DataSheet_4_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.csv

IntroductionTransmembrane 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.
MethodsTraesTM9SF 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.
Results and discussionForty-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.
ConclusionThese findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.

引言：跨膜9超家族（Transmembrane 9 superfamily, TM9SF）蛋白在植物生理过程中发挥关键作用，但目前小麦（Triticum aestivum）中该家族蛋白尚未得到充分表征。本研究旨在开展小麦潜在TM9SF蛋白（命名为TraesTM9SF）的全基因组分析，并探究其在氮限制和解淀粉芽孢杆菌（Bacillus amyloliquefaciens）PDR1处理下的潜在响应功能。
材料与方法：从小麦基因组中检索得到TraesTM9SF基因，随后对其理化性质、序列比对、系统发育分析、基序结构、顺式调控元件（cis-regulatory element）、共线性、蛋白质-蛋白质相互作用（protein-protein interaction, PPI）以及转录因子（transcription factor, TF）预测展开系统性分析。同时通过转录组测序与实时定量聚合酶反应（quantitative real-time polymerase reaction, qRT-PCR），检测小麦根系在单独或联合施加氮限制与解淀粉芽孢杆菌PDR1处理下的基因表达水平。
结果与讨论：本研究在小麦基因组中共鉴定出47个TraesTM9SF基因，凸显了该基因家族在小麦中的重要地位。部分小麦染色体上未分布TraesTM9SF基因，其余染色体上的基因分布亦不均衡，表明潜在的调控功能与进化事件共同塑造了TraesTM9SF基因家族的演化模式。在TraesTM9SF基因的启动子区域，共识别到54种顺式调控元件，涵盖光响应、激素响应、生物/非生物胁迫响应以及发育相关顺式调控元件。小麦基因组中未检测到TraesTM9SF基因的复制事件，同时预测得到177个转录因子可通过复杂调控网络靶向这47个TraesTM9SF基因。上述研究结果为解析尚未被表征的TM9SF基因的潜在功能提供了宝贵的数据支撑。此外，转录组分析与qRT-PCR验证结果表明，TraesTM9SF基因在小麦根系中均有表达，且可能参与植物响应单独或联合施加的氮限制与解淀粉芽孢杆菌PDR1处理的过程，提示其在植物生长发育与胁迫响应中发挥功能性作用。
结论：本研究结果可为后续探究小麦TM9SF基因的功能与生物学应用提供重要参考依据。