Role of Chromosome Changes in Crocodylus Evolution and Diversity

Srikulnath, Kornsorn,Thapana, Watcharaporn,Muangmai, Narongrit Korea Genome Organization 2015 Genomics & informatics Vol.13 No.4

The karyotypes of most species of crocodilians were studied using conventional and molecular cytogenetics. These provided an important contribution of chromosomal rearrangements for the evolutionary processes of Crocodylia and Sauropsida (birds and reptiles). The karyotypic features of crocodilians contain small diploid chromosome numbers (30~42), with little interspecific variation of the chromosome arm number (fundamental number) among crocodiles (56~60). This suggested that centric fusion and/or fission events occurred in the lineage, leading to crocodilian evolution and diversity. The chromosome numbers of Alligator, Caiman, Melanosuchus, Paleosuchus, Gavialis, Tomistoma, Mecistops, and Osteolaemus were stable within each genus, whereas those of Crocodylus (crocodylians) varied within the taxa. This agreed with molecular phylogeny that suggested a highly recent radiation of Crocodylus species. Karyotype analysis also suggests the direction of molecular phylogenetic placement among Crocodylus species and their migration from the Indo-Pacific to Africa and The New World. Crocodylus species originated from an ancestor in the Indo-Pacific around 9~16 million years ago (MYA) in the mid-Miocene, with a rapid radiation and dispersion into Africa 8~12 MYA. This was followed by a trans-Atlantic dispersion to the New World between 4~8 MYA in the Pliocene. The chromosomes provided a better understanding of crocodilian evolution and diversity, which will be useful for further study of the genome evolution in Crocodylia.

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.

Role of Chromosome Changes in Crocodilian Evolution and Diversity

Kornsorn Srikulnath,Watcharaporn Thapana,Narongrit Muangmai 한국유전체학회 2015 Genomics & informatics Vol.13 No.4

The karyotypes of most species of crocodilians were studied using conventional and molecular cytogenetics. These provided an important contribution of chromosomal rearrangements for the evolutionary processes of Crocodylia and Sauropsida (birds and reptiles). The karyotypic features of crocodilians contain small diploid chromosome numbers (30∼42), with little interspecific variation of the chromosome arm number (fundamental number) among crocodiles (56∼60). This suggested that centric fusion and/or fission events occurred in the lineage, leading to crocodilian evolution and diversity. The chromosome numbers of Alligator, Caiman, Melanosuchus, Paleosuchus, Gavialis, Tomistoma, Mecistops, and Osteolaemus were stable within each genus, whereas those of Crocodylus (crocodylians) varied within the taxa. This agreed with molecular phylogeny that suggested a highly recent radiation ofcrocodilians. Karyotype analysis also suggests the direction of molecular phylogenetic placement among crocodilians and their migration from the Indo-Pacific to Africa and The New World. Crocodilians originated from an ancestor in the Indo-Pacific around 9∼16 million years ago (MYA) in the mid-Miocene, with a rapid radiation and dispersion into Africa 8∼12 MYA. This was followed by a trans-Atlantic dispersion to the New World between 4∼8 MYA in the Pliocene. The chromosomes provided a better understanding of crocodilian evolution and diversity, which will be useful for further study of the genome evolution in Crocodylia.

Structural variations generated by simian foamy virus-like (SFV) in Crocodylus siamensis

Panupon Twilprawat,김송미,Kornsorn Srikulnath,Kyudong Han 한국유전학회 2017 Genes & Genomics Vol.39 No.10

Endogenous retrovirus (ERV) integrates into the germline of its host and could remain in the genome as a molecular fossil. ERV is one of sources that cause INDEL and recombination events in the vertebrate genomes, leading to various genomic and genetic changes in their hosts. There have been many studies conducted on ERVs in the vertebrate genomes to elucidate their evolutionary history. However, ERVs have not been studied well in Crocodylus siamensis. Here, we report structural variations among SFV1 elements (simian foamy virus-like), ERVs in C. siamensis. We initially identified 26 SFV1 candidates in the genome and experimentally verified 9 SFV1_1 and 5 SFV1_10 elements using PCR display. Their structural analyses showed that most of them are solitary-LTRs but two SFV1_1 elements are full-length. Through further analyses, we found that the two full-length elements retain intact ORFs. We examined transcription factor binding sites within their LTR sequences to predict promoter/enhancer activities. In sum, we identified 14 crocodile-specific SFV1 elements and the results of their structural analyses suggest that they could contribute to genomic or phenotypic variations in C. siamensis population.

Characterization of GA20ox genes in tall and dwarf types coconut (Cocos nucifera L.)

Tippawan Boonkaew,Chareerat Mongkolsiriwatana,Ananya Vongvanrungruang,Kornsorn Srikulnath,Surin Peyachoknagul 한국유전학회 2018 Genes & Genomics Vol.40 No.7

Coconuts (Cocos nucifera L.) are divided by the height into tall and dwarf types. In many plants the short phenotype was emerged by mutation of the GA20ox gene encoding the enzyme involved in gibberellin (GA) biosynthesis. Two CnGA20ox genes, CnGA20ox1 and CnGA20ox2, were cloned from tall and dwarf types coconut. The sequences, gene structures and expressions were compared. The structure of each gene comprised three exons and two introns. The CnGA20ox1 and CnGA20ox2 genes consisted of the coding region of 1110 and 1131 bp, encoding proteins of 369 and 376 amino acids, respectively. Their amino acid sequences are highly homologous to GA20ox1 and GA20ox2 genes of Elaeis guineensis, but only 57% homologous to each other. However, the characteristic amino acids two histidines and one aspartic acid which are the two iron ( Fe2+) binding residues, and arginine and serine which are the substrate binding residues of the dioxygenase enzyme in the 20G-FeII_Oxy domain involved in GA biosynthesis, were found in the active site of both enzymes. The evolutionary relationship of their proteins revealed three clusters in vascular plants, with two subgroups in dicots and three subgroups in monocots. This result confirmed that CnGA20ox was present as multi-copy genes, and at least two groups CnGA20ox1 and CnGA20ox2 were found in coconut. The nucleotide sequences of CnGA20ox1 gene in both coconut types were identical but its expression was about three folds higher in the leaves of tall coconut than in those of dwarf type which was in good agreement with their height. In contrast, the nucleotide sequences of CnGA20ox2 gene in the two coconut types were different, but the expression of CnGA20ox2 gene could not be detected in either coconut type. The promoter region of CnGA20ox1 gene was cloned, and the core promoter sequences and various cis-elements were found. The CnGA20ox1 gene should be responsible for the height in coconut, which is different from other plants because no mutation was present in CnGA20ox1 gene of dwarf type coconut.

Comparison of digital PCR platforms using the molecular marker

Cherl-Joon Lee,Wonseok Shin,Minsik Song,Seung-Shick Shin,Yujun Park,Kornsorn Srikulnath,Dong Hee Kim,Kyudong Han Korea Genome Organization 2023 Genomics & informatics Vol.21 No.2

Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.

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.

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.