Comparative genome analysis and genetic variability in populations of ‘Candidatus Phytoplasma citri’, the causative agent of Witches’ broom disease of lime

Phytopathogens represent a major threat to crop productivity. In the case of citrus, in particular Citrus aurantifolia (Christm.) Swingle, a major pathogen is ‘Candidatus Phytoplasma citri’, the causative agent of Witches’ broom disease of lime (WBDL). Although the taxonomy of this pathogen is established, molecular aspects of the disease it causes and its genetic variability have received little attention. Here, we use a draft genome to obtain insights into genomic features and pathogenicity factors of this phytoplasma. We also provide new information about genetic variability within ‘Ca. P. citri’ populations in Oman, a country that has been greatly affected by WBDL. Comparative analyses with other phytoplasma species show that the vast majority of protein coding genes, including the secretome, are shared between the WBDL phytoplasmas and ‘Ca. P. asteris’ strain AY-WB. A multi-locus sequence typing analysis in ‘Ca. P. citri’ strain populations from plants and insect vectors revealed substantial genetic homogeneity among ‘Ca. P. citri’ populations, suggesting a recent clonal replication of a phytoplasma strain in Oman. Our data add taxon sampling to genomic studies of phytoplasmas, as well as offering insights into the genetic variability of ‘Ca. P. citri’ populations of plant and insect hosts from different locations in Oman.