水稻Trihelix转录因子家族全基因组分析及功能预测

doi:10.16288/j.yczz.15-196

遗传 ›› 2015, Vol. 37 ›› Issue (12): 1228-1241.doi: 10.16288/j.yczz.15-196

水稻Trihelix转录因子家族全基因组分析及功能预测

纪剑辉, 周颖君, 吴贺贺, 杨立明

淮阴师范学院生命科学学院,江苏省环洪泽湖生态农业生物技术重点实验室,江苏省区域现代农业与环境保护协同创新中心,淮安 223300

收稿日期:2015-05-07 出版日期:2015-12-20 发布日期:2015-11-26
通讯作者: 杨立明,副教授,研究方向：植物抗逆分子生物学。E-mail: yanglm@hytc.edu.cn E-mail:zhouzhou@hytc.edu.cn
作者简介:作者简介:纪剑辉,讲师,研究方向：水稻分子生物学。E-mail: jijianhui@hytc.edu.cn;周颖君,实验员,研究方向：植物分子生物学。E-mail: zhouzhou@hytc.edu.cn;纪剑辉和周颖君并列第一作者。
基金资助:
国家自然科学基金项目(编号：31400169,30900871),江苏省自然科学基金项目(编号：BK20140454,BK2011409),淮安市科技计划项目(编号：HAC2014012),江苏高校品牌专业建设工程项目(编号：PPZY2015A018)和江苏省高校“青蓝工程”项目资助

Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice

Jianhui Ji, Yingjun Zhou, Hehe Wu, Liming Yang

Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture &Environment Protection(JCIC-RMAEP), School of Life Sciences, Huaiyin Normal University, Huai'an 223300, China

Received:2015-05-07 Online:2015-12-20 Published:2015-11-26

摘要/Abstract

摘要： Trihelix转录因子家族在植物生长发育以及响应逆境胁迫等方面发挥着重要作用,但目前基于水稻全基因组水平鉴定和分析该基因家族的研究尚未见相关报道。本文利用生物信息学方法在水稻基因组数据库中鉴定到Trihelix家族成员31个,序列聚类和功能结构域分析发现该家族均含有高度保守的、特征性的Trihelix结构域;根据亲缘关系远近和结构域特点,将其分为5个亚家族(Ⅰ~Ⅴ)。通过与拟南芥、二穗短炳草和高粱中Trihelix家族的聚类分析发现,这4个物种中Trihelix家族的分类相一致,但每个物种均含有不同亚家族的成员,表明该基因家族的分化早于物种的分化。基于MEME程序分析水稻Trihelix转录因子家族的保守基序与聚类分析结果具有较高的一致性。染色体区段复制分析表明,部分Trihelix家族成员在水稻以及水稻与其他物种之间存在种内和种间的染色体区段复制;生物芯片数据分析发现,Trihelix基因家族在水稻不同组织中、以及对6种不同植物激素的响应呈现多样化的表达谱。采用RiceFREND在线数据库分析发现,水稻Trihelix转录因子家族的20个成员与其他蛋白存在互作关系。本研究结果初步明确了水稻Trihelix转录因子家族的进化特点、染色体分布、染色体区段复制关系、组织表达、激素应答,以及该家族蛋白与其他蛋白质的互作情况,为进一步揭示Trihelix转录因子家族的分子进化规律和生物学功能奠定了基础。

关键词: 水稻, Trihelix, 转录因子家族, 进化

Abstract: The Trihelix transcription factor family plays an essential role in plant growth, development and stress response. However, the studies about identification and analysis of this gene family in rice on the genome-wide level have not been reported. In this study, 31 members of the Trihelix family, which contain highly conserved and characteristic trihelix domain through sequence clustering and functional domains analysis, were identified in rice genome database using bioinformatic tools. These members could be classified into 5 subfamilies (I~V) based on the evolutionary relationship and domain characteristics. Clustering analyses of the Trihelix family in rice, Arabidopsis, Brachypodium distachyom and Sorghum bicolor showed that each species contained different members of subfamily although the classification of the Trihelix family were consistent in these four species, which indicated that the differentiation of the Trihelix gene family occur earlier than that of these species. The conserved motifs in the Trihelix family of rice analyzed using the MEME program were highly consistent with the results of clustering analyses. Intraspecific and interspecific chromosomal replication in partial Trihelix family members were found to exist in rice and between rice and other species through chromosome replication analysis. Microarray data analysis revealed diverse expression patterns of Trihelix family genes in different tissues of rice or in response to six different phytohormones. Moreover, 20 members of the Trihelix transcription factor family were found to interact with other proteins in rice using RiceFRIEND online database analysis. Therefore, our results preliminarily identified the evolution, chromosome distribution and replication, expression patterns, phytohormones response of the Trihelix transcription factor family and the interaction between trihelix family proteins and other proteins in rice, which will provide a basis to further reveal the molecular evolution and biological function of the Trihelix transcription factor family.

Key words: rice, Trihelix, transcription factor family, evolution

纪剑辉, 周颖君, 吴贺贺, 杨立明. 水稻Trihelix转录因子家族全基因组分析及功能预测[J]. 遗传, 2015, 37(12): 1228-1241.

Jianhui Ji, Yingjun Zhou, Hehe Wu, Liming Yang. Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice[J]. HEREDITAS(Beijing), 2015, 37(12): 1228-1241.

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水稻Trihelix转录因子家族全基因组分析及功能预测

Genome-wide analysis and functional prediction of the Trihelix transcription factor family in rice

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