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Open Access Correspondence

"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes

Jianfeng Ren13, Xiao Liu1, Guofan Zhang1, Bin Liu12* and Ximing Guo4*

Author Affiliations

1 Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China

2 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, PR China

3 The Graduate University of Chinese Academy of Sciences, Beijing 100039, PR China

4 Haskin Shellfish Research Laboratory, Institute of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ 08349, USA

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BMC Genomics 2009, 10:84  doi:10.1186/1471-2164-10-84

Published: 19 February 2009

Abstract

Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9:477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK1, trnC, trnQ1 and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.