In silico analysis of secreted proteins via Sec- and Tat-pathways of Clavibacter spp. unravels functional diversity related to plant host range

Clavibacter genus comprises phytopathogenic and non-phytopathogenic species in a range of plant hosts. We applied structural and functional approaches for comparative genomics to unveil the adaptation of Clavibacter to plant hosts. The structural approach consisted of phylogeny and whole-genome alignment. The phylogeny suggested that C. tessallarius, C. zhangzhiyongii, C. capcisi, C. phaseoli depicted the more divergent species. Notably, C. nebraskensis, C. insidiosus, C. sepedonicus, Clavibacter sp. A6099, C. californiensis, and C. michiganensis formed a recent monophyletic clade. A synteny degree and genome rearrangements were noted. The functional approach based on prediction-annotation of secreted proteins via Sec and Tat pathways, and the prediction of metabolite biosynthetic potential. Regarding to Sec- and Tat-secreted proteins, we focused on carbohydrate-active enzymes (CAZymes) and expansins. The repertoire of secreted CAZymes exhibited variation related to taxonomy of Clavibacter. The predicted expansins harbored domain variability, related to horizontal gene transfer. A heterogeneous distribution-conservation of biosynthetic genetic clusters (BGCs) regarding Clavibacter phylogeny was observed. Our results suggested that farm practices of plant hosts likely influence the evolutive history of Clavibacter spp. Furthermore, Sec-, Tat-mediated secreted proteins and metabolite diversity may underpin plant-Clavibacter interactions. Biological knowledge drives sustainable strategies aimed to control plant diseases caused by Clavibacter spp.