Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species

First author: Deling Sun; Affiliations: Tianjin Academy of Agricultural Sciences (天津农科院): Tianjin, China

Corresponding author: Deling Sun

Cauliflower is an important variety of Brassica oleracea and is planted worldwide. Here, the high-quality genome sequence of cauliflower was reported. The assembled cauliflower genome was 584.60 Mb in size, with a contig N50 of 2.11 Mb, and contained 47,772 genes; 56.65% of the genome was composed of repetitive sequences. Among these sequences, long terminal repeats (LTRs) were the most abundant (32.71% of the genome), followed by transposable elements (TEs) (12.62%). Comparative genomic analysis confirmed that after an ancient paleohexaploidy (γ) event, cauliflower underwent two whole-genome duplication (WGD) events shared with Arabidopsis and an additional whole-genome triplication (WGT) event shared with other Brassica species. The present cultivated cauliflower diverged from the ancestral B. oleracea species ~3.0 million years ago (Mya). The speciation of cauliflower (~2.0  Mya) was later than that of B. oleracea L. var. capitata (approximately 2.6  Mya) and other Brassica species (over 2.0  Mya). Chromosome no. 03 of cauliflower shared the most syntenic blocks with the A, B, and C genomes of Brassica species and its eight other chromosomes, implying that chromosome no. 03 might be the most ancient one in the cauliflower genome, which was consistent with the chromosome being inherited from the common ancestor of Brassica species. In addition, 2,718 specific genes, 228 expanded genes, 2 contracted genes, and 1,065 positively selected genes in cauliflower were identified and functionally annotated. These findings provide new insights into the genomic diversity of Brassica species and serve as a valuable reference for molecular breeding of cauliflower.

花椰菜是一个重要的甘蓝品种，在全球均有栽培。本文中，作者报道了花椰菜的高质量参考基因组。花椰菜基因组组装共584.60Mb，contig N50长2.11Mb，共注释47772个基因，重复序列含量56.65%。其中，长末端重复LTR含量最多，占基因组32.71%，其次是转座因子TE，占基因组的12.62%。比较基因组分析显示在古六倍化之后，花椰菜还经历了两次与拟南芥共享的全基因组复制事件，以及一次与其它芸薹属植物共享的全基因组三倍化事件。现代栽培种花椰菜来自于三百万年前的古老的甘蓝物种。花椰菜的分化时间大约在2个百万年前左右，而卷心菜的分化时间则在2.6个百万年前，其它芸薹属植物分化时间均要超过2个百万年前。花椰菜的3号染色体与芸薹属植物的A、B、C三套亚基因组以及花椰菜本身其它8条染色体具有最多的共线性块，表明3号染色体可能是花椰菜基因组中比较古老的一个染色体。另外，作者还在花椰菜基因组中鉴定并功能注释了2718个特异基因，228个扩张基因，2个收缩基因，以及1065个受到选择的基因。本文的研究为芸薹属物种的基因组多样性提供了新的视野，同时也为将来花椰菜的分子育种提供了可贵的参考基因组资源。

通讯：孙德岭

研究方向：菜花（花椰菜）育种及分子标记辅助育种研究工作。

doi: https://doi.org/10.1038/s41438-019-0164-0

Journal: Horticulture Research

Published date: July 01, 2019