| Summary: | <p>Abstract</p> <p>Background</p> <p>Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five <it>Crassostrea </it>species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (<it>C. iredalei </it>and <it>Saccostrea mordax</it>) for a comprehensive analysis.</p> <p>Results</p> <p>The six Asian <it>Crassostrea </it>mt genomes ranged from 18,226 to 22,446 bp in size, and all coded for 39 genes (12 proteins, 2 rRNAs and 25 tRNAs) on the same strand. Their genomes contained a split of the <it>rrnL </it>gene and duplication of <it>trnM</it>, <it>trnK </it>and <it>trnQ </it>genes. They shared the same gene order that differed from an Atlantic sister species by as many as nine tRNA changes (6 transpositions and 3 duplications) and even differed significantly from <it>S. mordax </it>in protein-coding genes. Phylogenetic analysis indicates that the six Asian <it>Crassostrea </it>species emerged between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago.</p> <p>Conclusions</p> <p>The complete conservation of gene order in the six Asian <it>Crassostrea </it>species over 43 Myr is highly unusual given the remarkable rate of rearrangements in their sister species and other bivalves. It provides strong evidence for the recent speciation of the six <it>Crassostrea </it>species in Asia. It further indicates that changes in mt gene order may not be strictly a function of time but subject to other constraints that are presently not well understood.</p>
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