Scientia Agricultura Sinica ›› 2016, Vol. 49 ›› Issue (23): 4656-4668.doi: 10.3864/j.issn.0578-1752.2016.23.018

• RESEARCH NOTES • Previous Articles     Next Articles

Bioinformatics and Expression Analysis of the Cellulose Synthase Supergene Family in Flax

YUAN Hong-mei1, GUO Wen-dong2, ZHAO Li-juan3, YU Ying1,WU Jian-zhong1, ZHANG Li-guo1, CHENG Li-li1, ZHAO Dong-sheng1, WU Guang-wen1, GUAN Feng-zhi1   

  1. 1 Industrial Crops Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086
    2 Nature and Ecology Institute of Heilongjiang Academy of Sciences, Harbin 150040
    3 Crop Breeding Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086
  • Received:2016-03-21 Online:2016-12-01 Published:2016-12-01

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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

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