Running title: A chromosome-level genome assembly of Chinese flowering cabbage
Guangguang Li1#, Juntao Wang2,3#, Yi Liao4#, Ding Jiang1, Yansong Zheng1, Xiuchun Dai1, Hailong Ren1, Jianjun Lei2,3, Guoju Chen2,3, Bihao Cao2,3, Hua Zhang1*, and Changming Chen2,3*
1 Guangzhou Institute of Agriculture Science, Guangzhou, 510308, China
2 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China
3 Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
4 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
# Equal contributors
Correspondence should be addressed to Changming Chen, cmchen@scau.edu.cn and Hua Zhang, Huangz123@163.com
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 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.
Keywords: Chinese flowering cabbage; Brassica rapa var.parachinensis ; genome structure evolution; assembly; PacBio; Hi-C