Mitochondrial recovery from shotgun metagenome sequencing enabling phylogenetic analysis of the common thresher shark (Alopias vulpinus)

The common thresher shark (Alopias vulpinus) is an important fisheries species in the northeastern Pacific Ocean along California, USA and Mexico; yet genetic understanding of this species is incomplete. Using IonTorrent PGM generated metagenomic libraries constructed from the skin surface, we recovered the complete mitogenome of the common thresher shark. The length of the mitogenome was 16,712 basepairs and consisted of 22 tRNA, two rRNA, 13 protein coding sequences, a replication origin and a control region, similar to other Alopias spp. The median coverage across the mitogenome was 21 ×, ranging from 1 to 48 × coverage. The mean GC content of the mitogenome was 37.83%. Using the 13 protein coding genes of the mitogenome, we show phylogenetic placement of the common thresher shark with the pelagic thresher (Alopias pelagicus; a posterior probability of 1). In addition, the inclusion of this mitogenome increased certainty for the placement of the Lamniformes family with the Carcharhiniformes family (a posterior probability of 1), rather than with the Orectolobeformes family, as has been previously reported. The availability of the common thresher shark mitogenome will aid phylogenetic inference and population based studies of this important fisheries species.