@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{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{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{ThongtamNaAyudhaya2019222,

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

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

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

doi = {10.1080/23802359.2018.1546145},

issn = {23802359},

year  = {2019},

date = {2019-01-01},

journal = {Mitochondrial DNA Part B: Resources},

volume = {4},

number = {1},

pages = {222-224},

publisher = {Taylor and Francis Ltd.},

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

note = {cited By 2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ThongtamnaAyudhaya2017198,

title = {Unveiling cryptic diversity of the anemonefish genera Amphiprion and Premnas (Perciformes: Pomacentridae) in Thailand with mitochondrial DNA barcodes},

author = {P. Thongtam na Ayudhaya and N. Muangmai and N. Banjongsat and W. Singchat and S. Janekitkarn and S. Peyachoknagul and K. Srikulnath},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028653591&doi=10.1016%2fj.anres.2017.07.001&partnerID=40&md5=6f73dac252fbced04754a37b13569f0e},

doi = {10.1016/j.anres.2017.07.001},

issn = {24681458},

year  = {2017},

date = {2017-01-01},

journal = {Agriculture and Natural Resources},

volume = {51},

number = {3},

pages = {198-205},

publisher = {Elsevier B.V.},

abstract = {The genera Amphiprion and Premnas comprise the common anemonefish that are widely distributed in tropical areas. Species identification of these two genera is difficult due to high, intraspecific, morphological variation. Recently, DNA barcoding has been employed as an efficient tool that uses a short genetic marker in an organism's DNA to enable the identification and recognition of cryptic species. This study applied three regions of mitochondrial DNA—cytochrome c oxidase I (COI), cytochrome b (Cytb) and 16S rRNA—as DNA barcodes for species identification of seven species of Amphiprion and one species of Premnas in Thailand. Three species-delimitation methods—general mixed Yule-coalescent (GMYC), automatic barcoding gap detection (ABGD) and a Bayesian implementation of the Poisson tree processes model (bPTP)—were also used to estimate the number of species. An overlap was found between the intra- and inter-specific genetic divergence values in Cytb and 16S rRNA, but not for the COI data. This indicated that COI was the most effective for identifying different anemonefish species. A three-gene phylogenetic analysis and species-delimitation methods based on both COI and Cytb data suggested cryptic diversity in Amphiprion clarkii, A. percula, A. ocellaris and Premnas biaculeatus. Different distributions were found also for two cryptic species of A. clarkia—one restricted to the Gulf of Thailand and the other to the Andaman Sea. The results confirmed the efficiency of COI as a suitable marker for species identification of anemonefish. © 2017 Kasetsart University},

note = {cited By 12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}