番茄WOX转录因子家族的鉴定及其进化、表达分析

doi:10.16288/j.yczz.15-499

遗传 ›› 2016, Vol. 38 ›› Issue (5): 444-460.doi: 10.16288/j.yczz.15-499

番茄WOX转录因子家族的鉴定及其进化、表达分析

李晓旭¹, 刘成^{1, 2}, 李伟¹, 张增林¹, 高晓明¹, 周慧^{1, 3}, 郭永峰¹

1. 中国农业科学院烟草研究所,烟草行业基因资源利用重点实验室,青岛 266101;
2. 曲靖市烟草公司,曲靖 655000;
3. 山东中烟颐中集团,青岛 266101

收稿日期:2015-12-14 修回日期:2016-01-22 出版日期:2016-05-20 发布日期:2016-04-05
通讯作者: 郭永峰,博士,研究员,研究方向：植物发育生物学。E-mail: guoyongfeng@caas.cn E-mail:moxuanpds@163.com
作者简介:李晓旭,硕士研究生,专业方向：作物分子育种。E-mail: moxuanpds@163.com

Genome-wide identification, phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum

Xiaoxu Li¹, Cheng Liu^{1, 2}, Wei Li¹, Zenglin Zhang¹, Xiaoming Gao¹, Hui Zhou^{1, 3}, Yongfeng Guo¹

1. Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
2. Qujing Tobacco Company of Yunnan, Qujing 655000, China;
3. Etsong Qingdao Industrial Co., Ltd., Qingdao 266101, China

Received:2015-12-14 Revised:2016-01-22 Online:2016-05-20 Published:2016-04-05

摘要/Abstract

摘要： WUSCHEL相关的同源异型盒(WUSCHEL-related homeobox,WOX)是一类植物特异的转录因子家族,具有调控植物干细胞分裂分化动态平衡等重要功能。本研究利用番茄(Solanum lycopersicum)基因组数据,通过建立隐马尔科夫模型并进行检索,鉴定了番茄10个WOX转录因子家族成员。多序列比对发现,番茄WOX转录因子家族成员具有高度保守的同源异型结构域;以拟南芥WOX转录因子家族成员序列为参照,通过邻接法、极大似然法、贝叶斯法重建了系统发育树,三者呈现出类似的拓扑结构,番茄和拟南芥WOX转录因子家族共25个成员被分为3个进化支(Clade)和9个亚家族(Subgroup);利用MEME和GSDS对WOX转录因子家族成员的蛋白保守结构域和基因结构进行了分析,同一亚家族内的WOX转录因子家族成员的保守结构域的种类、组织形式以及基因结构具有高度的一致性;利用Perl和Orthomcl对家族成员的染色体定位和同源性关系进行分析,结果表明串联重复的SlWOX3a和SlWOX3b可能来源于一次复制事件;利用番茄转录组数据和qRT-PCR进行表达分析,结果显示家族成员在不同组织中的表达存在差异,暗示了WOX家族的不同成员在功能上可能具有多样性。本研究对番茄WOX转录因子家族成员进行GO(Gene Ontology)注释和比较分析,结果表明该家族成员作为转录因子,可能在组织器官发育、细胞间通讯等过程中发挥作用。

关键词: 番茄, 生物信息学分析, WOX转录因子家族

Abstract: Members of the plant-specific WOX transcription factor family have been reported to play important roles in cell to cell communication as well as other physiological and developmental processes. In this study, ten members of the WOX transcription factor family were identified in Solanum lycopersicum with HMMER. Neighbor-joining phylogenetic tree, maximum-likelihood tree and Bayesian-inference tree were constructed and similar topologies were shown using the protein sequences of the homeodomain. Phylogenetic study revealed that the 25 WOX family members from Arabidopsis and tomato fall into three clades and nine subfamilies. The patterns of exon-intron structures and organization of conserved domains in Arabidopsis and tomato were consistent based on the phylogenetic results. Transcriptome analysis showed that the expression patterns of SlWOXs were different in different tissue types. Gene Ontology (GO) analysis suggested that, as transcription factors, the SlWOX family members could be involved in a number of biological processes including cell to cell communication and tissue development. Our results are useful for future studies on WOX family members in tomato and other plant species.

Key words: Solanum lycopersicum, bioinformatics analysis, WOX family

李晓旭, 刘成, 李伟, 张增林, 高晓明, 周慧, 郭永峰. 番茄WOX转录因子家族的鉴定及其进化、表达分析[J]. 遗传, 2016, 38(5): 444-460.

Xiaoxu Li, Cheng Liu, Wei Li, Zenglin Zhang, Xiaoming Gao, Hui Zhou, Yongfeng Guo. Genome-wide identification, phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum[J]. HEREDITAS(Beijing), 2016, 38(5): 444-460.

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番茄WOX转录因子家族的鉴定及其进化、表达分析

Genome-wide identification, phylogenetic analysis and expression profiling of the WOX family genes in Solanum lycopersicum

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