ArticleGenome biology2009
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed, 225 citations in OpenAlex.
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- Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa).BMC plant biology · 2023Article
- Enrichment of intrinsically disordered residues in ohnologs facilitates abiotic stress resilience in Brassica rapa.Journal of plant research · 2023Article
- Identification of Trehalose-6-Phosphate Synthase (TPS) Genes Associated with Both Source-/Sink-Related Yield Traits and Drought Response in Rapeseed (Plants (Basel, Switzerland) · 2023Article
- Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies.Plant communications · 2023Article
- Targeted genome editing in polyploids: lessons fromFrontiers in plant science · 2023Review
- Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield ofFrontiers in plant science · 2023Article
- DWARF AND ROBUST PLANT regulates plant height via modulating gibberellin biosynthesis in chrysanthemum.Plant physiology · 2022Article
- Genome-Wide Identification, Characterization, and Transcriptomic Analysis of the Cyclin Gene Family inInternational journal of molecular sciences · 2022Article
- Interacting partners of Brassica juncea regulator of G-protein signaling protein suggest its role in cell wall metabolism and cellular signaling.Bioscience reports · 2022Article
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- Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View.Plants (Basel, Switzerland) · 2022Review
57 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors at 7 institutions in 2 countries.
Funding
Abstract
backgroundBrassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics.
resultsWe assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago.
conclusionsThis work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.
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