Ion Torrent next-generation sequencing reveals the complete mitochondrial genome of black and reddish morphs of the Coral Trout Plectropomus leopardus

Abstract

Using Ion Torrent next-generation sequencing (NGS) technology, we sequenced the complete mitochondrial genome (mitogenome) of black and reddish morphs of the coral trout Plectropomus leopardus. High-throughput sequencing generated a total of 958,614 sequence reads covering 164.80 Mb of two mitogenomes with a coverage of 4800X. Thirty-seven mitochondrial genes and gene order of P. leopardus was quite similar to that of other teleostean fishes. Most genes were either abutted or overlapped, and all the protein-coding genes began with an ATG start codon except for COX1 and ATP6. The number of stop codon was different for the black and reddish P. leopardus. Comparisons between the mitochondrial sequences of the two morphs revealed a total of 74 variable sites and one indel. Nucleotide diversity across protein-coding gene varied from 0.0006 (16s rRNA) to 0.0070 (Cytochrome b). As expected, the highest level of nucleotide diversity (0.0291) was detected in the control region. Our results demonstrate the NGS technology based on Ion torrent platform can be used to assemble the mitogenome of fish species.