Genetic insights: mapping sex-specific loci in Siamese cobra (Naja kaouthia) sheds light on the putative sex determining region

Jaito Wattanawan,Panthum Thitipong,Ahmad Syed Farhan,Singchat Worapong,Muangmai Narongrit,Han Kyudong,Koga Akihiko,Duengkae Prateep,Srikulnath Kornsorn 한국유전학회 2024 Genes & Genomics Vol.46 No.1

The location of female-specific/linked loci identified in Siamese cobra (Naja kaouthia) previously has been determined through in silico chromosome mapping of the Indian cobra genome (N. naja) as a reference genome. In the present study, we used in silico chromosome mapping to identify sex-specific and linked loci in Siamese cobra. Many sex-specific and sex-linked loci were successfully mapped on the Z sex chromosome, with 227 of the 475 specific loci frequently mapped in a region covering 57 Mb and positioned at 38,992,675–95,561,177 bp of the Indian cobra genome (N. naja). This suggested the existence of a putative sex-determining region (SDR), with one specific locus (PA100000600) homologous to the TOPBP1 gene. The involvement of TOPBP1 gene may lead to abnormal synaptonemal complexes and meiotic chromosomal defects, resulting in male infertility. These findings offer valuable insights into the genetic basis and functional aspects of sex-specific traits in the Siamese cobra, which will contribute to our understanding of snake genetics and evolutionary biology.

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

Kornsorn Srikulnath,Worapong Singchat,Nararat Laopichienpong,Syed Farhan Ahmad,Maryam Jehangir,Navapong Subpayakom,Aorarat Suntronpong,Kornsuang Jangtarwan,Tavun Pongsanarm,Thitipong Panthum,Nattakan 한국유전학회 2021 Genes & Genomics Vol.43 No.2

Background The Siamese fghting fsh (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 eforts 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 scientifc 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.

Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication

Panthum Thitipong,Ariyaphong Nattakan,Wattanadilokchatkun Pish,Singchat Worapong,Ahmad Syed Farhan,Kraichak Ekaphan,Dokkaew Sahabhop,Muangmai Narongrit,Han Kyudong,Duengkae Prateep,Srikulnath Kornsorn 한국유전학회 2023 Genes & Genomics Vol.45 No.2

Background The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories. Objective This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool. Methods A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species. Results The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set. Conclusion The COI gene should thus be used as the main barcoding marker for fighting fish.

Disclosing the hidden nucleotide sequences: a journey into DNA barcoding of raptor species in public repositories

Jaito Wattanawan,Sonongbua Jumaporn,Panthum Thitipong,Wattanadilokcahtkun Pish,Ariyaraphong Nattakan,Thong Thanyapat,Singchat Worapong,Ahmad Syed Farhan,Kraichak Ekaphan,Muangmai Narongrit,Han Kyudong 한국유전학회 2024 Genes & Genomics Vol.46 No.1

Background In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data. Objective Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae). Methods Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed. Results The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively. Conclusion Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors. Background In nucleotide public repositories, studies discovered data errors which resulted in incorrect species identification of several accipitrid raptors considered for conservation. Mislabeling, particularly in cases of cryptic species complexes and closely related species, which were identified based on morphological characteristics, was discovered. Prioritizing accurate species labeling, morphological taxonomy, and voucher documentation is crucial to rectify spurious data. Objective Our study aimed to identify an effective DNA barcoding tool that accurately reflects the efficiency status of barcodes in raptor species (Accipitridae). Methods Barcode sequences, including 889 sequences from the mitochondrial cytochrome c oxidase I (COI) gene and 1052 sequences from cytochrome b (Cytb), from 150 raptor species within the Accipitridae family were analyzed. Results The highest percentage of intraspecific nearest neighbors from the nearest neighbor test was 88.05% for COI and 95.00% for Cytb, suggesting that the Cytb gene is a more suitable marker for accurately identifying raptor species and can serve as a standard region for DNA barcoding. In both datasets, a positive barcoding gap representing the difference between inter-and intra-specific sequence divergences was observed. For COI and Cytb, the cut-off score sequence divergences for species identification were 4.00% and 3.00%, respectively. Conclusion Greater accuracy was demonstrated for the Cytb gene, making it the preferred primary DNA barcoding marker for raptors.

Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species

Piangjai Chalermwong,Thitipong Panthum,Pish Wattanadilokcahtkun,Nattakan Ariyaraphong,Thanyapat Thong,Phanitada Srikampa,Worapong Singchat,Syed Farhan Ahmad,Kantika Noito,Ryan Rasoarahona,Artem Lisach Korea Genome Organization 2023 Genomics & informatics Vol.21 No.3

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.