Functional genome analysis of
Gibbsiella quercinecans FRB97 (T), Brenneria goodwinii FRB141 (T) and Rahnella victoriana BRK18a. ( a) Circular representations of B. goodwinii FRB141, G. quercinecans FRB97 and R. victoriana BRK18a genomes. From outside to inside, circles represent: (1) Assembled bacterial genomes, outermost (orange) circle, with encoded secretion system annotated at their genomic loci. (2) Metatranscriptome heatmap. Alignment of two in silico combined metatranscriptomes recovered from two necrotic lesions of AOD-affected trees against the bacterial genomes. Blue saturation represents increasing transcript alignments. (3–9) Seven metagenomes from necrotic lesions on AOD-affected trees and one healthy tree (metagenomes were extracted from two sites, Attingham and Runs Wood) were aligned through their coding domains to homologous regions in the bacterial genomes. (3) Attingham healthy (AT1) aligned metagenome-coding domains (light purple). (4) Attingham diseased (AT7) aligned metagenome-coding domains (aqua). (5) Attingham diseased (AT8) aligned metagenome-coding domains (blue). (6) Attingham diseased (AT9) aligned metagenome-coding domains (orange). (7) Runs Wood diseased (RW1) aligned metagenome-coding domains (green). (8) Runs Wood diseased (RW2) aligned metagenome-coding domains (pink). (9) Runs Wood diseased (RW3) aligned metagenome-coding domains (grey). (10) G+C content across the bacterial genome. (11) G+C skew across the bacterial genome. ( b) Schematic diagram of transporters and transported proteins recovered from lesion metatranscriptomes and aligned against each bacterial genome. The number of significantly expressed (>3 aligned transcripts, covering >20% of the gene) genes is shown in parentheses. ( c) Number of transcripts aligned against selected virulence genes encoded within B. goodwinii FRB141, G. quercinecans FRB97 and R. victoriana BRK18a. Gene categories are represented by the following colours: red—PCWDE, purple—general secretory pathway (GSP), yellow—type II secretion system (T2SS), blue—type III secretion system (T3SS), pink—type III secretion system effectors (T3SS effectors), and green—global regulators (GR).