Open AccessMultilocus Sequence Type System for the Plant Pathogen Xylella fastidiosa and Relative Contributions of Recombination and Point Mutation to Clonal Diversity
Author(s) -
Mark Scally,
Erin Schuenzel,
Richard Stouthamer,
Leonard Nunney
Publication year - 2005
Publication title -
applied and environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.552
H-Index - 324
eISSN - 1070-6291
pISSN - 0099-2240
DOI - 10.1128/aem.71.12.8491-8499.2005
Subject(s) - multilocus sequence typing , xylella fastidiosa , biology , housekeeping gene , genetics , phylogenetic tree , multiplex , microbiology and biotechnology , genotype , gene , bacteria , gene expression
Multilocus sequence typing (MLST) identifies and groups bacterial strains based on DNA sequence data from (typically) seven housekeeping genes. MLST has also been employed to estimate the relative contributions of recombination and point mutation to clonal divergence. We applied MLST to the plant pathogenXylella fastidiosa using an initial set of sequences for 10 loci (9.3 kb) of 25 strains from five different host plants, grapevine (PD strains), oleander (OLS strains), oak (OAK strains), almond (ALS strains), and peach (PP strains). An eBURST analysis identified six clonal complexes using the grouping criterion that each member must be identical to at least one other member at 7 or more of the 10 loci. These clonal complexes corresponded to previously identified phylogenetic clades; clonal complex 1 (CC1) (all PD strains plus two ALS strains) and CC2 (OLS strains) defined theX. fastidiosa subsp.fastidiosa andX. fastidiosa subsp.sandyi clades, while CC3 (ALS strains), CC4 (OAK strains), and CC5 (PP strains) were subclades ofX. fastidiosa subsp.multiplex . CC6 (ALS strains) identified anX. fastidiosa subsp.multiplex -like group characterized by a high frequency of intersubspecific recombination. Compared to the recombination rate in other bacterial species, the recombination rate inX. fastidiosa is relatively low. Recombination between different alleles was estimated to give rise to 76% of the nucleotide changes and 31% of the allelic changes observed. The housekeeping lociholC ,nuoL ,leuA ,gltT ,cysG ,petC , andlacF were chosen to form the basis of a public database for typingX. fastidiosa (www.mlst.net ). These loci identified the same six clonal complexes using the strain grouping criterion of identity at five or more loci with at least one other member.