Identification of genetic relationships and subspecies signatures in Xylella fastidiosa

Abstract

BackgroundThe phytopathogenic bacterium Xylella fastidiosa was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Genetically diverse, this species is divided into six subspecies but genetic traits governing this classification are poorly understood.ResultsSkIf (Specific k-mers Identification) was designed and exploited for comparative genomics on a dataset of 46 X. fastidiosa genomes, including seven newly sequenced individuals. It was helpful to quickly check the synonymy between strains from different collections. SkIf identified specific SNPs within 16S rRNA sequences that can be employed for predicting the distribution of Xylella through data mining. Applied to inter- and intra-subspecies analyses, it identified specific k-mers in genes affiliated to differential gene ontologies. Chemotaxis-related genes more prevalently possess specific k-mers in genomes from subspecies fastidiosa, morus and sandyi taken as a whole group. In the subspecies pauca increased abundance of specific k-mers was found in genes associated with the bacterial cell wall/envelope/plasma membrane. Most often, the k-mer specificity occurred in core genes with non-synonymous SNPs in their sequences in genomes of the other subspecies, suggesting putative impact in the protein functions. The presence of two integrative and conjugative elements (ICEs) was identified, one chromosomic and an entire plasmid in a single strain of X. fastidiosa subsp. pauca. Finally, a revised taxonomy of X. fastidiosa into three major clades defined by the subspecies pauca (clade I), multiplex (clade II) and the combination of fastidiosa, morus and sandyi (clade III) was strongly supported by k-mers specifically associated with these subspecies.ConclusionsSkIf is a robust and rapid software, freely available, that can be dedicated to the comparison of sequence datasets and is applicable to any field of research. Applied to X. fastidiosa, an emerging pathogen in Europe, it provided an important resource to mine for identifying genetic markers of subspecies to optimize the strategies attempted to limit the pathogen dissemination in novel areas.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5565-9) contains supplementary material, which is available to authorized users.

Pest survey card on Xylella fastidiosa

“…tashke -X. fastidiosa subsp. morus Sequence types (STs): Multilocus sequence typing (Maiden et al 1998) is a genetic typing methodology that is widely used to characterise X. fastidiosa (Scally et al, 2005;Yuan et al, 2010;Elbeaino et al, 2014;Nunney et al, 2014;Denancé et al, 2017Denancé et al, , 2019. Different STs have been identified in the different outbreaks in the EU as shown in Figure 1.…”

Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

“…There are three formally accepted subspecies of Xf , i.e. fastidiosa, pauca and multiplex , based on DNA–DNA hybridization, as recently confirmed by comparative genomic analysis (Schaad et al , 2002; Marcelletti and Scortichini, 2016; Denancé et al , 2019). However, the International Society of Plant Pathology Committee on the Taxonomy of Plant Pathogenic Bacteria (ISPP-CTPPB) considered valid names only the subsp.…”

“…The pathogen is transmitted by xylem sap feeding insects and colonizes the host xylem vessel, causing the typical leaf scorching. Xf is an endemic pathogen in America and only recently was identified in southern Italy on olive trees (Saponari et al , 2013), in Corsica and in the south-east Mediterranean coast of France on several hosts (Denancé et al , 2019). Subsequently, records of Xf were reported in Germany on oleander (EPPO, 2016a) and in Spain, Mallorca Island and Andalusia, on different plant species (Landa, 2017; Olmo et al , 2017).…”

Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues

“…This bacterial species is genetically diverse as five subspecies including fastidiosa, morus, multiplex, pauca, and sandyi are currently described (EFSA, 2018b). Although this subspecies delineation was initially associated to Xf host range and places of occurrence, more and more observations report infection of a given host by various subspecies (Denancé et al, 2017;EPPO, 2018b;Denancé et al, 2019;Nunney et al, 2019). Homologous recombination events were detected in Xf and were suspected to be associated with host-shift, as documented for the subspecies morus (Nunney et al, 2014).…”

“…But intrasubspecific homologous recombination events could be more frequent than intersubspecific events (Potnis et al, 2019). Based on genome sequence analyses, it was proposed to merge the subspecies fastidiosa, morus, and sandyi in the subspecies fastidiosa [hereafter referred to Xff sensu lato (Xffsl) to avoid confusion with classical Xff], the subspecies multiplex and pauca remaining coherent groups and distantly related from Xff (Marcelletti and Scortichini, 2016;Denancé et al, 2019). The method generally used to identify strains at the subspecies level is based on the sequencing of seven housekeeping genes (cysG, gltT, holC, leuA, malF, nuoL, and petC) of the dedicated multilocus sequence typing (MLST) scheme (Yuan et al, 2010).…”