Additional file 1 of Changes in root microbiome during wheat evolution
Creators: name: Gholizadeh, Somayeh
name: Mohammadi, Seyed Abolghasem
name: Salekdeh, Ghasem Hosseini
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Figure 1. Unconstrained PCoA reveals distinct clustering of microbiomes of different developmental stages (A) Unconstrained PCoA using the Bray-Curtis distance metric. (B) Unconstrained PCoA using the weighted UniFrac distance metric. (C) Unconstrained PCoA using the unweighted UniFrac distance metric. Supplementary Figure 2. The wheat rhizosphere microbiome was colonized by distinct taxa. (A) and (C) Correspond to rhizosphere vs bulk soil comparison in phylum and family level respectively, and (B) and (D) Correspond to the rhizosphere of vegetative stage vs. that of reproductive time respectively in phylum and family level. To find the most important up-regulated features among the differentially expressed bacterial taxa, the MicrobiomeSeq package was used to detect respectively the top 10 and 20 differentially abundant Phyla and families among different comparison groups, and mean decrease accuracy values of differentially abundant taxa were calculated. Supplementary Figure 3. Host signature reveals a second distinct clustering of the variation in the rhizosphere microbiomes of individual wheat species after accounting for the variation present among developmental stages. Ordination of CAP analysis using the Bray-Curtis metric constrained in genotypes of (A) T. aestivum, (B) T. durum, (C) T. turgidum, (D) T. urartu, (E) Ae. tauschii, (F) Ae. speltoides across two developmental stages. Supplementary Figure 4. Differentially family-level relative abundance exhibits differences between genotypes of six wheat species across two developmental stages. Differential families in genotypes of (A) T. aestivum, (B) T. durum, (C) T. turgidum, (D) T. urartu, (E) Ae. tauschii, (F) Ae. speltoides, during different developmental stages, were represented with different colors. The colors orange, blue, and green show differential families at vegetative, reproductive, and both sampling time points respectively. Supplementary Figure 5. Bacterial community structure differs significantly among rhizosphere samples of modern cultivars and landraces. Ordination of CAP analysis using the Bray-Curtis metric constrained to factor Breeding. Supplementary Table 1. Field and grassland soils used as a seed bank of the microbiome in this study. Supplementary Table 2. Soil chemical and physical analysis. Supplementary Table 3. Wild wheat accessions used in this study. Supplementary Table 4. Modern and Landrace varieties used in this study. Supplementary Table 5. PERMANOVA of the bacterial communities associated with wheat plants considering all factors and their interactions. Numbers in sub-indices indicate the degrees of freedom and residuals of each F test. Supplementary Table 6. Experimental factors predicting alpha-diversity of bacterial communities associated with the rhizosphere of wheat. Statistical support was done with the function “kruskall.test” or “pairwise.Wilcox.test” in the R base considering all factors and their interactions. All P values were corrected for multiple comparisons using the FDR correction. Numbers in sub-indices indicate the degrees of freedom and residuals of each F test.