Detecting Genetic Introgression: High Levels of Intersubspecific Recombination Found in Xylella fastidiosa in Brazil

Abstract

b Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…The availability of novel loci and alleles can result in the emergence of epidemic isolates that have the potential to exploit host plants previously not susceptible to disease as a result of X. fastidiosa infection. Although not conclusively demonstrated, independent studies have suggested that X. fastidiosa diseases can emerge via gene exchange between isolates (Almeida et al 2008;Nunes et al 2003;Nunney et al 2012). Therefore, increases in genetic diversity, driven by the introduction of foreign genotypes, carry risks that go beyond the potential host range of the newly arrived isolate.…”

“…Both the coffee and citrus isolates of subspecies pauca appear to have acquired alleles from subspecies multiplex (Nunney et al 2012). Likewise, subspecies multiplex has participated in recombination with subspecies fastidiosa (Nunney et al 2010;Kung et al 2013).…”

“…Published annotations indicate that these genomes each contain from 2,066 to 2,294 protein-coding sequences, 2 ribosomal RNA operons, 49-50 tRNA genes (43 different anti-codons), and 1 tmRNA gene (van Sluys et al 2003). Draft quality genomes are available for three other isolates, each appearing to be very similar to one of the finished genomes at the coarse scale (Bhattacharyya et al 2002;Schreiber et al 2010;Zhang et al 2011), as are contigs from the shotgun sequencing of a mixed sample of subspecies multiplex and sandyi (Bhattacharyya et al 2002;Nunney et al 2012). The diversity of available sequences will increase rapidly in the near future, as several projects are underway that are sequencing tens of genomes from isolates collected around the world.…”

Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards

“…Because X. fastidiosa is naturally competent (Kung and Almeida 2011) and X. fastidiosa subsp. pauca infecting coffee and citrus has been suggested to be of recombinogenic origin (Nunney et al 2012), the departure from linkage equilibrium observed here may be a consequence of geographic structuring, admixture events, and limited genotype flow among the regions. In this case, linkage disequilibrium would occur due to barriers to gene exchange (e.g., geographic or ecological) or by an epidemic expansion in which case linkage disequilibrium would be temporary.…”

“…Thus, it is plausible that the epidemiology of the diseases caused by X. fastidiosa subsp. pauca in citrus and coffee is similar, despite the fact that strains isolated from these host plants are distinct Nunney et al 2012).…”