ArticleGenome biology2010
Sequence and structure of Brassica rapa chromosome A3.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Review
- Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis ofFrontiers in plant science · 2022Article
- Improved Reference Genome Annotation ofFrontiers in plant science · 2022Article
- Meiotic chromosome axis remodelling is critical for meiotic recombination in Brassica rapa.Journal of experimental botany · 2021Article
- Article
- Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity inFrontiers in plant science · 2020Article
- Article
- Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution.Scientific reports · 2017Article
- Expression profiles ofFEBS open bio · 2017Article
- A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage.Scientific reports · 2017Article
- Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.Genetics · 2016Article
- Differential expression ofMolecular biology research communications · 2014Article
- Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene, a homologue of CLAVATA3 in Arabidopsis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2014Article
- Article
- Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.PloS one · 2014Article
- Genome triplication drove the diversification of Brassica plants.Horticulture research · 2014Review
- Review
- Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa.BMC genomics · 2013Article
- Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa.Plant cell reports · 2013Article
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38 authors.
Funding
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.
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