@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{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{Srikulnath202262,

title = {Importance of Thai macaque bioresources for biological research and human health},

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

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85119506276&doi=10.1111%2fjmp.12555&partnerID=40&md5=6ef3dbc91f36a0d4cfcfcf8fe121723a},

doi = {10.1111/jmp.12555},

issn = {00472565},

year  = {2022},

date = {2022-01-01},

journal = {Journal of Medical Primatology},

volume = {51},

number = {1},

pages = {62-72},

publisher = {John Wiley and Sons Inc},

abstract = {During the past century, macaque bioresources have provided remarkable scientific and biomedical discoveries related to the understanding of human physiology, neuroanatomy, reproduction, development, cognition, and pathology. Considerable progress has been made, and an urgent need has arisen to develop infrastructure and viable settings to meet the current global demand in research models during the so-called new normal after COVID-19 era. This review highlights the critical need for macaque bioresources and proposes the establishment of a designated primate research center to integrate research in primate laboratories for the rescue and rehabilitation of wild macaques. Key areas where macaque models have been and continue to be essential for advancing fundamental knowledge in biomedical and biological research are outlined. Detailed genetic studies on macaque bioresources of Thai origin can further facilitate the rapid pace of vaccine discovery. © 2021 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd},

note = {cited By 1},

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{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{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{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{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{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{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}

}