Assembly and variation analyses of Clarias batrachus mitogenome retrieved from WGS data and its phylogenetic relationship with other catfishes

Abstract

Whole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequencethe mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data ofClarias batrachus,generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome usingbothde novoand reference based approaches. Both the methods yielded almost similar results and the bestassembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotationresulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order wasfound to be identical with other catfishes. Variation analyses between assembled and the reference (GenBankAcc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequencesand tRNA supports the monophyly of catfishes. Two SSRs were identified inC. batrachusmitogenome, out ofwhich one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrialgenes were found to evolve at a much faster pace than theD-loop, which in turn are followed by the rRNAs; thetRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among thecoding genes,ND2evolves most rapidly. The variations present in the coding regions of the mitogenome andtheir comparative analyses with other catfish species may be useful in species conservation and management programs