A high-continuity genome assembly of Chinese flowering cabbage (Brassica rapa var. parachinensis) provides new insights into Brassica genome structure evolution

Abstract

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 LTRretrotransposon 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.

The Genome-Wide Identification of the R2R3-MYB Gene Family in Chinese Flowering Cabbage and the Characterization of Its Response to Pectobacterium carotovorum Infection

“…The clean data were subsequently mapped to the Brassica rapa var. parachinensis reference genome [28]. HTSeq (v0.6.1) was used to count the read numbers mapped to each gene, and the fragments per kilobase of transcript sequences per million sequenced base pairs (FPKM) were calculated based on the length of the gene and read counts mapped to this gene [29].…”