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

Jianfeng Ren, Xiao Liu, Guofan Zhang, Bin Liu, Ximing Guo

Research output: Contribution to journalArticle

17 Citations (Scopus)

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.

Original languageEnglish (US)
Article number84
JournalBMC genomics
Volume10
DOIs
StatePublished - Feb 19 2009

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Crassostrea
Ostreidae
Mitochondrial Genome
Genome
rRNA Genes
Gene Rearrangement
Genomics
Transfer RNA
Artifacts
Mitochondria
DNA
Genes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Biotechnology

Cite this

Ren, Jianfeng ; Liu, Xiao ; Zhang, Guofan ; Liu, Bin ; Guo, Ximing. / "Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes. In: BMC genomics. 2009 ; Vol. 10.
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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.",
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"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes. / Ren, Jianfeng; Liu, Xiao; Zhang, Guofan; Liu, Bin; Guo, Ximing.

In: BMC genomics, Vol. 10, 84, 19.02.2009.

Research output: Contribution to journalArticle

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