Supplementary Figure 5: Microbiota structures in the rhizospheres of Hawaii 7996 and Moneymaker based on whole-metagenome sequencing and comparison of the metagenomic gene contents.

(a) Relative abundances of the microbial domains in whole-metagenomic data of the tomato rhizospheres. Relative abundances of each domain were calculated using the small-subunit rDNA reads extracted from the whole-metagenome sequences by read alignment against the Silva database. (b) Taxonomic comparison at the class level using whole metagenome-derived 16S rDNA reads. Circles indicate the bacterial classes with ≥ 0.1% relative abundance in both samples. Colored circles indicate ≥ 15% abundant taxa with ≥ 0.5% relative abundance in Hawaii 7996 or Moneymaker, as compared with each other. (c) Correlation between the bacterial community structures derived from the datasets of 16S rDNA amplicon pyrosequencing and those from Illumina whole-metagenome sequencing. The values were calculated as the ratio between relative abundance of the bacterial classes in Hawaii 7996 and relative abundance of the bacterial classes in Moneymaker. (d) Taxonomic distribution of CDSs specific to Hawaii 7996 or Moneymaker. Among 4,180,636 CDSs in the rhizosphere of Hawaii 7996, 203,204 were detected only in Hawaii 7996 and among 4,165,753 CDSs in the rhizosphere of Moneymaker, 188,321 were detected only in Moneymaker. Among these, 73,031 CDSs in Hawaii 7996 and 67,808 CDSs in Moneymaker were taxonomically assigned to bacterial or archaeal classes. The abundance of each CDS was calculated using RPK, and taxonomic assignment of each CDS was conducted with BLASTP against the GenBank NR database. Taxonomic abundance was calculated using the sum of the RPKs of each CDS. (e) Difference in the relative abundance of cultivar-specific COG-assigned CDSs. Red bars indicate the COGs more abundant in Hawaii 7996 and blue bars indicate the COGs more abundant in Moneymaker. Among the cultivar-specific CDSs, 36,686 in Hawaii 7996 and 34,359 in Moneymaker were assigned to the COG categories. COG categories: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division, chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme metabolism; I, lipid metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination, and repair; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport, and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking and secretion; V, defense mechanisms; W, extracellular structures; Z, cytoskeleton. (f) Difference in the relative abundance of COG-assigned CDSs, which are more than twice abundant in either cultivar. Red bars indicate the COGs more abundant in Hawaii 7996 and blue bars indicate the COGs more abundant in Moneymaker. Among the CDSs that are abundant more than twice in each cultivar, 265,838 in Hawaii 7996 and 249,907 in Moneymaker were assigned to the COG categories.