The complete mitochondrial genome organization of Schizothorax Plagiostomus (Teleostei: Cyprinidae) from Northern Pakistan

Comparative mitochondrial genomics analysis of selected species of Schizothoracinae sub family to explore the differences at mitochondrial DNA level

A comprehensive analysis of the whole mitochondrial genomes of the Schizothoracinae subfamily of the family Cyprinidae has been revealed for the first time. The species analyzed include Schizothorax niger, Schizothorax esocinus, Schizothorax labiatus and Schizothorax plagoistomus. The total mitochondrial DNA (mtDNA) length was determined to be 16585 bp, 16583 bp, 16582 bp and 16576 bp, respectively with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding area genes. The combined mean base compositions of the four species were as follows: A: 29.91 % T: 25.47 % G: 17.65 % C 27.01 %. The range of the GC content is 45-44 %, respectively. All protein coding genes (PCGs) commenced with the typical ATG codon, except for the cytochrome c oxidase subunit 1 (COX1) gene with GTG. The analysis of vital amino acid biosynthesis genes (COX1, ATPase 6, ATPase 8) in four different species revealed no significant differences. All 13 PCGs had Ka/Ks ratios that were all lesser than one, demonstrating purifying selection on those molecules. These tRNA genes were predicted to fold into the typical cloverleaf secondary structures with normal base pairing and ranged in size from 66 to 75 nucleotides. Additionally, the phylogenetic tree analysis revealed that S. esocinus species that was most alike to S. labiatus. This study provides critical data for phylogenetic analysis of the Schizothoracinae subfamily, which will help to resolve taxonomic difficulties and identify evolutionary links. Detailed mtDNA data are an invaluable resource for studying genetic diversity, population structure, and gene flow. Understanding genetic makeup can help inform conservation plans, identify unique populations, and track genetic variation to ensure effective preservation.

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes

BACKGROUND

Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes.

METHODS

Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis.

RESULTS

The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%.

CONCLUSION

The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.

Resolving the phylogenetic relationship of Himalayan snow trout Schizothorax plagiostomus with other species of Schizothoracine using mitochondrial CO-I and Cyt b genes

BACKGROUND

The classification of the sub-family Schizothoracinae has been debatable due to the overlap in morphological characters. There are discrepancies between classical taxonomy and molecular taxonomy, as well. In the present study, mitochondrial genes CO-I and Cyt b were sequenced to elucidate the phylogenetic status of three species of the genus Schizothorax.

METHODS AND RESULTS

In total, 29 samples of three species viz., S. plagiostomus, S. progastus, and S. richardsonii, were collected from rivers of Uttarakhand, India. For phylogenetic analyses, 40 sequences of CO-I and 41 sequences of Cyt b of Schizothoracinae species were downloaded from NCBI. The highest genetic divergence based on CO-I (16.08%) is between S. plagiostomus and Ptychobarbus dipogon, while the lowest divergence (0.00%) is between 10 pairs of species. The highest divergence based on Cyt b (19.43%), is between S. niger and Gymnocypris eckloni, while the lowest divergence (0.00%) is between four pairs of species. The divergence (0.00% for CO-I and 2.38% for Cyt b) between S. chongi and S. kozlovi, seems a case of convergent molecular evolution of the CO-I gene and in this case, CO-I alone cannot be used to differentiate these two species.

CONCLUSION

The simultaneous use of two molecular markers along with morphomeristic data is a better strategy for the classification of the sub-family Schizothoracinae. These results will be a resource dataset for determining the taxonomical status of Schizothoracine species and will help in the conservation and commercial production of these commercially important fish species.

Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India)

Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.

Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration

The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.

The mitochondrial genome of Schizothorax esocinus (Cypriniformes: Cyprinidae) from Northern Pakistan

The mitochondrial DNA sequence represents a mainstay of phylogenetics. It allows biologists to elucidate the evolutionary relationships among species. It also permits an examination of the relatedness of populations, hence got importance in the field of biology. The current study was designed to know the mitochondrial sequence of Schizothorax esocinus, a delicious fish belonging to family Cyprinidae. In this study, the complete mitochondrial genome of S. esocinus from Northern Pakistan was determined. The mitogenome of S. esocinus was found to be 16 591 bp in length and consisted of 13 protein coding genes, 22 tRNA genes, two rRNA genes, and one control region. All genes were encoded on heavy strain except ND6 and few tRNA genes. The overall base composition was T 25.5%, C 27.0%, A 29.8% and G 17.7%, A + T content 55.3% and G + C content 47.7%. The length of control region (CR) was 938 bp and contained putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB) and control region also contained a microsatellite region (TA). This is the very first study reported from a reservoir of large cold water bodies in Pakistan which have a great potential for conservation of cold water fish species. This mitogenome sequence would be useful to know the phylogenetic status of the fish.