Distribution of PGP functions and BGCs. The phylogenetic tree is constructed using the high-quality representative genomes of each bacterial genus in the CRBC and public databases (STAR Methods). Phylum level taxonomy is colored (I). Genera containing CRBC genomes are labeled in blue (II). For each genus, plant growth-promoting (PGP) functions are illustrated as the percentage of genomes containing all the necessary genes for each function (III;STAR Methods). Bacterial PGP functions are categorized into three groups: nutrient utilization, growth promotion, and stress tolerance, according to the KEGG database and prior literatures. Nutrient utilization includes phosphorus nutrition (P), nitrogen fixation (N), and siderophore biosynthesis (Fe). Growth promotion includes biosynthesis of indole-3-acetic acid (IAA), gibberellin (GA), and cytokinin (CK). Stress tolerance includes the biosynthesis of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCd), salicylic acid (SA), and ethylene. The BGC compositions are presented as the average of genomes at the genus level (IV). BGC classes are shown with the following abbreviations: non-ribosomal peptide synthetases (NRPSs); polyketide synthase (PKS); ribosomally synthesized and post-translationally modified peptide (RiPP). The outermost bar chart (section V) shows the median number of BGCs in all genomes of each genus. See alsoTable S3C.
