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

Abstract

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.