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.
Highlights
Because of its nature of maternal inheritance, mitochondrial genome has a fast rate of evolution and is useful in phylogenetic analysis
We read with great interest an article appeared in a recent issue of BMC Genomics (9:477 2008) entitled 'Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis – a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea?' by Yu, Z.N., Wei, Z.P., Kong, X.Y., and Shi, W. [1]
To test our hypothesis that the gene block between duplicated rrnS failed to amplify in Yu et al.'s study, we synthesized the three primer pairs used by Yu et al
Summary
Because of its nature of maternal inheritance, mitochondrial (mt) genome has a fast rate of evolution and is useful in phylogenetic analysis. 0 0 21 130 108 1 21 3 15 67 7 178 0 0 29 17 1 58 0 0 5 512 608 42 34 60 2 7 1 11 33 5 35 35 20 5 3 0 and two duplicated or split rRNA genes (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' Cox (2575–3438) cob (3670–4875) cob-trnD (4876–4983) cox (5054–5755) cox2-trnS1(5756–5845) rrnS1(6452–7525) rrnL-trnN (8385–8442) rrnS2 (8509–9698)
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