Complete mitochondrial DNA sequence of the European flat oyster Ostrea edulis confirms Ostreidae classification

Danic-Tchaleu et al. BMC Research Notes 2011, 4:400 http://www.biomedcentral.com/1756-0500/4/400 RESEARCH ARTICLE Open Access Complete mitochondrial DNA sequence of the European flat oyster Ostrea edulis confirms Ostreidae classification Gwenaelle Danic-Tchaleu, Serge Heurtebise, Benjamin Morga and Sylvie Lapègue* Abstract Background: Because of its typical architecture, inheritance and small size, mitochondrial (mt) DNA is widely used for phylogenetic studies. Gene order is generally conserved in most taxa although some groups show considerable variation. This is particularly true in the phylum Mollusca, especially in the Bivalvia. During the last few years, there have been significant increases in the number of complete mitochondrial sequences available. For bivalves, 35 complete mitochondrial genomes are now available in GenBank, a number that has more than doubled in the last three years, representing 6 families and 23 genera. In the current study, we determined the complete mtDNA sequence of O. edulis, the European flat oyster. We present an analysis of features of its gene content and genome organization in comparison with other Ostrea, Saccostrea and Crassostrea species. Results: The Ostrea edulis mt genome is 16 320 bp in length and codes for 37 genes (12 protein-coding genes, 2 rRNAs and 23 tRNAs) on the same strand. As in other Ostreidae, O. edulis mt genome contains a split of the rrnL gene and a duplication of trnM. The tRNA gene set of O. edulis, Ostrea denselamellosa and Crassostrea virginica are identical in having 23 tRNA genes, in contrast to Asian oysters, which have 25 tRNA genes (except for C. ariakensis with 24). O. edulis and O. denselamellosa share the same gene order, but differ from other Ostreidae and are closer to Crassostrea than to Saccostrea. Phylogenetic analyses reinforce the taxonomic classification of the 3 families Ostreidae, Mytilidae and Pectinidae. Within the Ostreidae family the results also reveal a closer relationship between Ostrea and Saccostrea than between Ostrea and Crassostrea. Conclusions: Ostrea edulis mitogenomic analyses show a high level of conservation within the genus Ostrea, whereas they show a high level of variation within the Ostreidae family. These features provide useful information for further evolutionary analysis of oyster mitogenomes. Background Because of its typical architecture, inheritance and small size, animal mitochondrial (mt) DNA is widely used for phylogenetic studies. Combined with these characteristics, its typically maternal inheritance contributes to a fast rate of evolution. Nucleotide changes combined with gene order and rearrangement data can provide valuable information on major evolutionary changes at different taxonomic levels. Typically, animal mtDNA is a compact molecule (14 to 17 kb), though some mtDNA can be vastly larger (e.g., Plactopecten magellanicus [1]), and usually encodes 13 proteins, 22 transfer * Correspondence: IFREMER, Laboratoire de Génétique et Pathologie, F-17390 La Tremblade, France RNAs (tRNAs) and 2 ribosomal RNAs (rRNAs) [2]. There are often few intergenic nucleotides except for a single large non-coding region generally thought to contain elements that control the initiation of replication and transcription [3]. Size variation in mtDNA is usually due to the different length of the non-coding regions. Gene order is generally conserved in most taxa, although some groups show considerable variation. This is particularly so in the Mollusca phylum, especially in Bivalvia and Scaphopoda [4]. In addition to the fact that phylogenetic relationships among major molluscan groups are not well understood, the species classification of some of the most common mollusks remains difficult. A case in point is oysters, for which a plastic growth pattern is a major feature, resulting in a wide range of © 2011 Lapègue et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Danic-Tchaleu et al. BMC Research Notes 2011, 4:400 http://www.biomedcentral.com/1756-0500/4/400 Page 2 of 10 overlapping ecophenotypic variants [5,6]. Oysters are bivalve molluscs that are widely distributed in the world’s oceans. As benthic, sessile filter-feeders, they play an important role in estuarine ecosystems. Moreover, some species are of economic importance, like the Pacific cupped oyster, which is grown in 27 countries and is the most highly produced mollusc species in the world. Oysters have been introduced all over the world for culture and many species are sympatric. Numerous species (30-40 according to the classifications) of oysters of the genus Ostrea have been described. Their geographical range is particularly wide in warm and temperate waters of all oceans, although they have a predominantly tropical distribution [6,7]. In Europe, along the Atlantic and Mediterranean coasts, the European flat oyster, Ostrea edulis, is an important economic marine resource: in 2009 almost 3000 tons were produced in the world, mainly (91%) in Europe (Spain, France, Ireland ...) [8]. During the last few years, there have been significant increases in the number of complete mitochondrial sequences available for all species. The number has more than doubled for molluscs in the last three years [9], so that 98 complete mollusk mitochondrial genomes are now available in GenBank, mainly from gastropods (43), bivalves (35) and cephalopods (14). Among bivalves, the sequenced genomes represent 6 families and 23 genera. In the Ostreidae, the genus Crassostrea has been thoroughly studied, with 7 representatives (6 Asian oysters and 1 American oyster) [10]. In contrast, there is only one representative of the genus Saccostrea (Saccostrea mordax), and one of the genus Ostrea (Ostrea denselamellosa). Recent studies have provided a more comprehensive picture of the cupped oyster genome, showing an unusually high conservation of mitochondrial gene order in Asian Crassostrea species [11]. Even though molecular tools, such as mitochondrial or microsatellite markers, already exist for the European flat oyster and allow population genetics [12] or quantitative genetics [13] studies, the complete characterization of its mtDNA will allow a better study to be made of phylogenetic relationships among members of the genus, especially between the closely-related species O. edulis and O. angasi [14], to improve classification of the Ostreidae family within the Bivalvia. (16 532 bp for S. mordax to 22 446 bp for C. iredalei), and is within the size range of the Pteriomorphia mt genomes published to date: from 16 211 nt for Argopecten irradians [15] to 32 115 nt for Placopecten magellanicus [1]. In the mt genome of O. edulis, a total of 965 bp of non-coding nucleotides is spread (...truncated)