Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato.
Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato.
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DOI：
10.1186/s12864-017-4082-y
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发表时间：
2017-09-06
期刊：
影响因子：
4.4
通讯作者：
Chung MY
中科院分区：
文献类型：
--
作者：
Khatun K;Nath UK;Robin AHK;Park JI;Lee DJ;Kim MB;Kim CK;Lim KB;Nou IS;Chung MY
锌指同源结构域蛋白 (ZHD) 构成植物特异性转录因子家族，具有保守的 DNA 结合同源结构域和锌指基序。 ZHD 蛋白家族的成员在植物生长、发育和胁迫反应中发挥着重要作用。 ZHD 基因的全基因组表征已在几种模式植物中进行，包括拟南芥和稻，但尚未在番茄（Solanum lycopersicum）中进行。在这项研究中，我们首次对番茄（Solanum lycopersicum）中的 ZHD 基因家族进行了全面的全基因组表征和表达谱分析。我们鉴定了 22 个 SlZHD 基因，并根据系统发育将它们分为 6 个亚家族。 SlZHD 基因在每个亚科中总体上是保守的，在基因结构和基序分布上有微小的变化。 22 个 SlZHD 基因分布在 12 条番茄染色体中的 6 条上，在 4 个基因中检测到片段重复。 Ka/Ks 比率分析表明，重复的基因处于负选择或纯化选择之下。综合表达分析表明，SlZHD基因在多种组织中广泛表达，与其他组织相比，大多数基因优先在花蕾中表达。此外，许多基因对非生物胁迫和植物激素治疗有反应。系统分析揭示了番茄 ZHD 蛋白的结构多样性，这表明 SlZHD 基因在不同发育阶段以及对非生物胁迫的反应中发挥不同作用的可能性。我们对 SlZHD 基因在各种组织/器官中以及在各种非生物胁迫和植物激素治疗下的表达分析揭示了它们的功能差异。我们的研究结果为进一步分析探索番茄 ZHD 基因的生物学功能提供了宝贵的资源。本文的在线版本 (10.1186/s12864-017-4082-y) 包含补充材料，可供授权用户使用。
Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment. Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes. The online version of this article (10.1186/s12864-017-4082-y) contains supplementary material, which is available to authorized users.
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