Additional file 1 of Seed endophytes of malting barley from different locations are shaped differently and are associated with malt quality traits
Creators: name: Ajayi, Oyeyemi
name: Mahalingam, Ramamurthy
Publisher: name: figshare
Year: 2025
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1. S1 Fig. S1. Rarefaction curves for malting barley seed endophytes across four locations. Rarefaction curves were made for all samples to evaluate the species richness, depth of sampling and sequencing coverage for bacterial 16S (A) and fungal ITS (B). S1 Fig. S2. - Bacterial community composition of malting barley seed endophytes across four locations. A-I represents the PCoA of 16S rRNA amplicon sequencing data across location for each cultivar based on unweighted unifrac (A-C), Bray-Curtis (D-F) and Jaccard distances (G-I). A,E,H are for ND Genesis; B,E,H are for AAC Synergy while C,E,H are for Conlon genotypes. S1 Fig. S3. Fungal community composition of malting barley seed endophytes across four locations. A-F represents the PCoA of fungal ITS sequencing data across location for each cultivar based on Bray-Curtis (A-C) and Jaccard distances (D-F). A,D are for ND Genesis; B, E are for AAC Synergy and C,F are for Conlon genotypes/cultivars. S1 Fig. S4. Negative relationship between Shannon index, bacterial genus taxa and some malt quality traits. For free amino nitrogen (FAN) (A), and alpha amylase (AA) (B) based on linear regression after adjusting for covariates genotype and location. S1 Fig. S5. UpSet plots of bacterial and fungal ASVs present in each location of Conlon, ND Genesis and AAC Synergy.(A-C) UpSet plot showing the number of bacterial ASVs that are shared between or are unique for all locations for Conlon (A), ND Genesis (B) and AAC Synergy (C). (D-F) UpSet plot showing the number of fungal ASVs that are shared between or are unique for all locations for Conlon (D), ND Genesis (E) and AAC Synergy (F). Number in color in A-F indicates shared ASVs common to all locations, while filled-in black dots with an edge between the dots indicates that these ASVs are present in multiple locations. S1 Fig. S6. Heatmap of the relative abundance of the top 30 bacterial seed endophytic communities of malting barley genotypes/cultivars across four locations. S1 Fig. S7. Heatmap of the relative abundance of the top 30 fungal seed endophytic communities of malting barley genotypes/cultivars across four locations. S1 Fig. S8. Feature ID sequence identification and BlastN analysis of 16S rRNA partial sequence of Xanthomonas. (A) Feature ID colored in orange represents genus Xanthomonas (B) BlastN analysis of the 260 bp sequence shared 100% homology with Xanthomonas translucens. S1 Fig. S9. Genotype and location pairwise comparison of the seed endophytic bacteria microbial taxonomic composition. For Crookston vs. St. Paul (A),  Carrington vs. Casselton (B), AAC Synergy vs. Conlon (C), Conlon vs. ND Genesis (D), and AAC Synergy and ND Genesis (E). For A-E, dot plots of the LDA scores (log 10) computed for features with differential abundance in each pairwise assessments as indicated above. S1 Fig. S10. Genotype and location pairwise comparison of the seed endophytic fungal microbial taxonomic composition. For Carrington vs. Casselton (A), Crookston vs. St. Paul (B), AAC Synergy vs. Conlon (C), Conlon vs. ND Genesis (D), and AAC Synergy and ND Genesis (E). For A-E, dot plots of the LDA scores (log 10) computed for features with differential abundance in each pairwise assessments as indicated above. S1 Fig. S11. Differential abundance analysis of seed endophytic bacterial communities of malting barley grown across four locations. (A) Pairwise differential abundance analysis (based on logFC) between St. Paul and Crookston locations at the genus level. Positive logFC indicates increased endophytic bacterial (EB) abundance in St Paul (decrease EB in Crookston), while negative logFC indicates decreased EB in St. Paul (increased EB in Crookston). (B) Pairwise differential abundance analysis (based on logFC) between Carrington and Casselton locations at the genus level. The negative logFC indicates decreased EB in Casselton (increased EB in Carrington). Only some genera are reported (for complete list see Table S7) (C). Venn diagram showing unique and shared ASVs between pairwise location comparisons (Complete list is available in Table S7). (D -F) Pairwise differential abundance analysis (based on logFC) between Conlon and AAC Synergy (D), Conlon and ND Genesis (E) and AAC Synergy and ND Genesis (F) at the genus level. For D, Positive logFC indicates increased EB abundance in Conlon (decrease EB in AAC Synergy), while negative logFC indicates decreased EB in Conlon (increased EB in AAC Synergy). For E, Positive logFC indicates increased EB abundance in Conlon (decrease EB in ND Genesis), while negative logFC indicates decreased EB in Conlon (increased EB in ND Genesis). For F, Positive logFC indicates increased EB abundance in AAC Synergy (decrease EB in ND Genesis), while negative logFC indicates decreased EB in AAC Synergy (increased EB in ND Genesis). (G) Venn diagram showing unique and shared ASVs between pairwise genotype comparisons (Complete list is available in Table S7). S1 Fig. S12. Differential abundance analysis of seed endophytic fungal communities of malting barley grown across four locations. (A) Pairwise differential abundance analysis (based on logFC) between Carrington and Casselton locations at the genus level. Positive logFC indicates increased endophytic bacterial (EB) abundance in Carrington (decrease EB in Casselton), while negative logFC indicates decreased EB in Carrington (increased EB in Casselton). (B) Pairwise differential abundance analysis (based on logFC) between St. Paul and Crookston locations at the genus level. Positive logFC indicates increased endophytic bacterial (EB) abundance in St. Paul (decrease EB in Crookston), while negative logFC indicates decreased EB in St. Paul (increased EB in Crookston). (C) Venn diagram showing unique and shared ASVs between pairwise location comparisons (Complete list is available in Table S8). (D -F) Pairwise differential abundance analysis (based on logFC) between Conlon and AAC Synergy (D), ND Genesis and Conlon (E) and ND Genesis and AAC Synergy (F) at the genus level. For D, Positive logFC indicates increased EB abundance in Conlon (decrease EB in AAC Synergy), while negative logFC indicates decreased EB in Conlon (increased EB in AAC Synergy). For E, Positive logFC indicates increased EB abundance in ND Genesis (decrease EB in Conlon), while negative logFC indicates decreased EB in ND Genesis (increased EB in Conlon). For F, Positive logFC indicates increased EB abundance in ND Genesis (decrease EB in AAC Synergy), while negative logFC indicates decreased EB in ND Genesis (increased EB in AAC Synergy). (G) Venn diagram showing unique and shared ASVs between pairwise genotypes comparisons (Complete list is available in Table S8).