Comparative Analysis between Homoeologous Genome Segments ofBrassica napusand Its Progenitor Species Reveals Extensive Sequence-Level Divergence

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

doi:10.1105/tpc.108.060376

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.

Highlights

Polyploidy is widespread in angiosperms and is thought to have been a predominant factor in the evolution and success of these species (Leitch and Bennett, 1997; Wendel, 2000)
BACs were selected for sequencing defined regions of the genomes of B. rapa and B. napus on the basis of previous physical mapping analyses (Rana et al, 2004; Park et al, 2005), with substitution of the B. napus Contig A BACs listed in Rana et al (2004) for clones identified on the basis of BAC end sequence alignments
The analysis enabled the identification in the sequences derived from B. rapa and B. napus of many interspersed gene fragments, as first described in Brassica species in B. oleracea (Town et al, 2006)

Summary

Introduction

Polyploidy is widespread in angiosperms and is thought to have been a predominant factor in the evolution and success of these species (Leitch and Bennett, 1997; Wendel, 2000). Understanding the mechanisms involved in the structural and functional evolution of genomes during the process of diploidization following polyploidy is of major importance to plant biology. In contrast with tomato and rice, the lineages of which diverged from that of Arabidopsis ;150 and 200 million years ago (Mya), respectively (Yang et al, 1999; Wolfe et al., 1989), the Brassica and Arabidopsis lineages diverged only ;20. Brassica napus is an allopolyploid, arising from the hybridization of A and C genome progenitors (U, 1935), probably during human cultivation (i.e.,

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