高质量的雪里蕻XC (Brassica juncea var. multiceps)基因组为芥菜叶形变异提供新的见解

doi:10.1016/j.jia.2024.04.031

Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (4): 1461-1476.DOI: 10.1016/j.jia.2024.04.031

高质量的雪里蕻XC (Brassica juncea var. multiceps)基因组为芥菜叶形变异提供新的见解

收稿日期:2023-11-01 接受日期:2024-03-22 出版日期:2025-04-20 发布日期:2025-03-17

The high quality genome of potherb mustard Xuecai (Brassica juncea var. multiceps) provides new insights into leaf shape variation

Shuangping Heng^1#, Mengdi Cui¹, Xiaolin Li¹, Shaoheng Zhang¹, Guangzhi Mao¹, Feng Xing¹, Zhengjie Wan², Jing Wen³, Jinxiong Shen³, Tingdong Fu³

¹College of Life Sciences, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang 464000, China
²College of Horticulture and Forestry, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
³College of Plant Science and Technology, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

Received:2023-11-01 Accepted:2024-03-22 Online:2025-04-20 Published:2025-03-17
About author:#Correspondence Shuangping Heng, E-mail: shuangpingheng@126.com
Supported by:
This study was supported by grants from the National Natural Science Foundation of China (32002056), the Science and Technology Research Key Project of Henan Province, China (242102111138), and the Nanhu Scholars Program for Young Scholars of Xinyang Normal University, China.

摘要/Abstract

摘要：

叶用芥菜雪里蕻(XC)是一种十字花科蔬菜，作为一种新鲜的食用和腌制蔬菜而广受欢迎。雪里蕻由于叶片裂刻的存而表现出多回羽状全裂叶片。裂叶的叶片净光合速率高于非裂叶。然而，叶形变异的分子机制仍然是不清楚的。本研究利用HiFi和Hi-C测序技术组装了雪里蕻的基因组。雪里蕻基因组长度为961.72 Mb, N50为6.565 Mb。通过与已测序的四个芥菜基因组进行了比较，鉴定了基因组共线性区域、SNPs和indels。通过芥菜比较基因组测序，在雪里蕻XC A10染色体BjRCO候选区段发现了5个BjRCO基因。大片段重复序列导致了BjRCO基因的拷贝数增加。BjRCO基因在多回羽状全裂叶中的转录表达高于锯齿状叶。BjRCO基因拷贝数增加与高表达共同调控芥菜叶形由简单变复杂。BjRCO基因编辑使芥菜叶形由多回羽状全裂叶片变为简单叶。雪里蕻的高质量基因组测序不仅为叶用芥菜基因组提供了新的见解，而且有助于进一步解析叶型变异的分子机制。我们的研究表明，通过芥菜基因组的比较分析，可以更好地解析重要性状的变异和进化。

Abstract:

The potherb mustard Xuecai (XC) cultivar is a cruciferous vegetable that is popular either fresh or pickled. Due to the deep notches in the edges of leaves in mustard XC, this plant can be said to have multipinnately lobed leaves. The net photosynthesis of lobed leaves is significantly greater than that of simple leaves. However, the molecular mechanism of leaf shape variation has not been determined. Here, we used HiFi and Hi-C data to assemble the XC genome. The genome was 961.72 Mb in size, with a contig N50 value of 6.565 Mb. The XC genome was compared with four previously sequenced mustard genomes, and the genomic collinearity regions, SNPs, and indels were identified. Five BjRCO genes were found on chromosome (Chr.) A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B. juncea genomes. Segmental duplication was found to contribute to the BjRCO gene copy number. The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves. Together, these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B. juncea. Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple. The high-quality XC genome sequence not only provides new insight into B. juncea leaf-type genomics but also helps in deciphering leaf shape variation. Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.

Key words: Brassica juncea , genome sequence , multipinnately lobed leaves , segmental duplication , BjRCO , gene editing

Shuangping Heng, Mengdi Cui, Xiaolin Li, Shaoheng Zhang, Guangzhi Mao, Feng Xing, Zhengjie Wan, Jing Wen, Jinxiong Shen, Tingdong Fu. 高质量的雪里蕻XC (Brassica juncea var. multiceps)基因组为芥菜叶形变异提供新的见解[J]. Journal of Integrative Agriculture, 2025, 24(4): 1461-1476.

Shuangping Heng, Mengdi Cui, Xiaolin Li, Shaoheng Zhang, Guangzhi Mao, Feng Xing, Zhengjie Wan, Jing Wen, Jinxiong Shen, Tingdong Fu.

The high quality genome of potherb mustard Xuecai (Brassica juncea var. multiceps) provides new insights into leaf shape variation

[J]. Journal of Integrative Agriculture, 2025, 24(4): 1461-1476.

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高质量的雪里蕻XC (Brassica juncea var. multiceps)基因组为芥菜叶形变异提供新的见解

The high quality genome of potherb mustard Xuecai (Brassica juncea var. multiceps) provides new insights into leaf shape variation

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