First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order

Abstract

BackgroundFour species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management.Principal findingsThe complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic.ConclusionsSequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.

The complete mitochondrial genome and phylogenetic analysis of the dwarf surf clam Mulinia lateralis

“…Thirteen protein-coding genes, two ribosomal RNA genes, and twentytwo transfer RNA genes were annotated by MITOS (Bernt et al 2013). The 13 conserved protein-coding genes were cox (I, II, and III), nad (1, 2, 3, 4, 5, 6, and 4L), atp (6, and 8), and cob as in Venerida (Xu et al 2012;Dong et al 2016;Fernandez-Perez et al 2017;Zhong et al 2017). The sequence has been deposited in GenBank under accession number MN326303.…”

Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae)

“…The phylogenetic analyses inferred from 5S rDNA sequences provides a similar tree to that based on the 13 protein-coding genes of mitochondrial genome of the same species [ 20 ], the phylogeny based on several mitochondrial (16S, COI and Cytb) and nuclear (18S, 28S and H3) genes [ 21 ], and the phylogenetic tree derived from the mitochondrial COI gene [ 30 ]. This is in accordance with other bivalve studies where phylogenies have been successfully reconstructed by using the 5S region (e.g.…”

“…[ 55 , 101 ]). On the other hand, ITS phylogeny displays a different topology, but in all cases D. semistriatus and D. vittatus species are grouped in the same clade when markers of different nature are used [ 20 , 21 , 30 ]. In a previous study carried out by Chow et al [ 5 ] who studied the ITS1 in several marine animals was reported that ITS1 has a limited utility for phylogenetic analysis.…”

“…Four Donax species, Donax semistriatus , Donax trunculus , Donax variegatus and Donax vittatus , are common along the European littoral and live sympatrically in some areas [ 1 , 20 , 21 , 31 , 84 ]. These marine bivalves play an important socioeconomic role in some European coastal regions.…”

“…However, despite the economic importance that genus Donax has for the European seafood sector and of being an overexploited species, until a few years ago basic genetic studies in this organism were neglected. To date, with respect to the Donax genus, the complete female mitochondrial genomes have been sequenced and characterized [ 20 ] and three methods for the molecular identification of European Donax species have been developed [ 22 , 65 , 72 ]. Concerning D. vittatus , a work that deals with the description and study of the karyotype of D. vittatus and compares it with the karyotype of D. trunculus has recently been published [ 30 ] and its genetic diversity and population structure have been evaluated with mitochondrial and nuclear markers [ 21 ].…”