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
复制标题
多倍体小麦NAC转录因子家族全基因组序列及表达分析
DOI：
10.1101/141747
复制
发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Borrill P
中科院分区：
文献类型：
--
作者：
Borrill P
农业中的许多重要基因对应于转录因子（TF），其调节从开花到对疾病和非生物胁迫的响应的广泛途径。在这项研究中，我们鉴定了5776个六倍体小麦（Triticum aestivum）转座子，并将其归类为基因家族。我们进一步研究了NAC家族，探索了308个RNA-seq样品的同源性、C-末端结构域（CTD）保守性和表达谱。NAC结构域的系统发育树表明，小麦NAC与水稻（Oryza sativa）和大麦（Hordeum vulgare）相似，可分为8个类群。CTD基序经常保守的小麦，水稻和大麦的系统发育组内，然而，这种保守性并没有保持在整个系统发育组。58%的NAC存在三个同源基因拷贝，而33%的NAC存在单个同源基因丢失的证据。我们探讨了基因表达模式在广泛的发展阶段，组织和非生物胁迫。我们发现，与更远的NAC相比，更多遗传相关的NAC共享更相似的表达模式。然而，在每个系统发育组中，有不同的表达谱的分支。我们对所有小麦基因进行了共表达分析，鉴定了37个共表达基因模块，其中23个包含NAC。使用基因本体论（GO）术语富集，我们获得了推定的功能，包括响应热和非生物胁迫和响应水的共表达模块内的NAC：这些NAC可能代表育种或生物技术应用的目标。本研究为小麦NAC转录因子的进一步研究提供了理论框架和数据基础。
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.