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

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

机构地区：[1]State Key Laboratory of Subtropical Silviculture,Zhejiang A&F University,Lin’an 311300,Hangzhou,China [2]Institute of Tropical Biosciences and Biotechnology,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China [3]Institute of Advanced Biotechnology and School of Life Sciences,Southern University of Science and Technology,Shenzhen 518055,China [4]Center for Advanced Bioindustry Technologies,Chinese Academy of Agricultural Sciences,Beijing 100081,China

出　　处：《Plant Communications》2023年第6期148-162,共15页植物通讯（英文）

基　　金：supported by the National Natural Science Foundation of China(31871233);Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural Varieties(2021C02070-1);the Scientific Research Development Fund of Zhejiang A&F University(2022LFR082).

摘　　要：C-repeat binding factors(CBFs)are well-known transcription factors(TFs)that regulate plant cold acclimation.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 Arabidopsis 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.Integrative 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.

关 键 词：PHYLOGENOMICS phylotranscriptomics ORTHOGROUP cold acclimation BBX29 CBF-independent pathway 

分 类 号：Q94[生物学—植物学]