The code to generate the published figures is found here in the following scripts:
Figure 1A: ordination_analysis.R
Figure 1B: microbial_groups.R
Figure 1C: heritability_analysis.R
Figure 2: selection_analysis.R
Figure 3A: gwas_analysis.R
Figure 3BC: gene_expression_analysis.R
Figure 4: abundance_vs_phenotype.R
Figure 5: f_comamonadaceae_example.R
Supplementary Figure 1: (manually drawn)
Supplementary Figure 2A: ordination_analysis.R
Supplementary Figure 2B: heritability_analysis.R
Supplementary Figure 3: heritability_analysis.R
Supplementary Figure 4: abundance_vs_phenotype.R
Supplementary Figure 5: (manually drawn)
Supplementary Figure 6: ordination_analysis.R
Supplementary Figure 7B: ordination_analysis.R
Supplementary Figure 8: microbial_groups.R
Supplementary Figure 9ABC: ordination_analysis.R
Supplementary Figure 9DE: gwas_analysis.R
Supplementary Figure 10: f_comamonadaceae_example.R
Supplementary Figure 11: selection_analysis.R
intermediate results generated by the analysis scripts
abundance_vs_phenotype.rda: BLUPs of microbe abundance and plant traits for each maize genotype and N treatment
asv_taxonomy.rda : taxonomic information of ASVs
B73_RefGen_v4_gene_ids.rda : gene IDs from maize B73 reference genome v4
B73_RefGen_v4_gene_pos.rda : gene positions from maize B73 reference genome v4
blup_lowN_150_tax_groups.csv : BLUPs of microbe abundance log(relative abundance) for 150 microbial groups in 226 maize genotypes under -N treatment
blup_lowN_3618_asvs.csv : BLUPs of microbe abundance log(relative abundance) for 3618 ASVs in 226 maize genotypes under -N treatment
blup_stdN_150_tax_groups.csv : BLUPs of microbe abundance log(relative abundance) for 150 microbial groups in 226 maize genotypes under +N treatment
blup_stdN_3618_asvs.csv : BLUPs of microbe abundance log(relative abundance) for 3618 ASVs in 226 maize genotypes under +N treatment
corr_data.rda: correlation of microbe abundance with phenotypes for 2 N treatments and 150 microbial groups
group_data.rda: summary statistics for all 150 microbial groups H2_stdN_19, H2_lowN_19, p_values_stdN, p_values_lowN
gwas_dat_threshold7: Gwas results (combined separate GWAS for +N and -N) showing 1089 SNPs that had a significant signal (-log10(p) > 7.187346) for any of the 150 microbial groups
mean_gene_expression_by_tissue_type_4genotypes.rda: Gene expression of genes near MAPLs vs other genes in 4 genotypes and 2 tissue types(growth chamber experiment)
mean_gene_expression_by_tissue_type_kremling.rda: Gene expression of genes near MAPLs vs other genes in all genotypes and 7 tissue types (data by Kremling et. al.)
ps_asv.rda: R phyloseq object, ASV table with 3626 ASVs and 3306 samples, final set of ASVs table used in this study (after filter step 8 in Supplementary Methods).
ps_bothyears.rda: R phyloseq object, ASV table with 3728 ASVs and 3307 samples, filtered ps_common.rda, includes all ASVs that were observed at least once in both years (after filter step 7 in Supplementary Methods).
ps_grp.rda: R phyloseq object, feature table where ps_asv was agglomerated into the 150 microbial groups by adding the counts of all ASVs in each group. Table with 150 microbial groups (identified by a representative ASV id, see supplementary file 2 for taxonomy) and 3306 samples.
ps_common.rda: R phyloseq object, ASV table with 4632 ASVs and 3307 samples. Removed ASVs that were not observed in at least 5% (166) of all samples (after filter step 6 in Supplementary Methods). Includes phylogenetic tree generated with mafft/7.407 and fasttree/2.1
ps_noMC.rda: R phyloseq object, ASV table with 129767 ASVs and 3313 samples, filtered ASV table with mitochondria and chloroplast sequences removed (after filter step 5 in Supplementary Methods)
V3_V4.csv : gene names in B73 reference genome v3 and v4
Figures generated by the analysis scripts are stored here
This directory is not uploaded to GitHub (too large). Download this directory here (LINK) for the following files:
GWAS/: GWAS results in the form of .assoc.txt files
rna_seq_4genotypes.csv : FPKM reads of gene expression data (growth chamber experiment) rna_seq_kremling.txt : FPKM reads of gene expression data by Kremling et.al.
hapmap_chr10_23800k-24100k.txt: Cutout of the chr 10 allele information, derived from HapMap3
Datasets generated in this study on the Buckler-Goodman maize diversity panel that show the associations of rhisozphere microbial groups with host genomic loci and performance in the field under two nitrogen treatments. (Also supplied as supplementary files). Please make use of these datasets in your own research (and don't forget to cite our work!).
dataset1.csv: Feature table (3,306 samples by 3,626 ASVs) from which our results were generated, alongside the sample metadata collected in this study.
dataset2.csv: Taxonomically annotated list of 3,626 16S sequences that comprise the core maize microbiome used for this analysis and may serve as a reference to identify the same maize-associated ASVs in future experiments.
dataset3.csv: List of the 150 microbial groups defined in this study alongside relevant summary statistics, such as abundance, heritability, selection coefficients, and correlations with plant traits under both N treatments.
dataset4.csv: List of 229 Buckler-Goodman maize genotypes with the corresponding measurements of all 17 plant and 150 rhizobiome traits analyzed here under both N treatments.
dataset5.csv: List of 622 plant loci (10 kb genomic regions) that exhibit significant association with one or more microbial groups, including the IDs of nearby (+/- 10 kb) genes.