Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon.
Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon.
复制标题
二穗短柄草 AP2/ERF 转录因子家族的全基因组鉴定、系统发育及表达分析
DOI：
10.1186/s12864-016-2968-8
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发表时间：
2016-08-15
期刊：
影响因子：
4.4
通讯作者：
Nie X
中科院分区：
文献类型：
--
作者：
Cui L;Feng K;Wang M;Wang M;Deng P;Song W;Nie X
AP2/ERF转录因子是植物中最重要的基因家族之一，在调节植物生长发育和响应各种逆境中发挥着重要作用。虽然AP2/ERF在许多植物物种中已经得到了充分的研究，但对模式植物远端短臂草中的AP2/ERF家族知之甚少，特别是那些参与逆境过程调控网络的植物。本研究采用全基因组检索的方法，对青冈中的AP2/ERF基因家族进行鉴定，共获得141个BdAP2/ERF基因。系统发育分析将其划分为4个亚科，其中ERF亚科112个，RAV亚科4个，AP2亚科24个，SOLIST亚科1个，这与AP2结构域的数目和基因结构分析一致。进一步通过染色体定位、基因结构、保守蛋白基序和顺式调控元件以及基因复制事件分析，系统研究了这些BdAP2/ERF基因的进化特征。此外，利用正交法构建了BdAP2/ERF与其他基因之间的调控网络，发现39个BdAP2/ERF参与调控网络，并识别了517个网络分支。利用已有的RNA序列和基因芯片数据，研究了BdAP2/ERF在发育和不同胁迫条件下的表达谱，鉴定出10个组织特异性基因和几个胁迫响应基因。最后，选择了11个AP2/ERF基因，利用RT-PCR方法验证了它们在不同组织和不同胁迫处理下的表达，结果证实这些AP2/ERF基因参与了不同的发育和生理过程。这项研究首次报道了BdAP2/ERF家族的特征，这将为进一步研究短臂藻类中AP2/ERF的进化和功能提供宝贵的信息，也有助于更好地理解该模式物种和其他模式物种的发育和胁迫耐受性的分子基础。
The AP2/ERF transcription factor is one of the most important gene families in plants, which plays the vital role in regulating plant growth and development as well as in response to diverse stresses. Although AP2/ERFs have been thoroughly characterized in many plant species, little is known about this family in the model plant Brachypodium distachyon, especially those involved in the regulatory network of stress processes. In this study, a comprehensive genome-wide search was performed to identify AP2/ERF gene family in Brachypodium and a total of 141 BdAP2/ERFs were obtained. Phylogenetic analysis classified them into four subfamilies, of which 112 belonged to ERF, four to RAV and 24 to AP2 as well as one to soloist subfamily respectively, which was in accordance with the number of AP2 domains and gene structure analysis. Chromosomal localization, gene structure, conserved protein motif and cis-regulatory elements as well as gene duplication events analysis were further performed to systematically investigate the evolutionary features of these BdAP2/ERF genes. Furthermore, the regulatory network between BdAP2/ERF and other genes were constructed using the orthology-based method, and 39 BdAP2/ERFs were found to be involved in the regulatory network and 517 network branches were identified. The expression profiles of BdAP2/ERF during development and under diverse stresses were investigated using the available RNA-seq and microarray data and ten tissue-specific and several stress-responsive BdAP2/ERF genes were identified. Finally, 11 AP2/ERF genes were selected to validate their expressions in different tissues and under different stress treatments using RT-PCR method and results verified that these AP2/ERFs were involved in various developmental and physiological processes. This study for the first time reported the characteristics of the BdAP2/ERF family, which will provide the invaluable information for further evolutionary and functional studies of AP2/ERF in Brachypodium, and also contribute to better understanding the molecular basis for development and stresses tolerance in this model species and beyond.