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. 2021 May 5;19(1):93.
doi: 10.1186/s12915-021-01031-2.

Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification

Ning Guo #  1 , Shenyun Wang #  2 , Lei Gao #  3   4 , Yongming Liu #  5 , Xin Wang  3 , Enhui Lai  4   6 , Mengmeng Duan  1 , Guixiang Wang  1 , Jingjing Li  5 , Meng Yang  5 , Mei Zong  1 , Shuo Han  1 , Yanzheng Pei  5 , Theo Borm  7 , Honghe Sun  1 , Liming Miao  1 , Di Liu  1 , Fangwei Yu  2 , Wei Zhang  2 , Heliang Ji  8 , Chaohui Zhu  9 , Yong Xu  1 , Guusje Bonnema  10 , Jianbin Li  11 , Zhangjun Fei  12   13 , Fan Liu  14
Affiliations

Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification

Ning Guo et al. BMC Biol. .

Abstract

Background: Brassica oleracea includes several morphologically diverse, economically important vegetable crops, such as the cauliflower and cabbage. However, genetic variants, especially large structural variants (SVs), that underlie the extreme morphological diversity of B. oleracea remain largely unexplored.

Results: Here we present high-quality chromosome-scale genome assemblies for two B. oleracea morphotypes, cauliflower and cabbage. Direct comparison of these two assemblies identifies ~ 120 K high-confidence SVs. Population analysis of 271 B. oleracea accessions using these SVs clearly separates different morphotypes, suggesting the association of SVs with B. oleracea intraspecific divergence. Genes affected by SVs selected between cauliflower and cabbage are enriched with functions related to response to stress and stimulus and meristem and flower development. Furthermore, genes affected by selected SVs and involved in the switch from vegetative to generative growth that defines curd initiation, inflorescence meristem proliferation for curd formation, maintenance and enlargement, are identified, providing insights into the regulatory network of curd development.

Conclusions: This study reveals the important roles of SVs in diversification of different morphotypes of B. oleracea, and the newly assembled genomes and the SVs provide rich resources for future research and breeding.

Keywords: Brassica oleracea; Cabbage; Cauliflower; Curd development; Structural variants.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1.
Fig. 1.
Genomes of cauliflower Korso and point cabbage OX-heart. a Features of the Korso and OX-heart genomes. (i) Ideogram of the chromosomes. Red, green, blue, and black colors indicate the LF, MF1, and MF2 subgenomes and centromere regions, respectively. (ii) Gene density. (iii) Repeat density. (iv) Copia-type LTR density. (v) Gypsy-type LTR density. (vi) Synteny blocks between Korso and OX-heart genomes. b Phylogenetic tree of 14 plant species/varieties and their estimated divergence times (million years ago) based on 1638 single-copy orthologous genes
Fig. 2.
Fig. 2.
SVs in different B. oleracea morphotypes. a Percentages of SVs with different genotypes in accessions of different morphotypes. b Principal component analysis of B. oleracea accessions based on SVs. c Maximum-likelihood tree and model-based clustering of the 271 B. oleracea accessions using SVs. Branch colors of the tree indicate different morphotypes as in b. K, number of ancestral kinships
Fig. 3.
Fig. 3.
SV divergence between cauliflower and cabbage. a Scatter plot showing Korso-allele frequencies of SVs in cabbage and cauliflower groups. q-value, Bonferroni-corrected p value of Fisher’s exact test. b GO terms enriched in genes overlapping with SVs with significant allele frequency differences between cabbage and cauliflower groups
Fig. 4.
Fig. 4.
SV contribution to cauliflower curd formation. a SAM and curd at different stages of curd development. b Korso-allele frequencies of SVs overlapping with candidate genes in cauliflower, broccoli, and cabbage. Triangles, circles, and squares indicate SVs in promoter, CDS, and intron regions, respectively, and their different colors, green, red, and yellow, indicate different types of SVs, insertion, deletion, and substitution, respectively, in Korso compare to OX-heart. c Heatmaps showing expression of candidate genes at different stages of curd development. The expression values (FPKM) were normalized by Z-score. d Proposed regulatory network for curd formation and development of cauliflower. Genes with yellow background had selected SVs between cauliflower and cabbage
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