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Background  Mitochondrial DNA sequences are extensively used as genetic markers not only for studies of population or ecological genetics, but also for phylogenetic and evolutionary analyses. Complete mt-sequences can reveal information about gene order and its variation, as well as gene and genome evolution when sequences from multiple phyla are compared. Mitochondrial gene order is highly variable among mollusks, with bivalves exhibiting the most variability. Of the 41 complete mt genomes sequenced so far, 12 are from bivalves. We determined, in the current study, the complete mitochondrial DNA sequence of  Crassostrea hongkongensis . We present here an analysis of features of its gene content and genome organization in comparison with two other  Crassostrea  species to assess the variation within bivalves and among main groups of mollusks.    Results  The complete mitochondrial genome of  C. hongkongensis  was determined using long PCR and a primer walking sequencing strategy with genus-specific primers. The genome is 16,475 bp in length and contains 12 protein-coding genes (the  atp8  gene is missing, as in most bivalves), 22 transfer tRNA genes (including a suppressor tRNA gene), and 2 ribosomal RNA genes, all of which appear to be transcribed from the same strand. A striking finding of this study is that a DNA segment containing four tRNA genes ( trnk1, trnC, trnQ1  and  trnN ) and two duplicated or split rRNA gene ( rrnL5'  and  rrnS ) are absent from the genome, when compared with that of two other extant  Crassostrea  species, which is very likely a consequence of loss of a single genomic region present in ancestor of  C. hongkongensis . It indicates this region seem to be a "hot spot" of genomic rearrangements over the  Crassostrea  mt-genomes. The arrangement of protein-coding genes in  C. hongkongensis  is identical to that of  Crassostrea gigas  and  Crassostrea virginica , but higher amino acid sequence identities are shared between  C. hongkongensis  and  C. gigas  than between other pairs. There exists significant codon bias, favoring codons ending in A or T and against those ending with C. Pair analysis of genome rearrangements showed that the rearrangement distance is great between  C. gigas - C. hongkongensis  and  C. virginica , indicating a high degree of rearrangements within  Crassostrea . The determination of complete mt-genome of  C. hongkongensis  has yielded useful insight into features of gene order, variation, and evolution of  Crassostrea  and bivalve mt-genomes.    Conclusion  The mt-genome of  C. hongkongensis  shares some similarity with, and interesting differences to, other  Crassostrea  species and bivalves. The absence of  trnC  and  trnN  genes and duplicated or split rRNA genes from the  C. hongkongensis  genome is a completely novel feature not previously reported in  Crassostrea  species. The phenomenon is likely due to the loss of a segment that is present in other  Crassostrea  species and was present in ancestor of  C. hongkongensis , thus a case of "tandem duplication-random loss (TDRL)". The mt-genome and new feature presented here reveal and underline the high level variation of gene order and gene content in  Crassostrea  and bivalves, inspiring more research to gain understanding to mechanisms underlying gene and genome evolution in bivalves and mollusks.

bmc genomics

Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea?