Large- and small-scale population structure of Xanthomonas oryzae pv. oryzicola, a bacterial pathogen of rice

Xanthomonas oryzae pv. oryzicola is a pathogen of rice responsible for bacterial leaf streak, a disease that can cause up to 32% yield loss. While it was first reported a century ago in Asia, its first report in Africa was in the 1980s. Since then, it has been discovered in several countries of both East and West Africa. In this study, we used a combination of genomics and genotyping tools to shed light on its global and local diversity and population structure with a focus on West Africa. Our findings group X. oryzae pv. oryzicola strains into three clades, an Asian, an East African-Asian, and a West African clade, and provide evidence of several introduction events from Asia being at the origin of outbreaks in East Africa and probably in West Africa. Our results further highlight the role of human activities in the local spread of this pathogen and the possible role of several wild rice species and weeds as reservoirs. Finally, our results globally support a clonal evolution of X. oryzae pv. oryzicola. However, coinfection of plants with distinct strains of X. oryzae pv. oryzicola, observed in Mali and Senegal, may facilitate some degree of genetic exchange.IMPORTANCEWest Africa has faced a rapid expansion of rice cultivation with importation of rice varieties mostly from Asia, and rice now constitutes 37% of the cereal consumed in the region. The bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) is causing bacterial leaf streak and threatening rice production in West Africa. Little is known about the pathogen's reservoirs and its modes and routes of dissemination. We used genome sequencing and tandem repeat sequences to describe large- and small-scale population structure and molecular epidemiology. Our results support the role of rice seed trade in the local and global spread of Xoc. This study further suggests different introduction events from Asia to both East and West Africa. We describe local natural dispersal events with some clonal diversification and the possible role of wild rice and weed species as reservoirs. Overall, our results indicate that weed management and the enforcement of phytosanitary measures on rice seeds could help control the spread of bacterial leaf streak.