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大规模的结构变异引起的基因表达改变驱动了芸薹属甘蓝型多样化的表型。

Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea.

机构信息

State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.

Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.

出版信息

Nat Genet. 2024 Mar;56(3):517-529. doi: 10.1038/s41588-024-01655-4. Epub 2024 Feb 13.

DOI:10.1038/s41588-024-01655-4
PMID:38351383
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10937405/
Abstract

Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.

摘要

甘蓝型油菜在全球范围内因其蔬菜作物而被广泛种植，它包含非常多样化的形态类型，其特征是作为收获产品的特化增大器官。这使得甘蓝型油菜成为研究快速进化和驯化的理想模型。我们从代表所有形态类型及其野生近缘种的 27 个高质量基因组中构建了甘蓝型油菜泛基因组。我们在这些基因组之间鉴定了结构变异（SVs），并使用基于图的基因组工具在 704 个甘蓝型油菜品种中对这些变异进行了特征描述。我们表明，SVs 对许多基因的表达具有双向影响，通过 DNA 甲基化抑制或可能通过携带转录因子结合元件促进表达。以下例子说明了 SVs 调节基因表达的作用：SVs 在花椰菜/西兰花中促进 BoPNY 和抑制 BoCKX3，在白菜中抑制 BoKAN1 和 BoACS4，并在观赏羽衣甘蓝中促进 BoMYBtf。这些结果为 SVs 作为基因表达剂量调节因子的作用提供了确凿的证据，推动了甘蓝型油菜的驯化和多样化。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/db2dbd803923/41588_2024_1655_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/a67cd23522b3/41588_2024_1655_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/f84a6467ff98/41588_2024_1655_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/8391275dc1d7/41588_2024_1655_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/c747558db6c6/41588_2024_1655_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/de256be6288b/41588_2024_1655_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/db2dbd803923/41588_2024_1655_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/a67cd23522b3/41588_2024_1655_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/f84a6467ff98/41588_2024_1655_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/8391275dc1d7/41588_2024_1655_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/c747558db6c6/41588_2024_1655_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/de256be6288b/41588_2024_1655_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c862/10937405/db2dbd803923/41588_2024_1655_Fig6_HTML.jpg

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