Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives

Abstract

SummaryThe cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10 000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.

Repeated Polyploidy Drove Different Levels of Crossover Suppression between Homoeologous Chromosomes inBrassica napusAllohaploids

“…In principle, this difference could reflect chromosome rearrangements that accentuated the divergence between B. napus homoeologous chromosomes after the inception of this species. However, although a few genetic changes were detected in several B. napus cultivars (references cited in the introduction), accumulating evidence indicates that the B. napus A/C genomes remain essentially the same as the A/C genomes of their progenitors (Bohuon et al, 1996;Parkin and Lydiate, 1997;Rana et al, 2004;Suwabe et al, 2008;Cheung et al, 2009). This suggests that natural B. napus has evolved or inherited Pairinghomoeologous loci that ensure proper chromosome recombination and segregation (such as PrBn; Jenczewski et al, 2003;Liu et al, 2006;Nicolas et al, 2009).…”

Gene families and evolution of trehalose metabolism in plants

“…Two AtTPS1-like gene fragments (AJ856246 and DX046489) were also identified from Chinese cabbage, indicating the presence of at least one AtTPS1-like isoform in this species, in addition to the three shorter isoforms. On current evidence it appears that the duplication or transposition events that gave rise to the AtTPS2-3 and AtTPS4 genes may have occurred after the divergence of the Brassicaceae lineage from other flowering plants, but predated the divergence of the Arabidopsis and Brassica lineages, which is estimated to have occurred ∼20 million years ago (Rana et al 2004). However, this tentative conclusion may need to be revised as more sequence data become available from other families within the order Brassicales, which are at present less well represented in the NCBI GenBank sequence database than the Brassicaceae.…”

Karyotype and Identification of All Homoeologous Chromosomes of AllopolyploidBrassica napusand Its Diploid Progenitors

“…B. napus (AACC; 2n ¼ 38) is an allopolyploid species formed by the hybridization of ancestors of Brassica rapa (AA; 2n ¼ 20) and Brassica oleracea (CC, 2n ¼ 18), while allopolyploid Brassica carinata (BBCC, 2n ¼ 34) is formed from Brassica nigra (BB, 2n ¼ 16) and B. oleracea, and allopolyploid Brassica juncea (AABB, 2n ¼ 36) is formed from B. rapa and B. nigra (U, Nagahara 1935). Judging from sequence variations within chromosome segments, domesticated B. napus has A-and C-genome components that have had few genetic changes relative to the presumed progenitor lines of B. rapa and B. oleracea (Rana et al 2004;Cheung et al 2009). Genetic mapping studies of B. napus cultivars have revealed only a few chromosomal rearrangements caused by recombination between homoeologous regions of the A and C genomes Sharpe et al 1995;Jenczewski et al 2003;Osborn et al 2003a;Udall et al 2005).…”