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