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PMID: 19602626 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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

The Plant cell ·Vol. 21 ·No. 7 ·2009-07-00 ·Pages 1912-28

Cheung F, Trick M, Drou N, Lim YP, Park JY, Kwon SJ, Kim JA, Scott R, Pires JC, Paterson AH, Town C, Bancroft I

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 oleracea 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. oleracea, 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.

MeSH Terms
Brassica/genetics Brassica napus/genetics Evolution, Molecular Genome, Plant/genetics Molecular Sequence Data Sequence Analysis, DNA
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Cheung Foo
The J. Craig Venter Institute, Rockville, Maryland 20850, USA.
Trick Martin
Drou Nizar
Lim Yong Pyo
Park Jee-Young
Kwon Soo-Jin
Kim Jin-A
Scott Rod
Pires J Chris
Paterson Andrew H
Town Chris
Bancroft Ian
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.108.060376
Published
2009-07-00
Epub
2009-00-14
Pages
1912-28
Language
English
Region
England
NLM ID
9208688
PMCID
PMC2729604
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/E017363/1 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/E017363 · United Kingdom
Biotechnology and Biological Sciences Research Council · BBS/B/07330 · United Kingdom
External Links
PubMed source DOI: 10.1105/tpc.108.060376 PMC Full Text View journal details
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