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. 2019 Jul 1:6:82.
doi: 10.1038/s41438-019-0164-0. eCollection 2019.

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

Deling Sun #  1 , Chunguo Wang #  2 , Xiaoli Zhang #  3 , Wenlin Zhang #  4 , Hanmin Jiang  3 , Xingwei Yao  3 , Lili Liu  3 , Zhenghua Wen  3 , Guobao Niu  3 , Xiaozheng Shan  3
Affiliations

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

Deling Sun et al. Hortic Res. .

Abstract

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.

Keywords: Genome assembly algorithms; Plant evolution.

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Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1. Distribution of genes in cauliflower and other representative plant species.
a Distribution of single-copy orthologs (pink), multiple-copy orthologs (orange), unique genes (brown), and other unclassified genes (green) in cauliflower and other representative plant species. b Venn diagram of gene families in cauliflower and two other Brassica species with the C genome
Fig. 2
Fig. 2. Divergence time of cauliflower and other representative plant species.
The nodes represent the divergence time from present (million years ago, Mya). The blue number in the brackets indicates the confidence interval of the divergence time. a–c indicate the A, B and C genomes of Brassica species, respectively
Fig. 3
Fig. 3. Synteny analysis of genes in cauliflower, B. nigra, B. rapa and B. oleracea L. var. capitata.
a Syntenic blocks of cauliflower with B. nigra and B. rapa. b Syntenic blocks of cauliflower with B. oleracea L. var. capitata. The numbers indicate the corresponding chromosomes in each species. The detailed syntenic blocks and the associated genes are shown in Tables S6–S13
Fig. 4
Fig. 4. Circos diagram of different elements on the chromosomes of cauliflower.
Chrom. 01, 02, 03, 04, 05, 06, 07, 08, and 09 indicate the nine assembled chromosomes of cauliflower
Fig. 5
Fig. 5. Distribution of 4DTv distances.
The x axis indicates the 4Dtv distance. The y axis indicates the percentage of gene pairs. (C) shows the C subgenome of B. napus Darmor-bzh
See this image and copyright information in PMC

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