Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus).
Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus).
复制标题
菠萝 (Ananas comosus) 中 R2R3-MYB 转录因子家族的全基因组组织和表达谱
DOI：
10.1186/s12864-017-3896-y
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发表时间：
2017-07-01
期刊：
影响因子：
4.4
通讯作者：
He Y
中科院分区：
文献类型：
--
作者：
Liu C;Xie T;Chen C;Luan A;Long J;Li C;Ding Y;He Y
MYB 蛋白是最大的植物转录因子家族之一，参与多种植物生理和生化过程。菠萝（Ananas comosus）是世界上三种最重要的热带水果之一。菠萝基因组测序的完成为在全基因组水平上研究菠萝MYB基因的组织和进化特征提供了绝佳的机会。在本研究中，总共鉴定了 94 个菠萝 R2R3-MYB 基因，并根据保守的基因结构和基序组成，进一步在系统发育上分为 26 个亚科。共线性分析表明，片段重复事件在菠萝MYB基因家族的扩展中发挥着至关重要的作用。进一步的比较系统发育分析表明，MYB基因家族在植物进化过程中存在功能分化。来自不同组织和发育阶段的 RNA-seq 数据揭示了 AcMYB 基因不同的时间和空间表达谱。进一步的定量表达分析显示了选定的推定应激相关 AcMYB 基因响应不同的非生物应激和激素治疗的特定表达模式。对菠萝MYB基因，特别是组织偏好基因和应激反应基因的综合表达分析，可以为进一步的功能表征提供有价值的线索。在这项工作中，我们通过使用一组生物信息学方法分析菠萝基因组序列，系统地鉴定了 AcMYB 基因。我们的研究结果提供了对菠萝 R2R3-MYB 基因的组织、系统发育和表达模式的全面了解，从而有助于更好地了解它们在菠萝中的生物学作用。本文的在线版本 (doi:10.1186/s12864-017-3896-y) 包含补充材料，可供授权用户使用。
The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level. In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization. In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple. The online version of this article (doi:10.1186/s12864-017-3896-y) contains supplementary material, which is available to authorized users.