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A high-continuity genome assembly of Chinese flowering cabbage (Brassica rapa var. parachinensis) provides new insights into Brassica genome structure evolution
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  • Guangguang Li,
  • Juntao Wang,
  • Yi Liao,
  • Ding Jiang ,
  • Yansong Zheng,
  • Xiuchun Dai,
  • Hailong Ren,
  • Hua Zhang,
  • Changming Chen
Guangguang Li

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Juntao Wang
South China Agricultural University
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Ding Jiang
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Yansong Zheng
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Xiuchun Dai
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Hailong Ren
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Changming Chen
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Chinese flowering cabbage (Brassica rapa var. parachinensis) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality de novo assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA elements and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, Brassica juncea. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely drive by LTR-retrotransposon amplification. This lineage-specific expansion may play a role in the species divergence in the Brassica genus. Furthermore, we found that a large amount of structural variations (SVs) identified within B. rapa lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of B. rapa crops.