Genetic diversity and genome-scale population structure of wild Indian major carp, Labeo catla (Hamilton, 1822), revealed by genotyping-by-sequencing

Labeo catla (catla) is the second most commercially important and widely cultured Indian major carp (IMC). It is indigenous to the Indo-Gangetic riverine system of India and the rivers of Bangladesh, Nepal, Myanmar, and Pakistan. Despite the availability of substantial genomic resources in this important species, detailed information on the genome-scale population structure using SNP markers is yet to be reported. In the present study, the identification of genome-wide single nucleotide polymorphisms (SNPs) and population genomics of catla was undertaken by re-sequencing six catla populations of riverine origin from distinct geographical regions. DNA isolated from 100 samples was used to perform genotyping-by-sequencing (GBS). A published catla genome with 95% genome coverage was used as the reference for mapping reads using BWA software. From a total of 472 million paired-end (150 × 2 bp) raw reads generated in this study, we identified 10,485 high-quality polymorphic SNPs using the STACKS pipeline. Expected heterozygosity (He) across the populations ranged from 0.162 to 0.20, whereas observed heterozygosity (Ho) ranged between 0.053 and 0.06. The nucleotide diversity (π) was the lowest (0.168) in the Ganga population. The within-population variation was found to be higher (95.32%) than the among-population (4.68%) variation. However, genetic differentiation was observed to be low to moderate, with Fst values ranging from 0.020 to 0.084, and the highest between Brahmani and Krishna populations. Bayesian and multivariate techniques were used to further evaluate the population structure and supposed ancestry in the studied populations using the structure and discriminant analysis of principal components (DAPC), respectively. Both analyses revealed the existence of two separate genomic clusters. The maximum number of private alleles was observed in the Ganga population. The findings of this study will contribute to a deeper understanding of the population structure and genetic diversity of wild populations of catla for future research in fish population genomics

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

Statistics of microsatellite search in <i>Labeo rohita</i>.

<p>Statistics of microsatellite search in <i>Labeo rohita</i>.</p

QC report for fastQ files.

<p>¹* >70% of bases in a read with >20 phred score</p><p>QC report for fastQ files.</p

A,B,C,D,E.

<p>Comparison of relative expression ratio of 13 known transcripts in different tissues between <i>post-spawning</i> and <i>preparatory</i> phase using beta actin as reference (whisker-box plots), where the 13 transcripts are, 1 = Estrogen receptor binding site associated antigen 9 variant 1, 2 = Vitellogenin receptor, 3 = Insulin receptor b, 4 = Fibrinogen gamma chain, 5 = Green sensitive cone opsin, 6 = Steroid receptor homolog svp 46, 7 = Spermatogenic glyceraldehyde-3-phosphate dehydrogenase, 8 = Semaphorin 3fa, 9 = Follistatin-like 2, 10 = Cathepsin-Z, 11 = 11-beta-hydroxysteroid dehydrogenase, 12 = Prolactin and 13 = Activin receptor.</p

The oases contigs/transcripts blasted against the Salmon, Zebrafish, and Catfish mRNA sequences (from NCBI).

<p>Those contigs with more than 70% identity and 50% query coverage (mRNA) as cut offs was taken for analysis;</p

Distribution of reproduction-relevant transcripts identified in <i>Labeo rohita</i>.

<p>A total of 940 reproduction relevant genes were distributed among 184 reproduction related proteins (GO: 0000003), 223 related to hormone activity (GO: 0005179) and receptor binding related proteins (GO: 0005102), 178 receptor activity related proteins (GO: 0004872) and 355 embryonic development related proteins (GO: 0009792).</p

Comparison of number of contigs, N50 length, average contigs length, at different k-mer value.

<p>Comparison of number of contigs, N50 length, average contigs length, at different k-mer value.</p

Identification of SNPs from rohu contigs.

<p>Identification of SNPs from rohu contigs.</p

GnRH Pathway in rohu: 66 transcripts coding for 40 genes were mapped in rohu, out of 121 genes of GnRH pathway (KEGG databases).

<p>GnRH Pathway in rohu: 66 transcripts coding for 40 genes were mapped in rohu, out of 121 genes of GnRH pathway (KEGG databases).</p