遗传 ›› 2014, Vol. 36 ›› Issue (1): 77-84.doi: 10.3724/SP.J.1005.2014.00077

• 研究报告 • 上一篇    下一篇

番茄PPR基因家族的鉴定与生物信息学分析

丁安明1, 李凌1, 屈旭1, 孙亭亭1, 陈雅琼1, 宗鹏2, 李尊强3, 龚达平1, 孙玉合1   

  1. 1. 中国农业科学院烟草研究所, 烟草行业烟草基因资源利用重点实验室, 青岛 266100; 
    2. 大理州烟草公司弥渡县公司, 大理 675600; 
    3. 牡丹江烟草科学研究所, 牡丹江 157011
  • 收稿日期:2013-09-26 修回日期:2013-11-14 出版日期:2014-01-20 发布日期:2013-12-20
  • 通讯作者: 孙玉合, 博士, 研究员, 研究方向:烟草功能基因组学。E-mail: yhsun@163.com E-mail:yhsun@163.com
  • 作者简介:丁安明, 博士研究生, 研究方向:烟草功能基因组学。E-mail: anmingdsdau@163.com
  • 基金资助:

    国家高技术研究发展计划(“863”计划)项目(编号:2012AA021801)

Genome-wide identification and bioinformatic analysis of PPR gene family in tomato

Anming Ding1, Ling Li1, Xu Qu1, Tingting Sun1, Yaqiong Chen1, Peng Zong2, Zunqiang Li3, Daping Gong1, Yuhe Sun1   

  1. 1. Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266100, China; 
    2. Dali Tobacco Company Midu Branch, Dali 675600, China; 
    3. Tobacco Science Research Institute of Mudanjiang, Mudanjiang 157011, China
  • Received:2013-09-26 Revised:2013-11-14 Online:2014-01-20 Published:2013-12-20

摘要:

PPR(Pentatricopeptide repeats)基因家族在植物中广泛存在, 其在植物生长发育过程中至关重要。文章采用生物信息学方法, 利用Pfam已鉴定的PPR保守结构域序列检索番茄(Solanum lycopersicum L.)基因组计划注释的蛋白序列, 最终确定了番茄中可能存在的471个PPR编码基因; 根据拟南芥(Arabidopsis thaliana L.)中鉴定的各个结构域的特点对其进行了蛋白结构分析、分类和保守序列分析, 并对番茄PPR基因家族进行了系统进化树构建、染色体定位、亚细胞定位预测、表达和GO分析等。结果表明:番茄PPR基因家族分为P和PLS两个亚家族, 各占序列数目的一半, PLS亚家族又分为PLS、E、E+和DYW四类, 且在进化树中形成不同的分支; 各个结构域在植物中非常保守; PPR基因家族分布在番茄12条染色体上, 且多数无内含子结构; 大部分PPR蛋白具有线粒体或叶绿体定位序列, GO分析表明PPR蛋白参与RNA相关的生物学过程

关键词: 番茄, PPR基因家族, 生物信息学

Abstract:

Pentatricopeptide repeats (PPRs) genes constitute one of the largest gene families in plants, which play a broad and essential role in plant growth and development. In this study, the protein sequences annotated by the tomato (S. lycopersicum L.) genome project were screened with the Pfam PPR sequences. A total of 471 putative PPR-encoding genes were identified. Based on the motifs defined in A. thaliana L., protein structure and conserved sequences for each tomato motif were analyzed. We also analyzed phylogenetic relationship, subcellular localization, expression and GO analysis of the identified gene sequences. Our results demonstrate that tomato PPR gene family contains two subfamilies, P and PLS, each accounting for half of the family. PLS subfamily can be divided into four subclasses i.e., PLS, E, E+ and DYW. Each subclass of sequences forms a clade in the phylogenetic tree. The PPR motifs were found highly conserved among plants. The tomato PPR genes were distributed over 12 chromosomes and most of them lack introns. The majority of PPR proteins harbor mitochondrial or chloroplast localization sequences, whereas GO analysis showed that most PPR proteins participate in RNA-related biological processes.

Key words: tomato, PPR gene family, bioinformatics