Complete F mitochondrial genomes of the Biwa pearl mussel, Hyriopsis schlegelii: the first report from the species' native lake in Japan

Abstract

We determined two complete mitochondrial sequences of female-transmitted (F) mitogenomes of two Hyriopsis schlegelii specimens from this species' original habitat, Lake Biwa. The mitogenomes were both 15,951 bp in length, and the gene contents and orders agreed with those of the typical F mitogenome of Hyriopsis. Molecular phylogenetic analysis based on the previously identified 13 partial sequences confirmed that the two mitogenomes both belonged to H. schlegelii and not to a closely related Chinese species, Hyriopsis cumingii. The same analysis revealed that two mitogenomes (HQ641406 and FJ529186) previously published as H. schlegelii and H. cumingii might be misidentified.

Keywords: F mitogenome; Hyriopsis cumingii; Hyriopsis schlegelii; Illumina sequencing; Lake Biwa.

Figure 1.

Supermatrix tree of four whole mitochondrial (15,939–15,954 bp) and 13 partial COX2-COX1 region (1027 bp) sequences of female-transmitted (F) mitogenomes of Hyriopsis schlegelii and H. cumingii. Bootstrap support (80% or over) is indicated at the nodes. Accession numbers are indicated after the species names with haplotype names of Shirai et al. (2010) in parentheses for partial sequences. Species names and accession numbers of the four mitogenomes are boxed, and the two mitogenomes sequenced in this study are indicated by arrows. The tree backbone was first generated for the four mitogenomes by the neighbor-joining (NJ) method using the online version of MAFFT (https://mafft.cbrc.jp/alignment/server/). The obtained NJ tree was then used as a backbone constraint for the supermatrix tree. The supermatrix tree was constructed based on the dataset including the four mitogenome and 13 partial sequences, which were first multiple aligned using MAFFT and corrected by eye using Mesquite (version 3.31; http://www.mesquiteproject.org). For the resultant 16,003-bp dataset, maximum likelihood analysis was performed using RAxML BlackBox (https://embnet.vital-it.ch/raxml-bb/).