Genome-wide analysis of transmembrane 9 superfamily genes in wheat (Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions.
Genome-wide analysis of transmembrane 9 superfamily genes in wheat (Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions.
复制标题
DOI：
10.3389/fpls.2023.1324974
复制
发表时间：
2023
影响因子：
5.6
通讯作者：
中科院分区：
文献类型：
--
作者：
跨膜9超家族(TM9SF)蛋白在植物生理中具有重要作用。然而，这些蛋白质在小麦(Triticum Aestivum)中的特性很差。本研究旨在对可能的小麦TM9SF(TraesTM9SF)蛋白进行全基因组分析，以及它们在氮素限制和淀粉溶解芽孢杆菌PDR1处理中的潜在作用。从小麦基因组中检索到TraesTM9SF基因，并对其进行了理化性质、比对、系统发育、基序结构、顺式调控元件、共性、蛋白质相互作用(PPI)和转录因子(TF)预测分析。采用转录组测序和实时定量聚合酶链式反应(qRT-PCR)技术，检测了氮素限制和淀粉菌PDR1单独或复合处理下根中基因的表达。在小麦基因组中发现了47个TraesTM9SF基因，突出了这些基因在小麦中的重要性。TraesTM9SF基因在一些小麦染色体上缺失，在其他染色体上分布不均匀，这表明潜在的调控功能和进化事件可能形成了TraesTM9SF基因家族。TraesTM9SF启动子区域存在54个顺式调控元件，包括光反应、激素反应、生物/非生物胁迫和发育顺式调节元件。在小麦基因组中没有记录到TraesTM9SF基因的重复，在一个复杂的调控网络中，预测有177个TF针对47个TraesTM9SF基因。这些发现为预测未知的TM9SF基因的功能提供了有价值的数据。此外，转录组分析和qRT-PCR验证表明，TraesTM9SF基因在小麦的根系中表达，并可能参与该植物对氮素限制和淀粉菌PDR1单一或联合处理的反应，表明它们在植物生长、发育和逆境反应中发挥功能。这些发现可能对进一步研究TM9SF基因在小麦中的功能和生物学应用具有重要意义。
Transmembrane 9 superfamily (TM9SF) proteins play significant roles in plant physiology. However, these proteins are poorly characterized in wheat (Triticum aestivum). The present study aimed at the genome-wide analysis of putative wheat TM9SF (TraesTM9SF) proteins and their potential involvement in response to nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatments. TraesTM9SF genes were retrieved from the wheat genome, and their physiochemical properties, alignment, phylogenetic, motif structure, cis-regulatory element, synteny, protein-protein interaction (PPI), and transcription factor (TF) prediction analyses were performed. Transcriptome sequencing and quantitative real-time polymerase reaction (qRT-PCR) were performed to detect gene expression in roots under single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1. Forty-seven TraesTM9SF genes were identified in the wheat genome, highlighting the significance of these genes in wheat. TraesTM9SF genes were absent on some wheat chromosomes and were unevenly distributed on the other chromosomes, indicating that potential regulatory functions and evolutionary events may have shaped the TraesTM9SF gene family. Fifty-four cis-regulatory elements, including light-response, hormone response, biotic/abiotic stress, and development cis-regulatory elements, were present in the TraesTM9SF promoter regions. No duplication of TraesTM9SF genes in the wheat genome was recorded, and 177 TFs were predicted to target the 47 TraesTM9SF genes in a complex regulatory network. These findings offer valued data for predicting the putative functions of uncharacterized TM9SF genes. Moreover, transcriptome analysis and validation by qRT-PCR indicated that the TraesTM9SF genes are expressed in the root system of wheat and are potentially involved in the response of this plant to single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1, suggesting their functional roles in plant growth, development, and stress responses. These findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.
登录
查看更多内容
影响因子：
16.6
作者：
Dean P;Sendra KM;Williams TA;Watson AK;Major P;Nakjang S;Kozhevnikova E;Goldberg AV;Kunji ERS;Hirt RP;Embley TM
通讯作者：
Embley TM
影响因子：
5.6
作者：
通讯作者：
--
影响因子：
5.6
作者：
Luján MA;Soria-García Á;Claver A;Lorente P;Rubio MC;Picorel R;Alfonso M
通讯作者：
Alfonso M
影响因子：
14.9
作者：
Bailey TL;Johnson J;Grant CE;Noble WS
通讯作者：
Noble WS
模因套件：用于发现和搜索的工具。
影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
通讯作者：
Noble WS