Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Abstract

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.

Comparative Analysis of the nrDNA Repeat Unit of Manila Clam Ruditapes philippinarum and Quahog Mercenaria mercenaria

“…This finding agreed with Salvi and Mariottini (2012) [5]. The mitochondrial genome analysis showed that P. undulata was clustered with other Tapetinae species [3,6]. Just four partial ITS sequences of P. undulata were deposited in the GenBank database (JN996788, JN996787, JN996750 and EU183531), and the identity of ITS1 and ITS2 of them were just 36.16% and 58.25%, respectively.…”

“…Many Veneridae species are economically important due to their huge abundance in benthic environments, such as the Manila clam Ruditapes philippinarum, the northern quahog Mercenaria mercenaria, the western Pacific hard clam Meretrix petechialis, the equilateral clam Gomphina aequilatera and the Taca clam Protothaca theca [1][2][3]. The classification system and phylogenetic re-lationships of Veneridae have been based mainly on morphological characteristics and molecular data (mitochondrial and nuclear sequences) [1,2,[4][5][6], which are currently un-der debate. Problems with existing classification methods are attributed to (1) the con-vergence of the evolutionary and phenotypic plasticity of morphological traits in most venerids [6]; (2) double uniparental inheritance (DUI) of mitochondrial DNA in some Veneridae species [7][8][9];…”

“…The classification system and phylogenetic re-lationships of Veneridae have been based mainly on morphological characteristics and molecular data (mitochondrial and nuclear sequences) [1,2,[4][5][6], which are currently un-der debate. Problems with existing classification methods are attributed to (1) the con-vergence of the evolutionary and phenotypic plasticity of morphological traits in most venerids [6]; (2) double uniparental inheritance (DUI) of mitochondrial DNA in some Veneridae species [7][8][9];…”

Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia

“…It can be used to investigate the ancestral lineage of phylogeny, and to establish the mechanism of gene replication, regulation and rearrangement. Bivalves of molluscs have highly variable mitochondrial gene sequences, and are the most mutated species in metazoa [ 61 , 62 ]. In the study, we selected some species from four orders of the superorder Impardentia, Venerida, Cardiida, Adapedonta and Lucinida as representatives of bivalves to study mitochondrial gene rearrangement ( Fig 6 ).…”

Characteristics of Complete Mitochondrial Genomes Reveals a Potential Division of Genus Modiolus into Three Genera

“…Mitochondrial DNA (mtDNA) exhibits special characteristics that differ from the nuclear genome, such as rapid evolution, maternal inheritance, and lack of recombination [1], and has been an e cient tool and widely used in molluscan evolutionary and phylogenetic analyses [2,3]. Molluscan mtDNA is nearly a closed circular molecule, always containing 13 protein-coding genes (NADH dehydrogenase subunits 1-6 and 4L, ATPase subunits six and eight, cytochrome oxidase subunits 1-3, and cytochrome b), 22 transfer RNA genes and two ribosomal RNAs (rrnS and rrnL) [4,5], with missing ATPase subunits eight, variable tRNAs and extra rrnS in some species [6][7][8]. Different mtDNA composition would result in functional diversity, as mtDNA carries genetic information essential to mitochondrial function [9], thus it's interesting to explore the difference of mtDNA related to adaptive evolution.…”