@article{Lisachov2023,

title = {Emerging importance of bighead catfish (Clarias macrocephalus) and north African catfish (C. gariepinus) as a bioresource and their genomic perspective},

author = {A. Lisachov and D. H. M. Nguyen and T. Panthum and S. F. Ahmad and W. Singchat and J. Ponjarat and K. Jaisamut and P. Srisapoome and P. Duengkae and S. Hatachote and K. Sriphairoj and N. Muangmai and S. Unajak and K. Han and U. Na-Nakorn and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85153387018&doi=10.1016%2fj.aquaculture.2023.739585&partnerID=40&md5=5a3ce76de1bee0fe3127e6eba8d05248},

doi = {10.1016/j.aquaculture.2023.739585},

issn = {00448486},

year  = {2023},

date = {2023-01-01},

journal = {Aquaculture},

volume = {573},

publisher = {Elsevier B.V.},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Budi2023,

title = {Thai Local Chicken Breeds, Chee Fah and Fah Luang, Originated from Chinese Black-Boned Chicken with Introgression of Red Junglefowl and Domestic Chicken Breeds},

author = {T. Budi and W. Singchat and N. Tanglertpaibul and W. Wongloet and A. Chaiyes and N. Ariyaraphong and W. Thienpreecha and W. Wannakan and A. Mungmee and T. Thong and P. Wattanadilokchatkun and T. Panthum and S. F. Ahmad and A. Lisachov and N. Muangmai and R. Chuenka and P. Prapattong and M. Nunome and W. Chamchumroon and K. Han and S. Pornpipatsiri and T. Supnithi and M. -S. Peng and J. -L. Han and Y. Matsuda and P. Duengkae and P. Noinafai and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85156114135&doi=10.3390%2fsu15086878&partnerID=40&md5=a0f1eb8838b9ba2f331f76749a9c14e4},

doi = {10.3390/su15086878},

issn = {20711050},

year  = {2023},

date = {2023-01-01},

journal = {Sustainability (Switzerland)},

volume = {15},

number = {8},

publisher = {MDPI},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ariyaraphong2023,

title = {Should the Identification Guidelines for Siamese Crocodiles Be Revised? Differing Post-Occipital Scute Scale Numbers Show Phenotypic Variation Does Not Result from Hybridization with Saltwater Crocodiles},

author = {N. Ariyaraphong and W. Wongloet and P. Wattanadilokchatkun and T. Panthum and W. Singchat and T. Thong and A. Lisachov and S. F. Ahmad and N. Muangmai and K. Han and P. Duengkae and Y. Temsiripong and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85154033202&doi=10.3390%2fbiology12040535&partnerID=40&md5=992a447a9f4076e4e43e5bb5f56fba61},

doi = {10.3390/biology12040535},

issn = {20797737},

year  = {2023},

date = {2023-01-01},

journal = {Biology},

volume = {12},

number = {4},

publisher = {MDPI},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wongloet2023,

title = {Genetic Monitoring of the Last Captive Population of Greater Mouse-Deer on the Thai Mainland and Prediction of Habitat Suitability before Reintroduction},

author = {W. Wongloet and P. Kongthong and A. Chaiyes and W. Singchat and W. Suksavate and N. Ariyaraphong and T. Panthum and A. Lisachov and K. Jaisamut and J. Sonongbua and T. Budi and W. Wannakan and W. Thienpreecha and P. Paansri and S. F. Ahmad and K. Sribuarod and U. Prayoon and P. Aramsirirujiwet and W. Chamchumroon and N. Muangmai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85149261233&doi=10.3390%2fsu15043112&partnerID=40&md5=3bf6e1a61599129ea2bfc299ff643fb5},

doi = {10.3390/su15043112},

issn = {20711050},

year  = {2023},

date = {2023-01-01},

journal = {Sustainability (Switzerland)},

volume = {15},

number = {4},

publisher = {MDPI},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Panthum2023169,

title = {Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication},

author = {T. Panthum and N. Ariyaphong and P. Wattanadilokchatkun and W. Singchat and S. F. Ahmad and E. Kraichak and S. Dokkaew and N. Muangmai and K. Han and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85143889290&doi=10.1007%2fs13258-022-01353-7&partnerID=40&md5=fb08b2c6e08b2e7db474604a9790209e},

doi = {10.1007/s13258-022-01353-7},

issn = {19769571},

year  = {2023},

date = {2023-01-01},

journal = {Genes and Genomics},

volume = {45},

number = {2},

pages = {169-181},

publisher = {Genetics Society of Korea},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikulnath2023,

title = {Asian Elephant Evolutionary Relationships: New Perspectives from Mitochondrial D-Loop Haplotype Diversity},

author = {K. Srikulnath and N. Ariyaraphong and W. Singchat and T. Panthum and A. Lisachov and S. F. Ahmad and K. Han and N. Muangmai and P. Duengkae},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85146018440&doi=10.3390%2fsu15010720&partnerID=40&md5=d3d2223fd30351cd5e8a4043df88f799},

doi = {10.3390/su15010720},

issn = {20711050},

year  = {2023},

date = {2023-01-01},

journal = {Sustainability (Switzerland)},

volume = {15},

number = {1},

publisher = {MDPI},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2022b,

title = {Population Scale Analysis of Centromeric Satellite DNA Reveals Highly Dynamic Evolutionary Patterns and Genomic Organization in Long‐Tailed and Rhesus Macaques},

author = {W. Singchat and S. F. Ahmad and K. Jaisamut and T. Panthum and N. Ariyaraphong and E. Kraichak and N. Muangmai and P. Duengkae and S. Payungporn and S. Malaivijitnond and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85132688631&doi=10.3390%2fcells11121953&partnerID=40&md5=d6a9ece8ee3edc2be0b9381647654d2b},

doi = {10.3390/cells11121953},

year  = {2022},

date = {2022-01-01},

journal = {Cells},

volume = {11},

number = {12},

abstract = {Centromeric satellite DNA (cen‐satDNA) consists of highly divergent repeat monomers, each approximately 171 base pairs in length. Here, we investigated the genetic diversity in the centromeric region of two primate species: long‐tailed (Macaca fascicularis) and rhesus (Macaca mulatta) macaques. Fluorescence in situ hybridization and bioinformatic analysis showed the chromosome‐specific organization and dynamic nature of cen‐satDNAsequences, and their substantial diversity, with distinct subfamilies across macaque populations, suggesting increased turnovers. Comparative genomics identified high level polymorphisms spanning a 120 bp deletion region and a remarkable interspecific variability in cen‐satDNA size and structure. Population structure analysis detected admixture patterns within populations, indicating their high divergence and rapid evolution. However, differences in censatDNA profiles appear to not be involved in hybrid incompatibility between the two species. Our study provides a genomic landscape of centromeric repeats in wild macaques and opens new avenues for exploring their impact on the adaptive evolution and speciation of primates. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ariyaraphong2022,

title = {Standard Identification Certificate for Legal Legislation of a Unique Gene Pool of Thai Domestic Elephants Originating from a Male Elephant Contribution to Breeding},

author = {N. Ariyaraphong and D. Ho My Nguyen and W. Singchat and W. Suksavate and T. Panthum and W. Langkaphin and S. Chansitthiwet and T. Angkawanish and A. Promking and K. Kaewtip and K. Jaisamut and S. F. Ahmad and S. Trirongjitmoah and N. Muangmai and O. Taesumrith and S. Inwiset and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142685212&doi=10.3390%2fsu142215355&partnerID=40&md5=3b0a0870a4fce356c31b735dcbbbd1ec},

doi = {10.3390/su142215355},

issn = {20711050},

year  = {2022},

date = {2022-01-01},

journal = {Sustainability (Switzerland)},

volume = {14},

number = {22},

publisher = {MDPI},

note = {cited By 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wattanadilokchatkun2022,

title = {Characterization of Microsatellite Distribution in Siamese Fighting Fish Genome to Promote Conservation and Genetic Diversity},

author = {P. Wattanadilokchatkun and T. Panthum and K. Jaisamut and S. F. Ahmad and S. Dokkaew and N. Muangmai and P. Duengkae and W. Singchat and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140613608&doi=10.3390%2ffishes7050251&partnerID=40&md5=1f13628dd05eb4bb0a5d9c10fc0da28b},

doi = {10.3390/fishes7050251},

issn = {24103888},

year  = {2022},

date = {2022-01-01},

journal = {Fishes},

volume = {7},

number = {5},

publisher = {MDPI},

note = {cited By 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chaiyes2022,

title = {Evidence of Genetic Connectivity among Lyle’s Flying Fox Populations in Thailand for Wildlife Management and One Health Framework},

author = {A. Chaiyes and N. Ariyaraphong and N. Sukgosa and K. Jangtarwan and S. F. Ahmad and N. Laopichienpong and W. Singchat and T. Panthum and S. Duangjai and N. Muangmai and S. Wacharapluesadee and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85137920388&doi=10.3390%2fsu141710791&partnerID=40&md5=d4897a533e5877e909547407efd72ccf},

doi = {10.3390/su141710791},

issn = {20711050},

year  = {2022},

date = {2022-01-01},

journal = {Sustainability (Switzerland)},

volume = {14},

number = {17},

publisher = {MDPI},

abstract = {Bats are important reservoir hosts of emerging viruses. Recent viral outbreaks and pandemics have resulted in an increased research focus on the genetic diversity, population structure, and distribution of bat species. Lyle’s flying fox (Pteropus lylei) is widely distributed throughout central Thailand, with most colonies congregating in temples within proximity to humans. A lack of knowledge regarding the genetic connectivity among different colonies hinders the investigation of zoonotic disease epidemiology and wildlife management. In this study, we hypothesized that genetic material may be exchanged between Lyle’s flying fox colonies that live in proximity. We assessed the mitochondrial displacement loop and cytochrome b nucleotide sequences of samples collected from 94 individuals from ten colonies across different roosting sites and detected limited genetic differentiation but increased nucleotide divergence within colonies. This suggests that genetic connectivity among Lyle’s flying fox colonies has experienced frequent and recent gene flow. These findings indicate that this species has maintained demographic equilibrium in a stable population, with a slight expansion event in certain populations. These data provide insights into the dynamics of bat populations, and the genetic knowledge gained presents opportunities for the improved monitoring of bat population structure. © 2022 by the authors.},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Duengkae2022,

title = {Coincidence of low genetic diversity and increasing population size in wild gaur populations in the Khao Phaeng Ma Non- Hunting Area, Thailand: A challenge for conservation management under humanwildlife conflict},

author = {P. Duengkae and N. Ariyaraphong and W. Tipkantha and W. Jairak and S. Baicharoen and D. H. M. Nguyen and O. Korboon and W. Singchat and T. Panthum and S. F. Ahmad and E. Kaewkhunjob and C. Chaisonkhram and U. Maikaew and N. Muangmai and G. Ieamsaard and S. Sripiboon and P. Paansri and W. Suksavate and A. Chaiyes and S. Winitpornsawan and U. Prayoon and T. Sornsa and R. Chokcharoen and A. Buanual and B. Siriaroonrat and Y. Utara and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85137125631&doi=10.1371%2fjournal.pone.0273731&partnerID=40&md5=de7e0531452fda78ec82d7dded7c2cdc},

doi = {10.1371/journal.pone.0273731},

issn = {19326203},

year  = {2022},

date = {2022-01-01},

journal = {PLoS ONE},

volume = {17},

number = {8 August},

publisher = {Public Library of Science},

abstract = {The gaur (Bos gaurus) is found throughout mainland South and Southeast Asia but is listed as an endangered species in Thailand with a decreasing population size and a reduction in suitable habitat. While gaur have shown a population recovery from 35 to 300 individuals within 30 years in the Khao Phaeng Ma (KPM) Non-Hunting Area, this has caused conflict with villagers along the border of the protected area. At the same time, the ecotourism potential of watching gaurs has boosted the local economy. In this study, 13 mitochondrial displacement-loop sequence samples taken from gaur with GPS collars were analyzed. Three haplotypes identified in the population were defined by only two parsimony informative sites (from 9 mutational steps of nucleotide difference). One haplotype was shared among eleven individuals located in different subpopulations/herds, suggesting very low genetic diversity with few maternal lineages in the founder population. Based on the current small number of sequences, neutrality and demographic expansion test results also showed that the population was likely to contract in the near future. These findings provide insight into the genetic diversity and demography of the wild gaur population in the KPM protected area that can inform long-term sustainable management action plans. © 2022 Duengkae et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {cited By 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chetruengchai2022,

title = {Genome of Varanus salvator macromaculatus (Asian Water Monitor) Reveals Adaptations in the Blood Coagulation and Innate Immune System},

author = {W. Chetruengchai and W. Singchat and C. Srichomthong and A. Assawapitaksakul and K. Srikulnath and S. F. Ahmad and C. Phokaew and V. Shotelersuk},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85133423820&doi=10.3389%2ffevo.2022.850817&partnerID=40&md5=42706ef85618835f883f74b76c990948},

doi = {10.3389/fevo.2022.850817},

issn = {2296701X},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Ecology and Evolution},

volume = {10},

publisher = {Frontiers Media S.A.},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2022,

title = {Population Scale Analysis of Centromeric Satellite DNA Reveals Highly Dynamic Evolutionary Patterns and Genomic Organization in Long‐Tailed and Rhesus Macaques},

author = {W. Singchat and S. F. Ahmad and K. Jaisamut and T. Panthum and N. Ariyaraphong and E. Kraichak and N. Muangmai and P. Duengkae and S. Payungporn and S. Malaivijitnond and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85132688631&doi=10.3390%2fcells11121953&partnerID=40&md5=d6a9ece8ee3edc2be0b9381647654d2b},

doi = {10.3390/cells11121953},

issn = {20734409},

year  = {2022},

date = {2022-01-01},

journal = {Cells},

volume = {11},

number = {12},

publisher = {MDPI},

abstract = {The domestication of wild animals represents a major milestone for human civilization. Chicken is the largest domesticated livestock species and used for both eggs and meat. Chicken originate from the red junglefowl (Gallus gallus). Its adaptability to diverse environments and ease of selective breeding provides a unique genetic resource to address the challenges of food security in a world impacted by climatic change and human population growth. Habitat loss has caused population declines of red junglefowl in Thailand. However, genetic diversity is likely to remain in captive stocks. We determine the genetic diversity using microsatellite genotyping and the mitochondrial D-loop sequencing of wild red junglefowl. We identified potential distribution areas in Thailand using maximum entropy models. Protected areas in the central and upper southern regions of Thailand are highly suitable habitats. The Bayesian clustering analysis of the microsatellite markers revealed high genetic diversity in red junglefowl populations in Thailand. Our model predicted that forest ranges are a highly suitable habitat that has enabled the persistence of a large gene pool with a nationwide natural distribution. Understanding the red junglefowl allows us to implement improved resource management, species reintroduction, and sustainable development to support food security objectives for local people. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Panthum2022,

title = {Something Fishy about Siamese Fighting Fish (Betta splendens) Sex: Polygenic Sex Determination or a Newly Emerged Sex-Determining Region?},

author = {T. Panthum and K. Jaisamut and W. Singchat and S. F. Ahmad and L. Kongkaew and W. Wongloet and S. Dokkaew and E. Kraichak and N. Muangmai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131004974&doi=10.3390%2fcells11111764&partnerID=40&md5=02f594f19ba254389bd0182a92783922},

doi = {10.3390/cells11111764},

issn = {20734409},

year  = {2022},

date = {2022-01-01},

journal = {Cells},

volume = {11},

number = {11},

publisher = {MDPI},

abstract = {Fishes provide a unique and intriguing model system for studying the genomic origin and evolutionary mechanisms underlying sex determination and high sex-chromosome turnover. In this study, the mode of sex determination was investigated in Siamese fighting fish, a species of commercial importance. Genome-wide SNP analyses were performed on 75 individuals (40 males and 35 females) across commercial populations to determine candidate sex-specific/sex-linked loci. In total, 73 male-specific loci were identified and mapped to a 5.6 kb region on chromosome 9, sug-gesting a putative male-determining region (pMDR) containing localized dmrt1 and znrf3 functional sex developmental genes. Repeat annotations of the pMDR revealed an abundance of transposable elements, particularly Ty3/Gypsy and novel repeats. Remarkably, two out of the 73 male-specific loci were located on chromosomes 7 and 19, implying the existence of polygenic sex determination. Besides male-specific loci, five female-specific loci on chromosome 9 were also observed in certain populations, indicating the possibility of a female-determining region and the polygenic nature of sex determination. An alternative explanation is that male-specific loci derived from other chromosomes or female-specific loci in Siamese fighting fish recently emerged as new sex-determining loci during domestication and repeated hybridization. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikulnath2022,

title = {Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation?},

author = {K. Srikulnath and S. F. Ahmad and W. Singchat and T. Panthum},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85128361141&doi=10.3390%2flife12040522&partnerID=40&md5=2c2420707bd9c71eb590eaf4707a9cbe},

doi = {10.3390/life12040522},

issn = {20751729},

year  = {2022},

date = {2022-01-01},

journal = {Life},

volume = {12},

number = {4},

publisher = {MDPI},

abstract = {Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Suntronpong2022,

title = {Implications of genome-wide single nucleotide polymorphisms in jade perch (Scortum barcoo) reveals the putative XX/XY sex-determination system, facilitating a new chapter of sex control in aquaculture},

author = {A. Suntronpong and T. Panthum and N. Laopichienpong and D. H. M. Nguyen and E. Kraichak and W. Singchat and N. Ariyaraphong and S. F. Ahmad and N. Muangmai and P. Duengkae and S. Peyachoknagul and T. Ezaz and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85117398752&doi=10.1016%2fj.aquaculture.2021.737587&partnerID=40&md5=d8ceaa9e3927c765629f3b8e844c9509},

doi = {10.1016/j.aquaculture.2021.737587},

issn = {00448486},

year  = {2022},

date = {2022-01-01},

journal = {Aquaculture},

volume = {548},

publisher = {Elsevier B.V.},

abstract = {Jade perch (Scortum barcoo) is a new teleost in the developing aquaculture freshwater finfish grow-out sector in Australia and China. However, key information on the breeding sex determination system (SDS) remains poorly understood, hampering sex control programs and genetic improvement. In this study, the jade perch SDS was examined by investigating genome-wide single-nucleotide polymorphisms (SNPs) using diversity arrays technology and cytogenetics analysis to identify the genomic variants associated with sex-linked regions. Although the cytogenetic results showed no variation in the chromosomal patterns between males and females, one male-specific locus and 13 male-linked loci were observed, suggesting that jade perch exhibits male heterogametic XX/XY SDS. Male-specific loci on the putative Y sex chromosome were also identified as an extremely small proportion of the genome. A homology search of the SNP loci revealed the male-specific loci were homologous to the Gypsy transposable element. This might be a remnant of an initial accumulation of repeats on the Y chromosome at the early stage of sex chromosome differentiation. The results provide a base for sex control breeding biotechnologies and genetic improvements to promote sexual size dimorphism and other new approaches to improve the commercial value of jade perch. © 2021},

note = {cited By 3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nguyen2022,

title = {Genome-Wide SNP Analysis of Hybrid Clariid Fish Reflects the Existence of Polygenic Sex-Determination in the Lineage},

author = {D. H. M. Nguyen and J. Ponjarat and N. Laopichienpong and T. Panthum and W. Singchat and S. F. Ahmad and E. Kraichak and N. Muangmai and P. Duengkae and S. Peyachoknagul and U. Na-Nakorn and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124894854&doi=10.3389%2ffgene.2022.789573&partnerID=40&md5=c78b59b7aeedf1a243e832ac3c27b858},

doi = {10.3389/fgene.2022.789573},

issn = {16648021},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Genetics},

volume = {13},

publisher = {Frontiers Media S.A.},

abstract = {The African catfish (Clarias gariepinus) may exhibit the co-existence of XX/XY and ZZ/ZW sex-determination systems (SDSs). However, the SDS of African catfish might be influenced by a polygenic sex-determination (PSD) system, comprising multiple independently segregating sex “switch” loci to determine sex within a species. Here, we aimed to detect the existence of PSD using hybrid. The hybrid produced by crossing male African catfish with female bighead catfish (C. macrocephalus, XX/XY) is a good animal model to study SDSs. Determining the SDS of hybrid catfish can help in understanding the interactions between these two complex SDS systems. Using the genotyping-by-sequencing “DART-seq” approach, we detected seven moderately male-linked loci and seventeen female-linked loci across all the examined hybrid specimens. Most of these loci were not sex-linked in the parental species, suggesting that the hybrid exhibits a combination of different alleles. Annotation of the identified sex-linked loci revealed the presence of one female-linked locus homologous with the B4GALNT1 gene, which is involved in the spermatogenesis pathway and hatchability. However, this locus was not sex-linked in the parental species, and the African catfish might also exhibit PSD. Copyright © 2022 Nguyen, Ponjarat, Laopichienpong, Panthum, Singchat, Ahmad, Kraichak, Muangmai, Duengkae, Peyachoknagul, Na-Nakorn and Srikulnath.},

note = {cited By 4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thapana2022,

title = {Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers},

author = {W. Thapana and N. Ariyaraphong and P. Wongtienchai and N. Laopichienpong and W. Singchat and T. Panthum and S. F. Ahmad and E. Kraichak and N. Muangmai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85122374536&doi=10.3390%2fani12020148&partnerID=40&md5=c9e5f871f9cb9d95e422f73d0dc911c8},

doi = {10.3390/ani12020148},

issn = {20762615},

year  = {2022},

date = {2022-01-01},

journal = {Animals},

volume = {12},

number = {2},

publisher = {MDPI},

abstract = {Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Panthum2021b,

title = {Genome-wide snp analysis of male and female rice field frogs, hoplobatrachus rugulosus, supports a non-genetic sex determination system},

author = {T. Panthum and W. Singchat and N. Laopichienpong and S. F. Ahmad and E. Kraichak and P. Duengkae and N. Muangmai and N. Kitana and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118178291&doi=10.3390%2fd13100501&partnerID=40&md5=9d906b9b139a03f9200a85cf543220e5},

doi = {10.3390/d13100501},

year  = {2021},

date = {2021-01-01},

journal = {Diversity},

volume = {13},

number = {10},

abstract = {Sex determination systems (SDSs) in anurans are diverse and have undergone independent evolutionary transitions among species. The mode of sexual reproduction of the rice field frog (Hoplobatrachus rugulosus)—an economically viable, edible amphibian species—is not well known. Previous studies have proposed that threshold temperature conditions may determine sex in these frogs. To elucidate the SDS in H. rugulosus, we karyotyped 10 male and 12 female frogs, and performed fluorescence in situ hybridization combined with sequencing analyses using DArTseq™. Our results revealed a highly conserved karyotype with no sex chromosome heteromorphism, and the sequencing analyses did not identify any consistent sex-linked loci, supporting the hypothesis of temperature-dependent sex determination. The results of this study, and others, on SDSs in the rice field frog and related species also provide support for the theory that heteromorphic sex chromosomes may lead to an evolutionary trap that prevents variable SDSs. These findings add important information to the body of knowledge on H. rugulosus and are likely to have a significant impact on the productivity and economic success of rice field frog farming. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ariyaraphong2021b,

title = {High-level gene flow restricts genetic differentiation in dairy cattle populations in thailand: Insights from large-scale mt d-loop sequencing},

author = {N. Ariyaraphong and N. Laopichienpong and W. Singchat and T. Panthum and S. F. Ahmad and D. Jattawa and P. Duengkae and N. Muangmai and T. Suwanasopee and S. Koonawootrittriron and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85107209977&doi=10.3390%2fani11061680&partnerID=40&md5=768fbcc498091ca40fd667bc46b56cc4},

doi = {10.3390/ani11061680},

year  = {2021},

date = {2021-01-01},

journal = {Animals},

volume = {11},

number = {6},

abstract = {Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nguyen2021b,

title = {An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish (Clarias gariepinus, Burchell, 1822)},

author = {D. H. M. Nguyen and T. Panthum and J. Ponjarat and N. Laopichienpong and E. Kraichak and W. Singchat and S. F. Ahmad and N. Muangmai and S. Peyachoknagul and U. Na-Nakorn and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099658568&doi=10.3389%2ffgene.2020.562856&partnerID=40&md5=9a346e1d25138630e1050f2dcad0e6a7},

doi = {10.3389/fgene.2020.562856},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Genetics},

volume = {11},

abstract = {An investigation of sex-specific loci may provide important insights into fish sex determination strategies. This may be useful for biotechnological purposes, for example, to produce all-male or all-female fish for commercial breeding. The North African catfish species, Clarias gariepinus, has been widely adopted for aquaculture because its superior growth and disease resistance render the species suitable for hybridization with other catfish to improve the productivity and quality of fish meat. This species has either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing as Diversity Arrays Technology. This approach was effective in identifying moderately sex-linked loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 perfectly sexed individuals of C. gariepinus. However, SNPs based markers were not found in this study. In total, 41 loci met the criteria for being moderately male-linked (with male vs. female ratios 80:20 and 70:30), while 25 loci were found to be moderately linked to female sex. No strictly male- or female-linked loci were detected. Seven moderately male-linked loci were partially homologous to some classes of transposable elements and three moderately male-linked loci were partially homologous to functional genes. Our data showed that the male heterogametic XX/XY sex determination system should co-exist with the ZZ/ZW system in C. gariepinus. Our finding of the co-existence of XX/XY and ZZ/ZW systems can be applied to benefit commercial breeding of this species in Thailand. This approach using moderately sex-linked loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs. © Copyright © 2021 Nguyen, Panthum, Ponjarat, Laopichienpong, Kraichak, Singchat, Ahmad, Muangmai, Peyachoknagul, Na-Nakorn and Srikulnath.},

note = {cited By 8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2021,

title = {Remnant of unrelated amniote sex chromosomal linkage sharing on the same chromosome in house gecko lizards, providing a better understanding of the ancestral super-sex chromosome},

author = {W. Singchat and T. Panthum and S. F. Ahmad and S. Baicharoen and N. Muangmai and P. Duengkae and D. K. Griffin and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118213200&doi=10.3390%2fcells10112969&partnerID=40&md5=89f78e39074fd3013099bddfb22d4da9},

doi = {10.3390/cells10112969},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {11},

publisher = {MDPI},

abstract = {Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages—the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Panthum2021,

title = {Genome-wide snp analysis of male and female rice field frogs, hoplobatrachus rugulosus, supports a non-genetic sex determination system},

author = {T. Panthum and W. Singchat and N. Laopichienpong and S. F. Ahmad and E. Kraichak and P. Duengkae and N. Muangmai and N. Kitana and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118178291&doi=10.3390%2fd13100501&partnerID=40&md5=9d906b9b139a03f9200a85cf543220e5},

doi = {10.3390/d13100501},

issn = {14242818},

year  = {2021},

date = {2021-01-01},

journal = {Diversity},

volume = {13},

number = {10},

publisher = {MDPI},

abstract = {The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikulnath2021,

title = {Why do some vertebrates have microchromosomes?},

author = {K. Srikulnath and S. F. Ahmad and W. Singchat and T. Panthum},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85115898577&doi=10.3390%2fcells10092182&partnerID=40&md5=2cb2a6f060dafe8bf9dfbfe885e42511},

doi = {10.3390/cells10092182},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {9},

publisher = {MDPI},

abstract = {With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes. © 2021 by the authors.},

note = {cited By 5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thintip2021,

title = {Reduced genetic variability in a captive-bred population of the endangered Hume's pheasant (Syrmaticus humiae, Hume 1881) revealed by microsatellite genotyping and Dloop sequencing},

author = {J. Thintip and W. Singchat and S. F. Ahmad and N. Ariyaraphong and N. Muangmai and W. Chamchumroon and K. Pitiwong and W. Suksavate and S. Duangjai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85113905155&doi=10.1371%2fjournal.pone.0256573&partnerID=40&md5=272e0667916ad9b63cc0773597147fe5},

doi = {10.1371/journal.pone.0256573},

issn = {19326203},

year  = {2021},

date = {2021-01-01},

journal = {PLoS ONE},

volume = {16},

number = {8 August},

publisher = {Public Library of Science},

abstract = {Captive breeding programs are crucial to ensure the survival of endangered species and ultimately to reintroduce individuals into the wild. However, captive-bred populations can also deteriorate due to inbreeding depression and reduction of genetic variability. We genotyped a captive population of 82 individuals of the endangered Hume's pheasant (Syrmaticus humiae, Hume 1881) at the Doi Tung Wildlife Breeding Center to assess the genetic consequences associated with captive breeding. Analysis of microsatellite loci and mitochondrial D-loop sequences reveal significantly reduced genetic differentiation and a shallow population structure. Despite the low genetic variability, no bottleneck was observed but 12 microsatellite loci were informative in reflecting probable inbreeding. These findings provide a valuable source of knowledge to maximize genetic variability and enhance the success of future conservation plans for captive and wild populations of Hume's pheasant. © 2021 Thintip et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {cited By 6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ahmad2021,

title = {Impact of repetitive dna elements on snake genome biology and evolution},

author = {S. F. Ahmad and W. Singchat and T. Panthum and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85114082924&doi=10.3390%2fcells10071707&partnerID=40&md5=9e7ce1fede690239781527c28a23eee3},

doi = {10.3390/cells10071707},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {7},

publisher = {MDPI},

abstract = {The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is inter-linked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite re-peats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ariyaraphong2021,

title = {High-level gene flow restricts genetic differentiation in dairy cattle populations in thailand: Insights from large-scale mt d-loop sequencing},

author = {N. Ariyaraphong and N. Laopichienpong and W. Singchat and T. Panthum and S. F. Ahmad and D. Jattawa and P. Duengkae and N. Muangmai and T. Suwanasopee and S. Koonawootrittriron and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85107209977&doi=10.3390%2fani11061680&partnerID=40&md5=768fbcc498091ca40fd667bc46b56cc4},

doi = {10.3390/ani11061680},

issn = {20762615},

year  = {2021},

date = {2021-01-01},

journal = {Animals},

volume = {11},

number = {6},

publisher = {MDPI AG},

abstract = {The Chinese goral (Naemorhedus griseus) is a small goat-like animal, which is considered “vulnerable” due to its rapid decline in population in the wild. Captive breeding programs are necessary to prevent the extinction of Chinese gorals; however, reproduction in captivity reduces genetic diversity due to inbreeding. In 2020, a total of six wild Chinese gorals were introduced into a captive population of 73 individuals to improve the allelic gene pool. An assessment of captive gorals was conducted to trace and understand genetic diversity in the new captive state. Microsatellite genotyping and mitochondrial D-loop sequence analyses were performed to examine the genetic diversity and population structure. The results showed very low haplotype diversity, with a significant difference between He (0.477 ± 0.065) and Ho (0.196 ± 0.056), suggesting a high degree of inbreeding. This resulted in a limited ability to adapt to environmental change and low natural reproductive fitness, thus increasing the risk of population decline and eventual extinction. Management of captive breeding plans based on different subpopulations and haplotypes has been proposed to maximize genetic variability and enhance the success of future conservation plans. © 2021 The Authors},

note = {cited By 6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikulnath202191,

title = {Overview of the betta fish genome regarding species radiation, parental care, behavioral aggression, and pigmentation model relevant to humans},

author = {K. Srikulnath and W. Singchat and N. Laopichienpong and S. F. Ahmad and M. Jehangir and N. Subpayakom and A. Suntronpong and K. Jangtarwan and T. Pongsanarm and T. Panthum and N. Ariyaraphong and J. Camcuan and P. Duengkae and S. Dokkaew and N. Muangmai},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099913076&doi=10.1007%2fs13258-020-01027-2&partnerID=40&md5=efbc01fa20db1405a1aea9b4d18960c4},

doi = {10.1007/s13258-020-01027-2},

issn = {19769571},

year  = {2021},

date = {2021-01-01},

journal = {Genes and Genomics},

volume = {43},

number = {2},

pages = {91-104},

publisher = {Genetics Society of Korea},

abstract = {Background: The Siamese fighting fish (Betta splendens, also known as the betta) is well known in aquarium markets, and also presents an exciting new research model for studying parental care, aggressive behavior, and cryptically diverse pigmentation. However, concentrated efforts are required, both in the context of conservation biology and in its genetics, to address the problems of ongoing outbreeding depression, loss of biodiversity, and lack of scientific biological information. Objective: The evolutionary dynamics of the betta must be better understood at the genomic scale in order to resolve the phylogenetic status of unrecognized species, develop molecular markers to study variation in traits, and identify interesting sets of genes encoding various bioresource functions. Methods: The recent revolution in multi-omics approaches such as genomics, transcriptomics, epigenomics, and proteomics has uncovered genetic diversity and gained insights into many aspects of betta bioresources. Results: Here, we present current research and future plans in an ongoing megaproject to characterize the betta genome as de novo assemblies, genes and repeat annotations, generating data to study diverse biological phenomena. We highlight key questions that require answers and propose new directions and recommendations to develop bioresource management to protect and enhance the betta genus. Conclusion: Successful accomplishment of these plans will allow the creation of a reference annotated genome and provide valuable information at the molecular level that can be utilized to sustain biodiversity and eco-management of the betta to improve breeding programs for future biomedical research. © 2021, The Genetics Society of Korea.},

note = {cited By 7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wongtienchai2021484,

title = {Genetic management of a water monitor lizard (Varanus salvator macromaculatus) population at Bang Kachao Peninsula as a consequence of urbanization with Varanus Farm Kamphaeng Saen as the first captive research establishment},

author = {P. Wongtienchai and S. Lapbenjakul and K. Jangtarwan and P. Areesirisuk and R. Mahaprom and N. Subpayakom and W. Singchat and S. Sillapaprayoon and N. Muangmai and R. Songchan and S. Baicharoen and P. Duengkae and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096706549&doi=10.1111%2fjzs.12436&partnerID=40&md5=413e2c19b3f4f30afd1e34d79c2c19bd},

doi = {10.1111/jzs.12436},

issn = {09475745},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Zoological Systematics and Evolutionary Research},

volume = {59},

number = {2},

pages = {484-497},

publisher = {Blackwell Publishing Ltd},

abstract = {Water monitors (Varanus salvator macromaculatus) are large lizards that inhabit wetlands. However, populations seem to be declining due to habitat fragmentation resulting from urban development. To develop an effective strategic conservation plan, the genetic diversity and population structure of water monitors at Bang Kachao Peninsula, a rich urban ecosystem in Bangkok, were analyzed using mitochondrial (mt) D-loop II sequences and microsatellite genotyping. Both genetic markers indicated a high degree of population-level genetic diversity. The consistency of the star-shaped haplotype network and results of neutrality tests strongly suggest the occurrence of a recent expansion in the population, possibly driven by anthropogenic urbanization. Subpopulations at Bang Kachao Peninsula are unlikely but gene flow between water monitors has occurred, which is suggestive of female-based dispersal. The large population of water monitors at Bang Kachao Peninsula creates conflict with local residents. Long-term population management through translocation has been conducted by captive management at Varanus Farm Kamphaeng Saen. The results of genetic monitoring indicate that the captive research population was soundly established. Comparison of allelic profiles between the two populations is necessary before translocation of water monitor groups from Bang Kachao Peninsula to Varanus Farm Kamphaeng Saen to reduce human-wildlife conflict. This work is the first step toward establishment of long-term ecological monitoring and an in situ/ex-situ conservation program, which are part of attempts to promote biodiversity in Thailand, following scientific principles. © 2020 Wiley-VCH GmbH},

note = {cited By 8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nguyen2021,

title = {An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish (Clarias gariepinus, Burchell, 1822)},

author = {D. H. M. Nguyen and T. Panthum and J. Ponjarat and N. Laopichienpong and E. Kraichak and W. Singchat and S. F. Ahmad and N. Muangmai and S. Peyachoknagul and U. Na-Nakorn and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099658568&doi=10.3389%2ffgene.2020.562856&partnerID=40&md5=9a346e1d25138630e1050f2dcad0e6a7},

doi = {10.3389/fgene.2020.562856},

issn = {16648021},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Genetics},

volume = {11},

publisher = {Frontiers Media S.A.},

abstract = {Bighead catfish (Clarias macrocephalus, Günther, 1864) is an important aquacultural species that plays a crucial role in the economy of Southeast Asia. Crossbreeding between female bighead catfish and male African catfish (C. gariepinus, Burchell, 1822) is used to produce hybrids with vigorous phenotypes. However, sterility of the hybrid is a major obstacle to their mass production. There is an emerging hypothesis that the complexity of the sex-determination system between two parental species might affect sterility. Previous studies investigated the co-existence of XX/XY and ZZ/ZW sex-determination systems in the African catfish population in Thailand, but in bighead catfish the sex-determination system remains poorly understood. In this study, the sex-determination system of the bighead catfish was examined using Diversity Arrays Technology to identify the genomic variants associated with sex-linked regions. The results support the hypothesis of the previous study that the bighead catfish might exhibit a male heterogametic XX/XY sex-determination system with multiple male-linked loci. One of the male-linked loci showed homology with the GTSF1L gene, which shows a testis-enriched expression pattern. Two of the male-linked loci were partially homologous to transposable element. Male-linked loci on the putative Y sex chromosome were identified as an extremely small proportion of the genome. A PCR-based DNA marker was developed to validate the male-linked loci in the bighead catfish. Our findings provide novel insights into sex-determination mechanisms in clariid catfish and will contribute to genetic improvements in breeding programs. © 2021 Elsevier B.V.},

note = {cited By 15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thintip20212251,

title = {Mitochondrial genome of bronze-winged jacana (Metopidius indicus, Latham 1790)},

author = {J. Thintip and S. F. Ahmad and W. Singchat and N. Laopichienpong and A. Suntronpong and T. Panthum and D. Ho My Nguyen and N. Ariyaraphong and N. Muangmai and W. Suksawet and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111835903&doi=10.1080%2f23802359.2021.1945971&partnerID=40&md5=9bf711f19dab14a22253dc0f1c2d0a2f},

doi = {10.1080/23802359.2021.1945971},

issn = {23802359},

year  = {2021},

date = {2021-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {6},

number = {8},

pages = {2251-2253},

publisher = {Taylor and Francis Ltd.},

abstract = {We reported the mitochondrial genome (mitogenome) of bronze-winged jacana (Metopidius indicus, Latham 1790). The circular mitogenome was 17,208 base pairs (bp) in length, containing 13 protein-coding genes, two rRNAs, 22 tRNAs, and a non-coding control region. A DNA spacer 109 bp long was also detected between ND5 and Cytb. Phylogenetic analysis indicated that M. indicus was more closely related with the genera Himantopus, Jacana and Hydrophasianus. This annotated mitogenome reference can be utilized as a data resource for comparative mitogenomics of waders or shorebirds, with possible use in ecological and evolutionary studies. © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.},

note = {cited By 0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Laopichienpong2021776,

title = {Complete mitochondrial genome of Mekong fighting fish, Betta smaragdina (Teleostei: Osphronemidae)},

author = {N. Laopichienpong and S. F. Ahmad and W. Singchat and A. Suntronpong and T. Pongsanarm and K. Jangtarwan and J. Bulan and T. Pansrikaew and T. Panthum and N. Ariyaraphong and N. Subpayakom and S. Dokkaew and N. Muangmai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102445931&doi=10.1080%2f23802359.2021.1882893&partnerID=40&md5=b5c619487b002a671672981925640346},

doi = {10.1080/23802359.2021.1882893},

issn = {23802359},

year  = {2021},

date = {2021-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {6},

number = {3},

pages = {776-778},

publisher = {Taylor and Francis Ltd.},

abstract = {Mekong fighting fish (Betta smaragdina) are found in Northeast Thailand. A complete mitochondrial genome (mitogenome) of B. smaragdina was assembled and annotated. Mitogenome sequences were 16,372 bp in length, with slight AT bias (59.8%), containing 37 genes with identical order to most teleost mitogenomes. Phylogenetic analysis of B. smaragdina showed closer relationship with B. splendens and B. mahachaiensis as the bubble-nesting group, compared to the mouthbrooder group (B. apollon, B. simplex, and B. pi). Results will allow the creation of a reference annotated genome that can be utilized to sustain biodiversity and eco-management of betta bioresources to improve conservation programs. © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.},

note = {cited By 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Laopichienpong2021624,

title = {Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes},

author = {N. Laopichienpong and E. Kraichak and W. Singchat and S. Sillapaprayoon and N. Muangmai and S. Suntrarachun and S. Baicharoen and S. Peyachoknagul and L. Chanhome and T. Ezaz and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85092101908&doi=10.1016%2fj.ygeno.2020.09.058&partnerID=40&md5=4806a0ec36dab3978302ab307dac1a96},

doi = {10.1016/j.ygeno.2020.09.058},

issn = {08887543},

year  = {2021},

date = {2021-01-01},

journal = {Genomics},

volume = {113},

number = {1P2},

pages = {624-636},

publisher = {Academic Press Inc.},

abstract = {Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome. © 2020 Elsevier Inc.},

note = {cited By 11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2020b,

title = {Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes},

author = {W. Singchat and S. F. Ahmad and S. Sillapaprayoon and N. Muangmai and P. Duengkae and S. Peyachoknagul and R. E. O’Connor and D. K. Griffin and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090054927&doi=10.3389%2ffgene.2020.00948&partnerID=40&md5=f3c3cece0b1c16358c346d13c3738aa5},

doi = {10.3389/fgene.2020.00948},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Genetics},

volume = {11},

abstract = {Squamate reptile chromosome 2 (SR2) is thought to be an important remnant of an ancestral amniote super-sex chromosome, but a recent study showed that the Siamese cobra W sex chromosome is also a part of this larger ancestral chromosome. To confirm the existence of an ancestral amniote super-sex chromosome and understand the mechanisms of amniote sex chromosome evolution, chromosome maps of two snake species [Russell’s viper: Daboia russelii (DRU) and the common tiger snake: Notechis scutatus (NSC)] were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Sixteen BACs were mapped on the W sex chromosome of DRU and/or NSC, suggesting that these BACs contained a common genomic region shared with the W sex chromosome of these snakes. Two of the sixteen BACs were co-localized to DRU2 and NSC2, corresponding to SR2. Prediction of genomic content from all BACs mapped on snake W sex chromosomes revealed a large proportion of long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) retrotransposons. These results led us to predict that amplification of LINE and SINE may have occurred on snake W chromosomes during evolution. Genome compartmentalization, such as transposon amplification, might be the key factor influencing chromosome structure and differentiation. Multiple sequence alignments of all BACs mapped on snake W sex chromosomes did not reveal common sequences. Our findings indicate that the SR2 and snake W sex chromosomes may have been part of a larger ancestral amniote super-sex chromosome, and support the view of sex chromosome evolution as a colorful myriad of situations and trajectories in which many diverse processes are in action. © Copyright © 2020 Singchat, Ahmad, Sillapaprayoon, Muangmai, Duengkae, Peyachoknagul, O’Connor, Griffin and Srikulnath.},

note = {cited By 15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ahmad2020,

title = {Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics},

author = {S. F. Ahmad and W. Singchat and M. Jehangir and A. Suntronpong and T. Panthum and S. Malaivijitnond and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85099076665&doi=10.3390%2fcells9122714&partnerID=40&md5=a4430bc958c3cb6917e212ed2e430f13},

doi = {10.3390/cells9122714},

issn = {20734409},

year  = {2020},

date = {2020-01-01},

journal = {Cells},

volume = {9},

number = {12},

publisher = {NLM (Medline)},

abstract = {A substantial portion of the primate genome is composed of non-coding regions, so-called "dark matter", which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.},

note = {cited By 20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Puinongpo20201,

title = {Existence of Bov-B line retrotransposons in snake lineages reveals recent multiple horizontal gene transfers with copy number variation},

author = {W. Puinongpo and W. Singchat and S. Petpradub and E. Kraichak and M. Nunome and N. Laopichienpong and R. Thongchum and T. Intarasorn and S. Sillapaprayoon and C. Indananda and N. Muangmai and S. Suntrarachun and S. Baicharoen and L. Chanhome and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85093920264&doi=10.3390%2fgenes11111241&partnerID=40&md5=498ce6c4dec5b0b265726af4fb79cddb},

doi = {10.3390/genes11111241},

issn = {20734425},

year  = {2020},

date = {2020-01-01},

journal = {Genes},

volume = {11},

number = {11},

pages = {1-22},

publisher = {MDPI AG},

abstract = {Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Koomgun2020,

title = {Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana (Iguana iguana) Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes},

author = {T. Koomgun and N. Laopichienpong and W. Singchat and T. Panthum and R. Phatcharakullawarawat and E. Kraichak and S. Sillapaprayoon and S. F. Ahmad and N. Muangmai and S. Peyachoknagul and P. Duengkae and T. Ezaz and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85094972343&doi=10.3389%2ffgene.2020.556267&partnerID=40&md5=cfa3bc33657a953eab25bac197894369},

doi = {10.3389/fgene.2020.556267},

issn = {16648021},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Genetics},

volume = {11},

publisher = {Frontiers Media S.A.},

abstract = {The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken (Gallus gallus) chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseqTM) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (Iguana iguana). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes. © Copyright © 2020 Koomgun, Laopichienpong, Singchat, Panthum, Phatcharakullawarawat, Kraichak, Sillapaprayoon, Ahmad, Muangmai, Peyachoknagul, Duengkae, Ezaz and Srikulnath.},

note = {cited By 11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Suntronpong20203097,

title = {Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements},

author = {A. Suntronpong and W. Singchat and W. Kruasuwan and O. Prakhongcheep and S. Sillapaprayoon and N. Muangmai and S. Somyong and C. Indananda and E. Kraichak and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085594105&doi=10.1016%2fj.ygeno.2020.05.024&partnerID=40&md5=8a8fe3645e5a6aefaf86ddeb53b68b1c},

doi = {10.1016/j.ygeno.2020.05.024},

issn = {08887543},

year  = {2020},

date = {2020-01-01},

journal = {Genomics},

volume = {112},

number = {5},

pages = {3097-3107},

publisher = {Academic Press Inc.},

abstract = {Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species. © 2020 Elsevier Inc.},

note = {cited By 7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2020,

title = {Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes},

author = {W. Singchat and S. F. Ahmad and S. Sillapaprayoon and N. Muangmai and P. Duengkae and S. Peyachoknagul and R. E. O’Connor and D. K. Griffin and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090054927&doi=10.3389%2ffgene.2020.00948&partnerID=40&md5=f3c3cece0b1c16358c346d13c3738aa5},

doi = {10.3389/fgene.2020.00948},

issn = {16648021},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Genetics},

volume = {11},

number = {11},

publisher = {Frontiers Media S.A.},

abstract = {: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.},

note = {cited By 18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat20203077,

title = {Complete mitochondrial genome of Mahachai betta, Betta mahachaiensis (Teleostei: Osphronemidae)},

author = {W. Singchat and S. F. Ahmad and N. Laopichienpong and A. Suntronpong and T. Pongsanarm and T. Panthum and N. Ariyaraphong and N. Subpayakom and S. Dokkaew and N. Muangmai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089070058&doi=10.1080%2f23802359.2020.1797578&partnerID=40&md5=55da5604acdccc42e8b89b58f07be85b},

doi = {10.1080/23802359.2020.1797578},

issn = {23802359},

year  = {2020},

date = {2020-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {5},

number = {3},

pages = {3077-3079},

publisher = {Taylor and Francis Ltd.},

abstract = {Mahachai bettas (Betta mahachaiensis) are distributed in areas of brackish water with Nipa Palms in Samut Sakhon, Thailand but urbanization is restricting their biodiversity. A complete mitochondrial genome (mitogenome) of B. mahachaiensis was determined to support conservation programs. Mitogenome sequences were 16,980 bp in length with slight AT bias (61.91%), containing 37 genes with identical order to most teleost mitogenomes. Phylogenetic analysis of B. mahachaiensis showed a closer relationship with B. splendens. Results will allow the creation of a reference annotated genome that can be utilized to sustain biodiversity and eco-management of the betta to improve conservation programs. © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.},

note = {cited By 6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ahmad20201,

title = {Consequence of paradigm shift with repeat landscapes in reptiles: Powerful facilitators of chromosomal rearrangements for diversity and evolution (running title: Genomic impact of repeats on chromosomal dynamics in reptiles)},

author = {S. F. Ahmad and W. Singchat and M. Jehangir and T. Panthum and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088167320&doi=10.3390%2fgenes11070827&partnerID=40&md5=eedd3d555288c21bd4be8a1427708cc1},

doi = {10.3390/genes11070827},

issn = {20734425},

year  = {2020},

date = {2020-01-01},

journal = {Genes},

volume = {11},

number = {7},

pages = {1-27},

publisher = {MDPI AG},

abstract = {Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the “repeatome”, remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro-and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {cited By 18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2020209,

title = {Do sex chromosomes of snakes, monitor lizards, and iguanian lizards result from multiple fission of an “ancestral amniote super-sex chromosome”?},

author = {W. Singchat and S. Sillapaprayoon and N. Muangmai and S. Baicharoen and C. Indananda and P. Duengkae and S. Peyachoknagul and R. E. O’Connor and D. K. Griffin and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085105523&doi=10.1007%2fs10577-020-09631-4&partnerID=40&md5=4a270a6da3994c8b654465da3920a8a5},

doi = {10.1007/s10577-020-09631-4},

issn = {09673849},

year  = {2020},

date = {2020-01-01},

journal = {Chromosome Research},

volume = {28},

number = {2},

pages = {209-228},

publisher = {Springer},

abstract = {Sex chromosomes in some amniotes share linkage homologies with distantly related taxa in regions orthologous to squamate reptile chromosome 2 (SR2) and the snake W sex chromosome. Thus, the SR2 and W chromosomes may formerly have been part of a larger ancestral amniote super-sex chromosome. Comparison of various sex chromosomal linkage homologies in Toxicofera with those in other amniotes offers an excellent model to assess key cytological differences, to understand the mechanisms of amniote sex chromosome evolution in each lineage and the existence of an ancestral amniote super-sex chromosome. Chromosome maps of four species of Toxicofera were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Different macrochromosome linkage homologies were highly conserved among Toxicofera, and at least two BACs (CH261-125F1 and CH261-40D6) showed partial homology with sex chromosomes of amniotes associated with SR2, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial linkage homologies. The present data also suggest a possible multiple fission mechanism of an ancestral super-sex chromosome, which resulted in further development of various sex chromosomal linkages of Toxicofera based on particular properties that favored the role of sex chromosomes. © 2020, Springer Nature B.V.},

note = {cited By 15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ahmad20203856,

title = {Next-generation sequencing yields complete mitochondrial genome assembly of peaceful betta fish, Betta imbellis (Teleostei: Osphronemidae)},

author = {S. F. Ahmad and N. Laopichienpong and W. Singchat and A. Suntronpong and T. Pongsanarm and T. Panthum and N. Ariyaraphong and J. Bulan and T. Pansrikaew and K. Jangtarwan and N. Subpayakom and S. Dokkaew and N. Muangmai and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097991831&doi=10.1080%2f23802359.2020.1841582&partnerID=40&md5=06b7011c7216ed2aa20e9e54c2ec2e82},

doi = {10.1080/23802359.2020.1841582},

issn = {23802359},

year  = {2020},

date = {2020-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {5},

number = {4},

pages = {3856-3858},

publisher = {Taylor and Francis Ltd.},

abstract = {The complete mitochondrial genome (mitogenome) of the peaceful betta (Betta imbellis) was obtained using next-generation sequencing. The sample of B. imbellis was collected from its native habitat in Southern Thailand. The mitogenome sequence was 16,897 bp in length, containing 37 genes with identical order to most teleost mitogenomes. Overall nucleotide base composition of the complete mitogenome was determined as AT bias. Phylogenetic analysis of B. imbellis showed a closer relationship with bubble-nesting fighting fish. This annotated mitogenome reference can be utilized as a bioresource for phylogenetic studies to support betta conservation programs. © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.},

note = {cited By 5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thongchum2019,

title = {Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles},

author = {R. Thongchum and W. Singchat and N. Laopichienpong and P. Tawichasri and E. Kraichak and O. Prakhongcheep and S. Sillapaprayoon and N. Muangmai and S. Baicharoen and S. Suntrarachun and L. Chanhome and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074289724&doi=10.1038%2fs41598-019-51863-w&partnerID=40&md5=817072a72cbff4b31f29de8868a2382b},

doi = {10.1038/s41598-019-51863-w},

issn = {20452322},

year  = {2019},

date = {2019-01-01},

journal = {Scientific Reports},

volume = {9},

number = {1},

publisher = {Nature Publishing Group},

abstract = {To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194–210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia. © 2019, The Author(s).},

note = {cited By 11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jangtarwan2019,

title = {Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woollynecked storks (Ciconia episcopus)},

author = {K. Jangtarwan and T. Koomgun and T. Prasongmaneerut and R. Thongchum and W. Singchat and P. Tawichasri and T. Fukayama and S. Sillapaprayoon and E. Kraichak and N. Muangmai and S. Baicharoen and C. Punkong and S. Peyachoknagul and P. Duengkae and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85073095794&doi=10.1371%2fjournal.pone.0223726&partnerID=40&md5=e5b7cb35536deae69d51ad826eb4e8ea},

doi = {10.1371/journal.pone.0223726},

issn = {19326203},

year  = {2019},

date = {2019-01-01},

journal = {PLoS ONE},

volume = {14},

number = {10},

publisher = {Public Library of Science},

abstract = {The fragmentation of habitats and hunting have impacted the Asian woolly-necked stork (Ciconia episcopus), leading to a serious risk of extinction in Thailand. Programs of active captive breeding, together with careful genetic monitoring, can play an important role in facilitating the creation of source populations with genetic variability to aid the recovery of endangered species. Here, the genetic diversity and population structure of 86 Asian woollynecked storks from three captive breeding programs [Khao Kheow Open Zoo (KKOZ) comprising 68 individuals, Nakhon Ratchasima Zoo (NRZ) comprising 16 individuals, and Dusit Zoo (DSZ) comprising 2 individuals] were analyzed using 13 microsatellite loci, to aid effective conservation management. Inbreeding and an extremely low effective population size (Ne) were found in the KKOZ population, suggesting that deleterious genetic issues had resulted from multiple generations held in captivity. By contrast, a recent demographic bottleneck was observed in the population at NRZ, where the ratio of Ne to abundance (N) was greater than 1. Clustering analysis also showed that one subdivision of the KKOZ population shared allelic variability with the NRZ population. This suggests that genetic drift, with a possible recent and mixed origin, occurred in the initial NRZ population, indicating historical transfer between captivities. These captive stork populations require improved genetic variability and a greater population size, which could be achieved by choosing low-related individuals for future transfers to increase the adaptive potential of reintroduced populations. Forward-in-time simulations such as those described herein constitute the first step in establishing an appropriate source population using a scientifically managed perspective for an in situ and ex situ conservation program in Thailand. © 2019 Jangtarwan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {cited By 12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat20196366,

title = {Dynamics of telomere length in captive Siamese cobra (Naja kaouthia) related to age and sex},

author = {W. Singchat and E. Kraichak and P. Tawichasri and T. Tawan and A. Suntronpong and S. Sillapaprayoon and R. Phatcharakullawarawat and N. Muangmai and S. Suntrarachun and S. Baicharoen and V. Punyapornwithaya and S. Peyachoknagul and L. Chanhome and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85067395063&doi=10.1002%2fece3.5208&partnerID=40&md5=1df553c474dc381a57ac2d19ad1ef4b2},

doi = {10.1002/ece3.5208},

issn = {20457758},

year  = {2019},

date = {2019-01-01},

journal = {Ecology and Evolution},

volume = {9},

number = {11},

pages = {6366-6377},

publisher = {John Wiley and Sons Ltd},

abstract = {Telomeres comprise tandem repeated DNA sequences that protect the ends of chromosomes from deterioration or fusion with neighboring chromosomes, and their lengths might vary with sex and age. Here, age- and sex-related telomere lengths in male and female captive Siamese cobras (Naja kaouthia) were investigated using quantitative real-time polymerase chain reaction based on cross-sectional data. A negative correlation was shown between telomere length and body size in males but not in females. Age-related sex differences were also recorded. Juvenile female snakes have shorter telomeres relative to males at up to 5 years of age, while body size also rapidly increases during this period. This suggests that an accelerated increase in telomere length of female cobra results from sex hormone stimulation to telomerase activity, reflecting sexually dimorphic phenotypic traits. This might also result from amplification of telomeric repeats on sex chromosomes. By contrast, female Siamese cobras older than 5 years had longer telomeres than males. Diverse sex hormone levels and oxidative stress parameters between sexes may affect telomere length. © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.},

note = {cited By 7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ponjarat201984,

title = {Evidence of dramatic sterility in F 1 male hybrid catfish [male Clarias gariepinus (Burchell, 1822) × female C. macrocephalus (Günther, 1864)] resulting from the failure of homologous chromosome pairing in meiosis I},

author = {J. Ponjarat and W. Singchat and P. Monkheang and A. Suntronpong and P. Tawichasri and S. Sillapaprayoon and S. Ogawa and N. Muangmai and S. Baicharoen and S. Peyachoknagul and I. Parhar and U. Na-Nakorn and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061960886&doi=10.1016%2fj.aquaculture.2019.02.035&partnerID=40&md5=5ab9240fea3cbea60089f27b9903a101},

doi = {10.1016/j.aquaculture.2019.02.035},

issn = {00448486},

year  = {2019},

date = {2019-01-01},

journal = {Aquaculture},

volume = {505},

pages = {84-91},

publisher = {Elsevier B.V.},

abstract = {Sterile hybrid animals exhibit spermatogenic disruptions with a decreased number and/or malformation of mature sperm. F 1 hybrid catfish (2n = 55) is an important cultured fish derived from male North African catfish [Clarias gariepinus (Burchell, 1822); 2n = 56] and female bighead catfish [C. macrocephalus (Günther, 1864); 2n = 54]; they are sterile with gametogenic failure in males. Despite the generality of this phenomenon, the spermatogenic phenotype has not been well described and a comprehensive understanding of the genetic basis of the disruption remains elusive. Our observations in the F 1 male hybrid showed abnormal morphology of testes with small size, while meiotic configuration indicated that meiosis succeeded in the early pachytene stage but failed to progress beyond the diplotene-diakinesis stage in primary spermatocytes. This suggests the presence of a number of degenerated spermatocytes. Histological examination recorded no postmeiotic cells and spermatozoa in F 1 male hybrid testes. A high frequency of apoptotic testicular cells was also present in the F 1 male hybrid, as shown by histochemical results for activated Caspase-3 and TUNEL assays. Low expression levels of Caspase-3, p53 and MCL1 (isoform 2), which activate pro-apoptotic signals in the development process, were also observed in both parental species, but significantly high expression levels were observed in the F 1 male hybrid. By contrast, the level of BCL2 expression was very low in the F 1 male hybrid, supporting the state of apoptosis as BCL2 inhibits the actions of pro-apoptotic proteins. These results collectively suggest that sterility in male hybrids is caused by spermatogenic disruptions in the pachytene stage, resulting from the failure of homologous chromosome pairing due to chromosomal incompatibility between parental genomes, and subsequent elimination by apoptosis leading to spermatogenic breakdown in the F 1 male hybrid. © 2019 Elsevier B.V.},

note = {cited By 9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Srikulnath2019,

title = {Distribution and amplification of interstitial telomeric sequences (ITSs) in Australian dragon lizards support frequent chromosome fusions in Iguania},

author = {K. Srikulnath and B. Azad and W. Singchat and T. Ezaz},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061969083&doi=10.1371%2fjournal.pone.0212683&partnerID=40&md5=7c4f9feefcf9fa8d5092b5fa5789ab8b},

doi = {10.1371/journal.pone.0212683},

issn = {19326203},

year  = {2019},

date = {2019-01-01},

journal = {PLoS ONE},

volume = {14},

number = {2},

publisher = {Public Library of Science},

abstract = {Telomeric sequences are generally located at the ends of chromosomes; however, they can also be found in non-terminal chromosomal regions when they are known as interstitial telomeric sequences (ITSs). Distribution of ITSs across closely related and divergent species elucidates karyotype evolution and speciation as ITSs provide evolutionary evidence for chromosome fusion. In this study, we performed physical mapping of telomeric repeats by fluorescence in situ hybridisation (FISH) in seven Australian dragon lizards thought to represent derived karyotypes of squamate reptiles and a gecko lizard with considerably different karyotypic feature. Telomeric repeats were present at both ends of all chromosomes in all species, while varying numbers of ITSs were also found on microchromosomes and in pericentromeric or centromeric regions on macrochromosomes in five lizard species examined. This suggests that chromosomal rearrangements from ancestral squamate reptiles to Iguania occurred mainly by fusion between ancestral types of acrocentric chromosomes and/or between microchromosomes, leading to appearance of bi-armed macrochromosomes, and in the reduction of microchromosome numbers. These results support the previously proposed hypothesis of karyotype evolution in squamate reptiles. In addition, we observed the presence of telomeric sequences in the similar regions to heterochromatin of the W microchromosome in Pogona barbata and Doporiphora nobbi, while sex chromosomes for the two species contained part of the nucleolar organiser regions (NORs). This likely implies that these ITSs are a part of the satellite DNA and not relics of chromosome fusions. Amplification of telomeric repeats may have involved heterochromatinisation of sex-specific W chromosomes and play a role in the organisation of the nucleolus. © 2019 Srikulnath et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {cited By 20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Singchat2019577,

title = {Complete mitochondrial genome of Siamese cobra (Naja kaouthia) determined using next-generation sequencing},

author = {W. Singchat and P. Areesirisuk and S. Sillapaprayoon and N. Muangmai and S. Baicharoen and S. Suntrarachun and L. Chanhome and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85060335258&doi=10.1080%2f23802359.2018.1558123&partnerID=40&md5=3b3eedbd3755c0ff1d2cbad3128d4ef9},

doi = {10.1080/23802359.2018.1558123},

issn = {23802359},

year  = {2019},

date = {2019-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {4},

number = {1},

pages = {577-578},

publisher = {Taylor and Francis Ltd.},

abstract = {Siamese cobra (Naja kaouthia) exhibits highly toxic venom, which causes morbidity and mortality. Accurate species identification through molecular approaches is very important to administer correct antivenoms. The Siamese cobra mitogenome contains 17,203 bp with slight AT bias (58.2%) containing 37 genes in identical order to snake mitogenomes; no tandem repeat was found in the control region. Phylogenetic analysis indicated that Siamese and other cobras had highly supported monophyletic clades similar to the genus Naja and close relationships with other elapid snakes. Our results will facilitate clinical diagnosis and enrich genomic resources for future evolutionary studies and conservation management. © 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.},

note = {cited By 4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ThongtamNaAyudhaya2019222,

title = {Complete mitochondrial genome of 10 anemonefishes belonging to Amphiprion and Premnas},

author = {P. Thongtam Na Ayudhaya and P. Areesirisuk and W. Singchat and S. Sillapaprayoon and N. Muangmai and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059771540&doi=10.1080%2f23802359.2018.1546145&partnerID=40&md5=f916bfbc3997ac10314075c97eaf689b},

doi = {10.1080/23802359.2018.1546145},

issn = {23802359},

year  = {2019},

date = {2019-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {4},

number = {1},

pages = {222-224},

publisher = {Taylor and Francis Ltd.},

abstract = {Anemonefish are widely distributed in tropical areas with phenotypic color variation often observed in the same species. Complete mitochondrial genomes (mitogenomes) of 10 anemonefishes belonging to Amphiprion and Premnas were determined to support taxonomic status. Average mitogenome sequence was 16,838 ± 19.69 bp, containing 37 genes with identical gene order to most teleost mitogenomes. The percula complex comprised A. percula and A. ocellaris and was phylogenetically clustered with P. biaculeatus. Color morphs of A. ocellaris and P. biaculeatus were identified, suggesting large phenotypic variation at species level. Results will facilitate further genetic studies of mitochondrial variation and species diversity in anemonefish. © 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.},

note = {cited By 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}