Homologous recombination and Xylella fastidiosa host-pathogen associations in South America

Homologous recombination impacts the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity. Multi-locus sequence typing (MLST) has previously identified 6 sequence types (STs) among plant samples collected in Brazil (both subsp. pauca and multiplex). Here we report on a survey of X. fastidiosa genetic diversity (MLST-based) performed in 6 regions in Brazil and 2 in Argentina, by sampling 5 different plant species. In addition to the 6 previously reported STs, 7 new subsp. pauca and 2 new subsp. multiplex STs were identified. The presence of subsp. multiplex in South America is considered to be the consequence of a single introduction from its native range in North America more than 80 years ago. Different phylogenetic approaches clustered the South American STs into 4 groups, with strains infecting citrus (subsp. pauca), coffee/olive (subsp. pauca), coffee/hibiscus/plum (subsp. pauca), and plum (subsp. multiplex). In areas where these different genetic clusters occurred sympatrically, we found evidence of homologous recombination in the form of bidirectional allelic exchange between subsp. pauca and multiplex. In fact, the only strain of subsp. pauca isolated from a plum host had an allele that originated from subsp. multiplex. These signatures of bidirectional homologous recombination between endemic and introduced STs indicate that gene flow occurs in short evolutionary time frames in X. fastidiosa, despite the ecological isolation (i.e. host plant species) of genotypes.