Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat.
Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat.
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DOI：
10.1534/g3.117.043679
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发表时间：
2017-09-07
期刊：
影响因子：
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通讯作者：
Uauy C
中科院分区：
文献类型：
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作者：
Borrill P;Harrington SA;Uauy C
农业中的许多重要基因对应于转录因子（TFS），这些基因调节了从开花到对疾病和非生物应激的反应的广泛途径。在这项研究中，我们在十六世纪小麦（Triticum aestivum）中确定了5776个TF，并将其分类为基因家族。我们进一步研究了NAC家族，探索了308个RNA-Seq样品中的系统发育，C末端结构域（CTD）的保护和表达谱。 NAC结构域的系统发育树表明，小麦NAC分为八组，类似于大米（Oryza sativa）和大麦（Hordeum vulgare）。在系统发育群体中，小麦，大米和大麦之间经常保守CTD基序。但是，这种保护尚未在系统发育群体之间维持。 58％的NAC有三份同源副本，而单个同源基因损失的证据为33％的NAC。我们探索了各种发育阶段，组织和非生物应力的基因表达模式。我们发现，与更遥远的NAC相比，更多的系统发育相关的NAC具有更相似的表达模式。但是，在每个系统发育群体中，都有各种表达谱的进化枝。我们对所有小麦基因进行了共表达分析，并确定了37个共表达基因的模块，其中23个包含NAC。使用基因本体论（GO）术语富集，我们获得了共表达模块中NAC的推定功能，包括对热量和非生物压力的响应和对水的反应：这些NACS可能代表了繁殖或生物技术应用的靶标。这项研究为假设生成的框架和数据提供了有关小麦NAC TF的未来研究的框架和数据。
Many important genes in agriculture correspond to transcription factors (TFs) that regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5776 TFs in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain (CTD) conservation, and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). CTD motifs were frequently conserved between wheat, rice, and barley within phylogenetic groups; however, this conservation was not maintained across phylogenetic groups. Three homeologous copies were present for 58% of NACs, whereas evidence of single homeolog gene loss was found for 33% of NACs. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a coexpression analysis on all wheat genes and identified 37 modules of coexpressed genes of which 23 contained NACs. Using gene ontology (GO) term enrichment, we obtained putative functions for NACs within coexpressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC TFs in wheat.