@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{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{Areesirisuk2021,

title = {Haplogroup distribution of 309 thais from admixed populations across the country by hvi and hvii sanger-type sequencing},

author = {P. Areesirisuk and K. Srikulnath and P. Onsod and J. Jaroensuk and B. Rerkamnuaychoke},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118156781&doi=10.3390%2fd13100496&partnerID=40&md5=186caa991f88524ba12d8c8c616a7ec7},

doi = {10.3390/d13100496},

issn = {14242818},

year  = {2021},

date = {2021-01-01},

journal = {Diversity},

volume = {13},

number = {10},

publisher = {MDPI},

abstract = {The mitochondrial DNA (mtDNA) control region sequences for the hypervariable regions I (HVI) and II (HVII) of 309 Thai citizens were investigated using Sanger-type sequencing to generate an mtDNA reference dataset for forensic casework, and the haplogroup distribution within geographically proximal Asian populations was analyzed. The population sample set contained 264 distinct haplotypes and showed high haplotype diversity, low matching probability, and high powers of discrimination, at 0.9985, 0.4744%, and 0.9953, respectively, compared with previous reports. Sub-haplogroup F1a showed the highest frequency in the Thai population, similar to Southeast Asian populations. The haplotype frequencies in the northern, northeastern, and southern populations of Thailand illustrate the relevance of social, religious, and historical factors in the biogeographical origin of the admixed Thai population as a whole. The HVI and HVII reference datasets will be useful for forensic casework applications, with improved genetic information content and discriminatory power compared to currently available techniques. © 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{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{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{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{Miura20211,

title = {Evolution of a multiple sex-chromosome system by three-sequential translocations among potential sex-chromosomes in the taiwanese frog odorrana swinhoana},

author = {I. Miura and F. Shams and S. -M. Lin and M. Bello Cioffi and T. Liehr and A. Al-Rikabi and C. Kuwana and K. Srikulnath and Y. Higaki and T. Ezaz},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103863314&doi=10.3390%2fcells10030661&partnerID=40&md5=09da1bca3bcffbcb36c5b7d747be50be},

doi = {10.3390/cells10030661},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {3},

pages = {1-10},

publisher = {MDPI},

abstract = {Translocation between sex-chromosomes and autosomes generates multiple sex-chromosome systems. It happens unexpectedly, and therefore, the evolutionary meaning is not clear. The current study shows a multiple sex chromosome system comprising three different chromosome pairs in a Taiwanese brown frog (Odorrana swinhoana). The male-specific three translocations cre-ated a system of six sex-chromosomes, X1Y1X2Y2X3Y3-X1X1X2X2X3X3. It is unique in that the translocations occurred among three out of the six members of potential sex-determining chromosomes, which are known to be involved in sex-chromosome turnover in frogs, and the two out of three include orthologs of the sex-determining genes in mammals, birds and fishes. This rare case suggests sex-specific, nonrandom translocations and thus provides a new viewpoint for the evolutionary meaning of the multiple sex chromosome system. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

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{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{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{Wattanadilokchatkun2021,

title = {Complete genome sequence of Pseudoalteromonas sp. Strain LC2018020214, a bacterium isolated from natural seawater},

author = {Pish Wattanadilokchatkun and Pattanapon Kayansamrua and Jiao Pan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103486283&doi=10.1128%2fMRA.00075-21&partnerID=40&md5=b9d8f395c84b72ce8c673e7797f5ad42},

doi = {10.1128/MRA.00075-21},

year  = {2021},

date = {2021-01-01},

journal = {Microbiology Resource Announcements},

volume = {10},

number = {11},

abstract = {Pseudoalteromonas is a genus widely distributed in the ocean and displays antibacterial and antifouling activities. We isolated a Pseudoalteromonas sp. strain (LC2018020214) from coastal water of Qingdao, China, and assembled its complete genome. The genome consists of two circular chromosomes with lengths of 3,700,777 bp and 817,517 bp, respectively, and 3,866 coding sequences. © 2021 American Society for Microbiology. All rights reserved.},

note = {Cited by: 1; All Open Access, Gold Open Access, Green Open Access},

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{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{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{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{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}

}