Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops

文献类型： 外文期刊

第一作者： Xin, Hongjia

作者： Xin, Hongjia;Liu, Xin;Yang, Xueyong;Wang, Bowen;Xu, Yuanchao;Zhong, Xiaoyun;Xin, Hongjia;Chai, Sen;Zhang, Zhonghua;Liu, Xin;Li, Hongbo;Wang, Bowen;Xu, Yuanchao;Lin, Shengnan;Liu, Bin;Lu, Zefu

作者机构： Chinese Acad Agr Sci, Inst Vegetables & Flowers, State Key Lab Vegetable Biobreeding, Beijing 100081, Peoples R China;Qingdao Agr Univ, Coll Hort, Engn Lab Genet Improvement Hort Crops Shandong Pro, Qingdao 266109, Peoples R China;Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Shenzhen Branch,Minist Agr & Rural Affairs,Key Lab, Shenzhen 518120, Peoples R China;Huazhong Agr Univ, Coll Hort & Forestry Sci, Key Lab Hort Plant Biol, Wuhan 430070, Peoples R China;Xinjiang Acad Agr Sci, Hami Melon Res Ctr, Urumqi 830091, Peoples R China;Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resource & Genet Improve, Beijing 100081, Peoples R China

期刊名称：PLANT CELL （ 2022影响因子：11.6； 五年影响因子：12.9 ）

ISSN： 1040-4651

年卷期： 2024 年 36 卷 6 期

页码：

收录情况： SCI

摘要： A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved noncoding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865 to 43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2, and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution. Integrative analyses of conserved noncoding sequences and accessible chromatin regions provide insights into cis-regulatory elements and target sequences for fruit development in cucurbits.

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