亚麻纤维素合酶超基因家族的生物信息学及表达分析

doi:10.3864/j.issn.0578-1752.2016.23.018

摘要/Abstract

摘要： 【目的】全基因组水平鉴定亚麻纤维素合酶超家族基因CesA/Csls，并对基因的进化、基因结构及组织表达特性等进行分析，为亚麻纤维发育的机理研究奠定基础。【方法】利用Phytozome基因组数据库，通过生物信息学手段，鉴定亚麻纤维素合酶超基因家族成员，并进行蛋白理化特性分析；利用MEGA 5.0、GSDS、MEME等软件构建系统进化树，并进行基因结构、蛋白保守基序分析；根据RNA-Seq数据对CesA/Csls进行表达分析。【结果】系统分析鉴定了45个亚麻CesA/Csls超家族基因，该家族基因在scaffolds上是分散分布的，没有明显的成簇现象。CesA/Csls蛋白主要分布于质膜上，氨基酸数目为409—1 167，分子量为47 401.1—130 578.3，等电点分布在5.43—9.08。CesA/Csl蛋白均含有跨膜结构域，数目为2—8。根据系统进化分析将其分成CesA与Csl两类，细分为CesA、CslA、CslB、CslC、CslD、CslE、CslG共7组。基因结构分析显示，亚麻CesA/Csls基因的长度在2.1—6.8 kb，外显子数量在2—14。保守基序分析表明，不同组间Motif组成有一定的差异，Motif 1、Motif 2、Motif 3、Motif 4、Motif 12在CesA、CslB、CslD、CslE、CslG组蛋白中均有分布，Motif 18、Motif 20在CslA、CslC组蛋白中均有分布，而Motif 13、Motif 14、Motif 15、Motif 19的分布则表现出一定的组间特异性。表达谱分析结果表明，CesA/Csls家族成员在不同发育阶段表达模式不同，部分CesA/Csls可被NaCl、BR和Brz诱导上调或下调表达，预示CesA/Csls功能的多样性以及在植物发育过程中扮演着不同角色。【结论】鉴定出45个亚麻CesA/Csls家族基因成员，分属于两类，7组，分布于scaffolds上，基因结构和蛋白基序具有组间多样性和组内保守性。不同的基因在不同发育阶段具有一定的时空特异性。CesA/Csls中部分基因响应激素BR、Brz及NaCl胁迫。

关键词: 亚麻, 纤维素合酶, CesA/Csls, 基因家族, 表达分析

Abstract: 【Objective】 The CesA/Csls genes were identified in flax. Then the phylogeny, gene structure and tissue expression pattern were analyzed in order to provide a theoretical basis for studying the mechanism of flax fiber development.【Method】Based on flax genome database and bioinformatics method, CesA/Csls genes were identified and the physico-chemical characteristics were analyzed. The phylogenetic tree was constructed by MEGA 5.0 software. The gene structure and conservative motifs were analyzed by the bioinformatics softwares GSDS and MEME. Finally, the expression of CesA/Csl genes was analyzed by using the RNA-seq data. 【Result】 A total of 45 CesA/Csl genes were systematically identified in flax. The genes appeared to be dispersed within the chromosome and were not clustered. The CesA/Csl proteins were mainly located on the plasma membrane. The number of amino acid of the proteins ranged from 409 to 1 167. The isoelectric point distributed from 5.43 to 9.08. All of the 45 CesA/Csl proteins possessed the transmembrane domains, the number of which was from 2 to 8. The genes were classified into 2 classes (CesA and Csl) and seven groups (CesA, CslA, CslB, CslC, CslD, CslE, CslG) according to the phylogetic relationship. Gene structure prediction indicated that CesA/Csls genes ranged from 2.1 to 6.8 kb in size and most of them consist of 2 to 14 exons.The gene structure was conserved within a group. Obvious differences were observed in motif composition in genes from different groups. Motif 1 to motif 4, motif 12 were observed in most of CesA, CslB, CslD, CslE, and CslG group proteins，and motif 18, and motif 20 were observed in most of CslA, CslC group proteins. Motif 13, motif 14, motif 15, and motif 19 as the spectific motifs were observed in different groups. Futhermore, some CesA/Csl genes could be upregulated or downregulated by BR, Brz and NaCl stress. The results of digital gene expression profile showed that CesA/Csl were expressed differently at different development stages. It indicated that CesA/Csls had various functions and played different roles in the process of plant development. 【Conclusion】A total of 45 CesA/Csl genes in flax were systematically identified by genome-wide screening. The genes were classified into 2 classes and seven groups. The genes appeared to be dispersed within the scaffolds. The analysis of gene structure and conservative motifs indicated that there were obvious differences between groups, but the genes within a group varied slightly. RNA-seq expression profiling of the CesA/Csl genes revealed unique, homoeolog-specific expression patterns at different development stages. Some of them could be induced by BR, Brz or NaCl stress.

Key words: flax, cellulose synthase, CesA/Csls, gene family, expression analysis

袁红梅，郭文栋，赵丽娟，于莹，吴建忠，张利国，程莉莉，赵东升，吴广文，关凤芝. 亚麻纤维素合酶超基因家族的生物信息学及表达分析[J]. 中国农业科学, 2016, 49(23): 4656-4668.

YUAN Hong-mei, GUO Wen-dong, ZHAO Li-juan, YU Ying, WU Jian-zhong, ZHANG Li-guo, CHENG Li-li, ZHAO Dong-sheng, WU Guang-wen, GUAN Feng-zhi. Bioinformatics and Expression Analysis of the Cellulose Synthase Supergene Family in Flax[J]. Scientia Agricultura Sinica, 2016, 49(23): 4656-4668.

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