Sequence and structure of Brassica rapa chromosome A3

Abstract

BackgroundThe species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.ResultsWe have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3.ConclusionsWe report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.

The genome of the mesopolyploid crop species Brassica rapa

“…These assemblies show excellent agreement with 647 BACs 12 and previously assembled chromosome A3 13 (Figure 1), the transposon-related sequences were most abundant in the vicinity of centromeres, inversely related to the abundance of protein-coding genes. We estimated that transposon-related sequences occupy 39.51% of the genome, with the proportions of retrotransposons (with LTRs), DNA transposons and LINEs being 27.14%, 3.20% and 2.82%, respectively (Supplementary Table S3.1T4).…”

Centromere Locations inBrassicaA and C Genomes Revealed Through Half-Tetrad Analysis

“…Hence, our centromere-positioning analysis suggests that the short arm of chromosome A03 has not been assembled in the published Darmor reference genome. This is not surprising as the short arm of chromosome A03 is a known nucleolar organizing region (NOR), composed of repetitive elements and arrays; Mun et al (2010) were also unable to identify any BACs localized to this chromosome arm in their sequence and assembly of A03. Cheng et al (2013) performed an extensive investigation of paleocentromeres in B. rapa using a sequence-based approach.…”

Deciphering the Diploid Ancestral Genome of the MesohexaploidBrassica rapa

“…A comparison of the B. rapa genome sequence with previously reported linkage maps shows that block D on chromosome A01; blocks W, Q, X, M, and D on A03; S on A05; M, H, and U on A6; F, X, and S on A07; S on A08; K, L, and M on A09; and C on A10 were not detected by genetic mapping (Parkin et al, 2005;Panjabi et al, 2008;Kim et al, 2009;Trick et al, 2009). Although the assembly of B. rapa chromosome A03 by Mun et al (2010) identified 14 GBs or block segments, three additional blocks on the same chromosome were detected within the B. rapa reference genome . Similarly, the 2.4-Mb fragment of block W within the V/K/L/Wa/Q/X association was not detected by genetic mapping.…”