Orthogroup and phylotranscriptomic analyses identify transcription factors involved in the plant cold response: A case study of Arabidopsis BBX29

文献类型： 外文期刊

第一作者： Wang, Shuo

作者： Wang, Shuo;Shen, Yirong;Deng, Deyin;Guo, Liangyu;Zhang, Yixian;Nie, Yuqi;Du, Yunfei;Zhao, Xijuan;Huang, Jianqin;Huang, Huahong;Wu, Wenwu;Ye, Xiaoxue;Zhu, Jian-Kang;Zhu, Jian-Kang;Zhu, Jian-Kang

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关键词： phylogenomics; phylotranscriptomics; orthogroup; cold acclimation; BBX29; CBF-independent pathway

期刊名称：PLANT COMMUNICATIONS （ 影响因子：10.5； 五年影响因子：10.5 ）

ISSN： 2590-3462

年卷期： 2023 年 4 卷 6 期

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收录情况： SCI

摘要： C-repeat binding factors (CBFs) are well-known transcription factors (TFs) that regulate plant cold acclima-tion. RNA sequencing (RNA-seq) data from diverse plant species provide opportunities to identify other TFs involved in the cold response. However, this task is challenging because gene gain and loss has led to an intertwined community of co-orthologs and in-paralogs between and within species. Using orthogroup (closely related homologs) analysis, we identified 10,549 orthogroups in five representative eudicots. A phylotranscriptomic analysis of cold-treated seedlings from eudicots identified 35 high-confidence conserved cold-responsive transcription factor orthogroups (CoCoFos). These 35 CoCoFos included the well-known cold-responsive regulators CBFs, HSFC1, ZAT6/10, and CZF1 among others. We used Arabi-dopsis BBX29 for experimental validation. Expression and genetic analyses showed that cold-induction of BBX29 is CBF-and abscisic acid-independent, and BBX29 is a negative regulator of cold tolerance. Inte-grative RNA-seq and Cleavage Under Targets and Tagmentation followed by sequencing analyses revealed that BBX29 represses a set of cold-induced TFs (ZAT12, PRR9, RVE1, MYB96, etc.). Altogether, our analysis yielded a library of eudicot CoCoFos and demonstrated that BBX29 is a negative regulator of cold tolerance in Arabidopsis.

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