Host Adaptation and Interactions

Bacterial pathogens cause significant crop damage worldwide, limiting crop yields and threatening global food security. The main arsenals for virulence-associated with plant bacterial pathogens involve secretion of plant cell wall degrading enzymes and type secretion systems. These pathogens are highly heterogeneous with respect to pathogenicity determinants that play a significant role in virulence, suggesting their broad-range host adaptability. Our research group is interested to understand genomic and transcriptomic features related to xylem colonization and to ascertain mechanisms that confer advantages to the pathogen for adaptation to diverse hosts. This research will contribute to knowledge that leads to the development of broad-spectrum resistance in economically important plants. We are using omics-technologies including genome sequencing and RNA-seq (PacBio, Illumina and Nanopore Oxford), microscopy (Confocal Laser Microscope, Electron Microscope, Leica Fluorescent Thunder Microscope), advanced bioinformatics pipelines.

Two plant pathogenic bacteria co-infecting kale. The bacteria are labelled with mScarlet and mTurquoise2

Circos plot description of main genetic features, relevant virulence, and antibiotic biosynthesis clusters among all Pectobacterium species. Seven circular layers have been rendered to show unique features based upon the comparative genomic analyses. From the outermost layer to the innermost layer: the area of each genome; sizes of each genome (axis in kb); gene function types across the species, name of each species indicated in 3rd layer; virulence genes (pink lane) and key gene regulators (green lane), as indicated in the legend (5th layer); scattered dots of all genes, where the red and blue dots depict negative and positive gene orientation, respectively; and the inner layer showing the connection among homologues genes of all gene clusters covered in this study. The colors of the connector lanes of each cluster are labeled on the right side of the figure. T1SS (Type I secretion system), T2SS (Type II secretion system), T3SS (Type III secretion system), T4SS (Type IV secretion system), T5SS (Type V secretion system), T6SS (Type VI secretion system), Flp/Tad (Fimbrial low-molecular-weight protein/Tight adherence protein), cfa (coronofacic acid), NRPS (Non-Ribosomal Peptide-Synthetase) like syringomycin, 3H2B (3-hydroxy-2-butanone pathway), ECA (Enterobacteria Common Antigen), Cps-Poly (capsular polysaccharide), LOS/LPS (lipopolysaccharide/lipooligosaccharide), EPS—O-ag (Exopolysaccharide O-antigen), entAFECD (enterobactin), cbrABCD (achromobactin), fecIRABCD (ferric citrate uptake), hasRADEF (heme acquisition), hsmHFRS/pgaABCD (hemin storage), and fusABCD (ferredoxin uptake)
(Arizala and Arif, 2019)