Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus

PeerJ

article

Regina L. Cunha¹  Katy R. Nicastro¹  Gerardo I. Zardi³  Celine Madeira¹  Christopher D. McQuaid³  Cymon J. Cox¹  Rita Castilho¹ 

[1] Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas;CNRS, Univ. Littoral Côte d’Opale, UMR 8187 – LOG – Laboratoire d’Océanologie et de Géosciences, Université de Lille;Department of Zoology and Entomology, Rhodes University

关键词: Mitogenomics;    Perna perna;    Gene rearrangements;    Polyphyly;    Primer-walking;   

DOI  :  10.7717/peerj.13953

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the “primer-walking” method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.

【 授权许可】

CC BY