Modular evolution of secretion systems and virulence plasmids in a bacterial species complex
Year: 2021
Type: preprint
Abstract: Background Many bacterial taxa are species complexes and uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized Agrobacterium tumefaciens , a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. Results We utilized 35 genome assemblies to achieve a comprehensive and balanced sampling of A. tumefaciens . Our confident inference of gene content and core-genome phylogeny supported a quantitative guideline for delineating 12 species and allowed for robust investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. Conclusions We demonstrated that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. Our strategies for multi-level investigations at scales that range from whole-genomes to intragenic domains and phylogenetic depths of between- and within-species are applicable to other bacteria. Finally, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
Awards: G1337698996, G2205640134, G2494647904, Studies of the Secretion Mechanisms and Structural Insights of the Agrobacterium Type VI Secretion Tde DNAse Effectors, G4607736316, G497937365, Identification and Functional Characterization of Plant Virulence Genes in Agrobacterium Tumefaciens: Phenotypic, Genomic, and Transcriptomic Variations in Genomospecies 7 and 8( I ), G7354014674, G7480064622, Functional Studies of Type Vi Secretion Diverse Effectors and Delivery Mechanisms in Agrobacterium Tumefaciens
OpenAlex ID: W3161889610