Abstract

Background: 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
Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly
released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis.

Results: The six Asian Crassostrea 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 rrnL gene
and duplication of trnM, trnK and trnQ 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
S. mordax in protein-coding genes. Phylogenetic analysis indicates that the six Asian Crassostrea species emerged
between 3 and 43 Myr ago, while the Atlantic species evolved 83 Myr ago.

Conclusions: The complete conservation of gene order in the six Asian Crassostrea 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 Crassostrea 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.