New, complete circularized genomes of Xanthomonas citri pv. mangiferaeindicae produced from short- and long-read co-assembly shed light on strains that emerged a decade ago on mango and cashew in Burkina Faso.

We report high-quality genomes of three strains of Xanthomonas citri pv. mangiferaeindicae (Xcm), the causal agent of mango bacterial canker disease, including the pathotype strain of this pathovar and two strains from Burkina Faso that emerged a decade ago. These strains hosted two to three plasmids of sizes ranging from 19 to 86 kb. Genome mining revealed the presence of several secretion systems (SS) and effectors involved in virulence of xanthomonads with (i) a T1SS of the hlyDB group, (ii) xps and xcs T2SSs, (iii) a T3SS with several type three effectors (T3E), including transcription activator-like effectors (TALE), (iv) several T4SSs associated with plasmid or integrative conjugative elements (ICE) mobility, (v) three T5SS subclasses (Va, Vb and Vc) and (vi) a single i3* T6SS. The two strains isolated in Burkina Faso from mango (Mangifera indica L.) and cashew (Anacardium occidentale L.) differed by only 14 SNPs and shared identical secretion systems and T3E repertoire. Several TALEs were identified in each strain, some of which may target plant genes previously found implicated in disease development in other xanthomonad-associated pathosystems. These results support the emergence in Burkina Faso a decade ago of very closely related strains that became epidemic on mango and cashew, i.e., two distinct host genera of a same plant family. These new genomic resources will contribute to better understand the biology and evolution of this agriculturally major crop pathogen.