Complete mitochondrial genome sequence of Catla catla and its phylogenetic consideration

High Genetic Differentiation and Genetic Diversity in Endangered Mahseer Tor khudree (Sykes, 1839) as Revealed from Concatenated ATPase 6/8 and Cyt b Mitochondrial Genes

The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species.

Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes

Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.

Mitochondrial DNA reveals shallow population genetic structure in economically important Cyprinid fish Labeo rohita (Hamilton, 1822) from South and Southeast Asia

BACKGROUND

Assessment of genetic diversity and population genetic structure is important for species that are economically important, threatened, and are at global conservation priority. Analysis of mitochondrial DNA is broadly used in species identification and population genetics studies due to the availability of sufficient reference data and better evolutionary dynamics for phylogeographic investigation. Labeo rohita (Rohu) is an economically important species cultured under carp polyculture systems in Asia. The present study explores the genetic diversity, phylogeography, and population structure of L. rohita from different countries using cytochrome oxidase subunit I (COI) gene.

METHODS AND RESULTS

A total of 17 L. rohita specimens were sampled from River Beas, India. For the genetic study, we amplified and sequenced COI mitochondrial DNA region. The obtained genetic data was combined with 268 COI records available in the NCBI and BOLD databases originating from multiple populations/countries across South and Southeast Asia. As a result, 33 haplotypes were identified that displayed low nucleotide (π = 0.0233) and moderate haplotype diversity (Hd = 0.523). Tajima (D) was found to be negative (P > 0.05), whereas Fu's Fs showed a positive value (P > 0.05). The overall F_ST value between studied populations was 0.481 (P < 0.05).

CONCLUSION

AMOVA analysis indicated higher variation within than among the population examined. The neutrality tests suggested the presence of rare haplotypes and stable demography within studied populations of L. rohita. The Bayesian skyline plot indicated steady population growth until 1 Mya followed by population decline, whereas F_ST values indicated significant genetic differentiation. High heterogeneity was observed in the Pakistan population which could be indicative of long-term isolation and excessive culturing to meet market demands. The present results are the first global comparative analysis of L. rohita and pave the way forward for detailed genomic and ecological studies aimed at the development of improved stock and effective conservation plans. The study also makes recommendations to conserve the genetic integrity of wild species from aquaculture-reared fishes.

Complete mitochondrial genome of nearly threatened freshwater ornamental fish, Microphis deocata and its phylogenetic relationship within Syngnathidae

Microphis deocata (deocata pipefish), belonging to family Syngnathidae, is one of the important indigenous ornamental fish species listed as near threatened in the IUCN red list. Here, we first report the complete mitochondrial genome of deocata pipefish using Illumina next-generation sequencing platform. The total length of the mitogenome is 16,526 bp. It encompasses 13 protein coding genes, 2 ribosomal rRNAs, and 22 tRNAs. The WANCY region (a cluster of five tRNA genes) contains the 50 bp O_L light strand origin of replication. Phylogenetic analysis of Syngnathidae revealed M. deocata to cluster with Oostethus manadensis, forming a sister group with Doryrhamphus japonicas and Dunckerocampus dactyliophorus. The mitochondrial genome sequence data generated in the present study will play an important role in population genetic analysis and developing conservation strategies for this species.

The complete mitochondrial genome of Labeo catla (Hamilton, 1822) using long read sequencing

Labeo catla is a widely cultured species in monoculture and polyculture systems of the Indian subcontinent. In this study, the complete mitochondrial genome sequence of catla was reconstructed from Oxford Nanopore sequence data. The mitochondrial genome is 16,600 bp in length (accession no. is MN830943) which is larger than the previously reported catla mitogenomes. Like other vertebrate mitochondrial genomes, it has 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. Most of the mitogenes are encoded on H-strand. Phylogenetic analysis showed that Labeo catla is more closely related to Labeo rohita than other labeo species. The catla mtgenome reported here will facilitate population genetics, phylogenetics and molecular taxonomy of Indian major carps.

Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes

Sinorhodeus microlepis (S. microlepis) is recently described as a new species and represents a new genus Sinorhodeu of the subfamily Acheilognathinae. In this study, we first sequenced the complete mitogenome of S. microlepis and compared with the other 29 bitterling mitogenomes. The S. microlepis mitogenome is 16,591 bp in length and contains 37 genes. Gene distribution pattern is identical among 30 bitterling mitogenomes. A significant linear correlation between A+T% and AT-skew were found among 29 bitterling mitogenomes, except S. microlepis shows unusual AT-skew with slightly negative in tRNAs and PCGs. Bitterling mitogenomes exhibit highly conserved usage bias of start codon, relative synonymous codons and amino acids, overlaps and non-coding intergenic spacers. Phylogenetic trees constructed by 13 PCGs strongly support the polyphyly of the genus Acheilognathus and the paraphyly of Rhodeus and Tanakia. Together with the unusual characters of S. microlepis mitogenomes and phylogenetic trees, S. microlepis should be a sister species to the genus Rhodeu that might diverge about 13.69 Ma (95% HPD: 12.96-14.48 Ma).

Population structure and genetic diversity of hatchery stocks as revealed by combined mtDNA fragment sequences in Indian major carp, Catla catla

Catla catla is the second most important Indian major carp due to high growth rate and acceptance to consumers for food value. It is widely cultured in the Indian subcontinent as monoculture or polyculture. In the present study, genetic diversity among hatchery stocks (total 218 samples of catla) collected from different geographical regions of India was examined using mtDNA fragment sequence of Cyt b (306 bp) and D loop (710 bp). High numbers (57) of population specific haplotypes were observed in the present study. The results revealed significant genetic heterogeneity for the sequence data (F_ST = 0.27546, p < .05). Analysis of molecular variance revealed significant genetic differentiation among different catla populations. The information generated in present study could be useful to develop broad genetic base populations of catla.

Genetic diversity and population structure of Cirrhinus mrigala revealed by mitochondrial ATPase 6 gene

The genetic diversity and population structure of Cirrhinus mrigala were studied using partial mitochondrial ATPase 6 gene. 155 individuals were collected from six distant rivers of peninsular India. A total of 11 haplotypes were found with haplotype diversity value of 0.46711 and nucleotide diversity 0.00154 indicating a low degree of genetic divergence among populations. The result of AMOVA analysis also revealed that 97.53% of the genetic variation contained within populations and 2.47% occurred among populations. An overall fixation index was found to be 0.02466 (p < .05). Pairwise Fst analysis showed significant genetic differentiation between the Kaveri and rest of the populations. The minimum spanning tree of the haplotype data demonstrated a common ancestral origin of the mrigal populations in peninsular rivers. From the overall results of the present study it may be inferred that mrigal population in peninsular India have low genetic differentiation. This information would be very essential for setting up of genetic improvement programmes, effective management, and conservation of natural genetic resources of mrigal.

Rapid recovery of complete mitogenome of Indian major carp, Catla catla from low depth paired end Illumina sequencing

Here we report the reconstruction of the catla (Catla catla) complete mitochondrial genome sequence from low depth paired end Illumina sequencing. The genome is of 16,597 bp in size. Similar to other vertebrate mtgenomes, it consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. The present mtgenome is 3 bp longer than the earlier reported catla mtgenome from our laboratory. Majority of the mitochondrial genes are encoded by the H-strand. Phylogenetics analysis revealed that Catla catla is closer to Labeo rohita than other labeo species. Present study demonstrated the power of next generation sequencing towards hassle free and rapid sequencing of mitochondrial genomes of non-model organisms.

Complete mitochondrial genome sequence of E. suratensis revealed by next generation sequencing

The complete mitochondrial genome of Etroplus suratensis, the Green chromide cichlid, was determined for the first time through NGS method. The genome is 16,467 bp (Accession no. KU301747) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on plus strand was A: 28.3%, G: 15.2%, C: 30.9%, T: 25.6%, and the A + T content 53.9%. The control region contains a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cichlid fish of India.

India's Computational Biology Growth and Challenges

India's computational science is growing swiftly due to the outburst of internet and information technology services. The bioinformatics sector of India has been transforming rapidly by creating a competitive position in global bioinformatics market. Bioinformatics is widely used across India to address a wide range of biological issues. Recently, computational researchers and biologists are collaborating in projects such as database development, sequence analysis, genomic prospects and algorithm generations. In this paper, we have presented the Indian computational biology scenario highlighting bioinformatics-related educational activities, manpower development, internet boom, service industry, research activities, conferences and trainings undertaken by the corporate and government sectors. Nonetheless, this new field of science faces lots of challenges.

Complete mitochondrial genome sequence of Indian medium carp, Labeo gonius (Hamilton, 1822) and its comparison with other related carp species

In the present study, the complete mitochondrial genome sequence of Labeo gonius is reported using PGM sequencer (Ion Torrent). The complete mitogenome of L. gonius is obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP) which is 16 614 bp in length. The mitogenome of L. gonius comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and D-loop as control region along with gene order and organization, being similar to most of other fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of Labeo fimbriatus, as reported earlier. The phylogenetic analysis of Cypriniformes depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of L. gonius would be helpful in understanding the population genetics, phylogenetics, and evolution of Indian Carps.

Complete mitochondrial genome sequence of Labeo fimbriatus (Bloch, 1975)

The complete mitochondrial genome of Labeo fimbriatus, the fringe-lipped carp, was determined for the first time. The genome was 16,614 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on the plus strand was A: 32.35%, G: 15.46%, C: 27.54%, T: 24.647%, and the A + T content 57%. The control region contains a microsatellite, (TA)12, a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cultivable carps of India.

A comparative study of COI and 16 S rRNA genes for DNA barcoding of cultivable carps in India

The 5' region of the mitochondrial DNA gene cytochrome c oxidase subunit I (COI) is the standard marker for DNA barcoding. However, 16 S rRNA has also been advocated for DNA barcoding in many animal species. Herein, we directly compare the usefulness of COI and 16 S rRNA in discriminating six cultivable carp species: Labeo rohita, Catla catla, Cirrhinus mrigala, Labeo fimbriatus, Labeo bata and Cirrhinus reba from India. Analysis of partial sequences of these two gene fragments from 171 individuals indicated close genetic relationship between Catla catla and Labeo rohita. The results of the present study indicated COI to be more useful than 16 S rRNA for DNA barcoding of Indian carps.

Population divergence and structure of Cirrhinus mrigala from peninsular rivers of India, revealed by mitochondrial cytochrome b gene and truss morphometric analysis

Genetic diversity and population structure of Cirrhinus mrigala from peninsular riverine systems of India was studied using mitochondrial DNA gene, cytochrome b and truss morphometric analysis. Analysis of 982 bp of the cytochrome b gene from 182 samples collected from six rivers revealed the presence of 28 haplotypes with overall high haplotype diversity value of 0.78981 and nucleotide diversity value of 0.00215. Analysis of molecular variance (AMOVA) showed that genetic variation is mainly harbored within populations rather than among populations. The pairwise Fst values (-0.009 to 0.084) was indicative of a low genetic structure among mrigal populations. Morphometric examination of 243 samples using 10 truss landmarks and principal component analysis showed a similar trend when compared with genetic data. Overall, low genetic and morphometric differences were observed despite those populations from different geographic locations. The results of this study would provide essential information to resource recovery and help in delineating populations for fishery management. Besides, the data will provide a valuable baseline for further investigations on the geographic distribution of this commercially important fish species.