Phylogenomics & Evolution

The genomic revolution has made an enormous contribution to disease management strategies in plant pathology; it increases our understanding of the molecular mechanism of pathogenesis and resistance, population genetics and development of rapid and novel detection methods. Next-generation sequencing further enhanced our knowledge for developing genomic based strategies for improvement and management of disease resistance. The NGS-based comparative bacterial genomics provide insight on many important bacterial genomic regions responsible for pathogenicity; they also provide better resolution for understanding population biology and evolution of distinct pathogens from different geographical regions. Our aims are expected to have yielded thorough and comprehensive knowledge about the genomic biology of plant bacterial pathogens—this will include advancing our understanding of genetic exchange and species delineation. Identifying the recombination events that lead to novel variants or species is extremely important from a disease management point of view. The other important goal includes advancing the knowledge of pathogenicity determinants and their relationship to host specificity, geographical/temporal distribution, and phenotypic characteristics. This will produce a valuable genomic dataset that can be used to advance other aspects of the science—from molecular diagnostic developments, molecular plant-bacteria interactions to genome editing—to develop strategies for sustainable food security through improved disease management during crop production.

Reconstructed genealogy and recombination inference in Pectobacterium species (A) Pie chart depicting the number of core and accessory genes across 62 draft and complete Pectobacterium genomes. (B) Phylogenetic reconstruction and recombination analysis in the genus Pectobacterium estimated by ClonalFrameML. The image on the left shows the phylogenomic relationships between the strains after accounting for the impact of recombination. Each branch and node of the phylogenetic tree are aligned with a corresponding row in the heatmap on the right plot. This plot illustrates the location of recombination events marked with dark blue horizontal lines whereas white vertical lines indicate non-homoplastic substitutions or mutation sites in the core genome alignment of 1343 genes (green portion in the pie chart). Absence of substitutions or invariant sites are represented as light blue background-color. Polymorphic substitution sites are displayed as vertical lines colored from yellow to red based on the increased level of homoplasy. The colored line next to the phylogenetic tree highlights the 9 clusters inferred in Pectobacterium after the population structure analysis using RhierBAPS.  

Timeline highlighting the major events based on taxonomic and phylogenetic studies of the bacterial wilt pathogen, Ralstonia solanacearum species complex (RSSC)
​(Paudel et al, 2020)