Comparative analysis between homoeologous genome segments of brassica napus and its progenitor species reveals extensive sequence-level divergence

Foo Cheung, Martin Trick, Nizar Drou, Yong Pyo Lim, Jee Young Park, Soo Jin Kwon, Jin A. Kim, Rod Scott, J. Chris Pires, Andrew H. Paterson, Chris Town, Ian Bancroft

Research output: Contribution to journalArticlepeer-review

Abstract

Homoeologous regions of Brassica genomes were analyzed at the sequence level. These represent segments of the Brassica A genome as found in Brassica rapa and Brassica napus and the corresponding segments of the Brassica C genome as found in Brassica olerácea and B. napus. Analysis of synonymous base substitution rates within modeled genes revealed a relatively broad range of times (0.12 to 1.37 million years ago) since the divergence of orthologous genome segments as represented in B. napus and the diploid species. Similar, and consistent, ranges were also identified for single nucleotide polymorphism and insertion-deletion variation. Genes conserved across the Brassica genomes and the homoeologous segments of the genome of Arabidopsis thaliana showed almost perfect collinearity. Numerous examples of apparent transduplication of gene fragments, as previously reported in B. olerácea, were observed in B. rapa and B. napus, indicating that this phenomenon is widespread in Brassica species. In the majority of the regions studied, the C genome segments were expanded in size relative to their A genome counterparts. The considerable variation that we observed, even between the different versions of the same Brassica genome, for gene fragments and annotated putative genes suggest that the concept of the pan-genome might be particularly appropriate when considering Brassica genomes.

Original languageEnglish (US)
Pages (from-to)1912-1928
Number of pages17
JournalPlant Cell
Volume21
Issue number7
DOIs
StatePublished - Jul 2009

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology

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