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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #371627

Research Project: Identification of Novel Management Strategies for Key Pests and Pathogens of Grapevine with Emphasis on the Xylella Fastidiosa Pathosystem

Location: Crop Diseases, Pests and Genetics Research

Title: Variation among type I restriction modification systems in Xylella fastidiosa correlates with genetic lineage

item O'Leary, Michael
item Burbank, Lindsey
item Stenger, Drake

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 2/15/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Background: Xylella fastidiosa is a naturally competent bacterial plant pathogen composed of five distinct subspecies, i.e., fastidiosa, morus, multiplex, pauca, and sandyi. This pathogen causes disease on numerous economically important plant hosts including blueberry, citrus, grapevine, and olive. The X. fastidiosa genome is enriched in restriction-modification (RM) systems which can impede acquisition of foreign DNA; deletion or inhibition of Type I RM systems improves transformation efficiency. Type I RM systems depend on a specificity subunit (HsdS) with two target recognition domains (TRDs) to recognize target DNA sequences. In other bacterial pathogens with distinct lineages (e.g., Staphylococcus aureus), hsdS genes are divergent, providing different sequence specificity in different bacterial strains. Transformation efficiency of X. fastidiosa varies by genetic lineage, suggesting differences among RM systems. Here, Type I RM systems were compared across multiple X. fastidiosa strains based on the TRD domains of hsdS. Methods: Seventy-four X. fastidiosa genome assemblies were downloaded from Genbank. Eleven additional strains were sequenced using the Oxford-Nanopore MinIon platform with genomes assembled using Canu, for a combined total of 85 strains representing 26 strain types (STs) across the five subspecies. The core genome of all strains was aligned with Snippy and used to generate a recombination-sensitive phylogeny of X. fastidiosa strains with Gubbins. Assemblies were annotated with PROKKA; RM systems were identified by homology to REbase gold standard enzymes. Sequences of hsdS were extracted and classified by TRD sequence. Results: Xylella fastidiosa strains individually carry up to four Type I RM systems, although one is likely nonfunctional due to frameshift mutations. Two of the remaining Type I RM systems are present in 80 of 85 strains, whereas the fourth is only present in X. fastidiosa subsp. multiplex and X. fastidiosa subsp. pauca. Sequence of the hsdS subunit for each Type I RM system varies by strain, with at least 32 combinations of TRDs across functional Type I RM systems. Within STs, little variation among hsdS sequence was observed. No clear correlation was observed between hsdS genotype and host species or geographic origin of strains. Conclusion: Substantial diversity of Type I RM system hsdS subunits exists between STs of X. fastidiosa but is conserved within ST lineages. Further work will explore the functional role of these Type I RM systems in transformation efficiency of different strains.