Supplementary Data

Supplementary figure S1: A representative visual illustration of the slide culture technique for viewing <em>P. medicaginis</em>. Supplementary figure S2: A representative visual illustration of the biocontrol plate-based screening Supplementary tables S1.1-1.3 contain original list of differentially regulated proteins, obtained from the centre of proteomics and genomics research (CPGR). The data sets are comprised of the of differentially regulated proteins in response to endophytes (WWE), <em>P. medicaginis </em>(WWP) and the combination (WWPE) relative to the controls. Additionally, supplementary table S1.4 contains the list of all differentially regulated proteins (&gt; log2 fold change) in response to endophytes, <em>Phoma</em> and combined endophytes and <em>Phoma</em> under greenhouse conditions. Supplementary tables S2.1-2.3 contain original of differentially regulated proteins, obtained from the centre of proteomics and genomics research (CPGR). The data sets are comprised of the of differentially regulated proteins in response to endophytes (WWE), <em>P. medicaginis </em>(WWP) and the combination (WWPE) relative to the controls. Additionally, supplementary table S2.4 contains the list of all differentially regulated proteins (&gt; log2 fold change) in response to endophytes, <em>Phoma</em> and combined endophytes and <em>Phoma</em> under greenhouse conditions. Supplementary tables S3.1-3.3 contain original data files obtained from the centre of proteomics and genomics research (CPGR). Additionally, supplementary table S3.4 contains the list of all differentially regulated proteins (&gt; log2 fold change) in response to endophytes, water deficit and combined endophytes and water deficit under greenhouse conditions. Supplementary tables S4.1-4.3 contains the original files of differentially regulated proteins in response to endophytes (WWE), water deficit (WD) and the combination (WDE) relative to the controls. Additionally, supplementary table S4.4 contains the list of all differentially regulated proteins (&gt; log2 fold change) in response to endophytes, water deficit and combined endophytes and water deficit under field conditions. Supplementary table_S5.1.1 Blast2GO mapping omicsbox table <em>Phoma</em> greenhouse and table S5.2.1 Blast2GO mapping omicsbox table <em>Phoma</em> field contains detailed gene ontology (GO) obtained using Blast2GO program for greenhouse and field experiments respectively. The table contains the respective accessions in response to endophytes (WWE), <em>P. medicaginis </em>(WWP) and the combination (WWPE) and the sequences are associated to each GO term with analysis is based on the three main categories of GO distribution by level 2: Biological Process (BP) and Molecular Function (MF) and Cellular Components (CC). Supplementary table S5.1.2 KEGG pathway omicsbox <em>Phoma</em> greenhouse and supplementary table S5.2.2 KEGG pathway omicsbox <em>Phoma</em> field contains pathways identified in greenhouse and field experiments in response to endophytes (WWE), <em>P. medicaginis </em>(WWP) and the combination (WWPE). Additionally, file contains Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, which includes the pathway name and code, the number of sequences in pathway (#Seqs), KEGG orthologs (KO) as well as enzyme codes (EC) associated with the identified sequences Supplementary table S6.1.1 Blast2GO mapping omicsbox table drought greenhouse and Supplementary table S6.2.1 Blast2GO mapping omicsbox table drought field contains detailed Gene ontology (GO) obtained using Blast2GO program for greenhouse and field experiments respectively. The table contains the respective accessions in response to endophytes (WWE), water deficit (WD) and the combination (WDE) and the sequences are associated to each GO term with analysis is based on the three main categories of GO distribution by level 2: Biological Process (BP) and Molecular Function (MF) and Cellular Components (CC). Supplementary table S6.1.2 KEGG pathway omicsbox drought greenhouse and KEGG pathway omicsbox drought field, contains pathways identified in greenhouse and field experiments in response to endophytes (WWE), water deficit (WD) and the combination (WDE). Additionally, the file contains Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, which includes the pathway name and code, the number of sequences in pathway (#Seqs), KEGG orthologs (KO) as well as enzyme codes (EC) associated with the identified sequences. Supplementary table S7.1 contains the list of KEGG pathways found to be conserved between greenhouse and field plants in response to endophytes, <em>P. medicaginis</em> and combined endophyte and <em>P. medicaginis </em>infection. Furthermore, supplementary table S7.2 contains the conserved KEGG pathways between greenhouse and field grown <em>M. sativa </em>in response to endophytes, <em>P. medicaginis</em> and combined endophyte and <em>P. medicaginis </em>infection. The table include the main category as well as the pathway identified in that category. Supplementary table S8.1 the list of KEGG pathways found to be conserved between greenhouse and field plants in response to endophytes, water deficit and combined endophyte and water deficit. Additionally, supplementary table S8.2 contains the conserved KEGG pathways between greenhouse and field plants in response to endophytes, water deficit and combined endophyte and water deficit. The table include the main category as well as the pathway identified in that category. This study, to our knowledge, is the first reported comparative proteomic analyses investigating application of endophytes for improved <em>Phoma</em> disease resistance and drought tolerance in <em>Medicago sativa</em> under both greenhouse and field conditions补充图S1：紫苜蓿茎点霉（P. medicaginis）载片培养技术的代表性可视化图示。补充图S2：基于平板的生防筛选代表性可视化图示。 补充表S1.1~1.3收录了来自蛋白质组与基因组研究中心（CPGR）的差异表达蛋白原始列表。该数据集包含相对于对照组而言，经内生真菌（WWE）、紫苜蓿茎点霉（WWP）以及二者联合处理（WWPE）后得到的差异表达蛋白数据。此外，补充表S1.4收录了温室条件下，内生真菌、茎点霉属（Phoma）以及二者联合处理下所有差异表达蛋白（log₂倍变化>阈值）的列表。 补充表S2.1~2.3同样包含来自CPGR的差异表达蛋白原始数据，对应处理组为内生真菌（WWE）、紫苜蓿茎点霉（WWP）以及二者联合处理（WWPE）的对照组相对数据。补充表S2.4收录了温室条件下，内生真菌、茎点霉属（Phoma）以及二者联合处理下所有差异表达蛋白（log₂倍变化>阈值）的列表。 补充表S3.1~3.3均为来自CPGR的差异表达蛋白原始数据文件。此外，补充表S3.4收录了温室条件下，内生真菌、水分胁迫以及二者联合处理下所有差异表达蛋白（log₂倍变化>阈值）的列表。 补充表S4.1~4.3包含了相对于对照组而言，经内生真菌（WWE）、水分胁迫（WD）以及二者联合处理（WDE）后得到的差异表达蛋白原始文件。此外，补充表S4.4收录了田间条件下，内生真菌、水分胁迫以及二者联合处理下所有差异表达蛋白（log₂倍变化>阈值）的列表。 补充表S5.1.1为紫苜蓿茎点霉温室试验的Blast2GO注释组学盒映射表，补充表S5.2.1为紫苜蓿茎点霉田间试验的Blast2GO注释组学盒映射表，二者分别包含通过Blast2GO程序获得的温室与田间试验的详细基因本体（GO）注释信息。该类表格收录了内生真菌（WWE）、紫苜蓿茎点霉（WWP）以及二者联合处理（WWPE）对应的样本信息，每条序列均关联至相应GO术语，分析基于GO二级分类的三大核心类别：生物过程（BP）、分子功能（MF）与细胞组分（CC）。 补充表S5.1.2为紫苜蓿茎点霉温室试验的KEGG通路注释组学盒表格，补充表S5.2.2为紫苜蓿茎点霉田间试验的KEGG通路注释组学盒表格，收录了温室与田间试验中，内生真菌（WWE）、紫苜蓿茎点霉（WWP）以及二者联合处理（WWPE）下鉴定到的通路信息。该文件包含京都基因与基因组百科全书（KEGG）分析结果，涵盖通路名称与编号、通路内序列数（#Seqs）、KEGG同源基因（KO）以及与鉴定序列相关的酶编码（EC）。 补充表S6.1.1为干旱胁迫温室试验的Blast2GO注释组学盒映射表，补充表S6.2.1为干旱胁迫田间试验的Blast2GO注释组学盒映射表，二者分别包含通过Blast2GO程序获得的温室与田间试验的详细GO注释信息。该类表格收录了内生真菌（WWE）、水分胁迫（WD）以及二者联合处理（WDE）对应的样本信息，每条序列均关联至相应GO术语，分析基于GO二级分类的三大核心类别：生物过程（BP）、分子功能（MF）与细胞组分（CC）。 补充表S6.1.2为干旱胁迫温室试验的KEGG通路注释组学盒表格，补充表S6.2.2为干旱胁迫田间试验的KEGG通路注释组学盒表格，收录了温室与田间试验中，内生真菌（WWE）、水分胁迫（WD）以及二者联合处理（WDE）下鉴定到的通路信息。该文件包含KEGG分析结果，涵盖通路名称与编号、通路内序列数（#Seqs）、KEGG同源基因（KO）以及与鉴定序列相关的酶编码（EC）。 补充表S7.1收录了温室与田间植株经内生真菌、紫苜蓿茎点霉以及二者联合侵染处理后，保守存在的KEGG通路列表。此外，补充表S7.2收录了温室与田间种植的紫花苜蓿（Medicago sativa）经内生真菌、紫苜蓿茎点霉以及二者联合侵染处理后，保守存在的KEGG通路列表。该表格包含通路所属的核心类别以及对应类别中鉴定到的通路信息。 补充表S8.1收录了温室与田间植株经内生真菌、水分胁迫以及二者联合处理后，保守存在的KEGG通路列表。此外，补充表S8.2收录了温室与田间植株经内生真菌、水分胁迫以及二者联合处理后，保守存在的KEGG通路列表。该表格包含通路所属的核心类别以及对应类别中鉴定到的通路信息。 据我们所知，本研究是首次在温室与田间条件下开展比较蛋白质组学分析，探究内生真菌用于提升紫花苜蓿（Medicago sativa）抗茎点霉属病害与耐旱性的应用潜力。