Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria.

Edward W Davis Ii,Jeff H Chang,Javier F Tabima,Niklaus J Grunwald,Alexandra J Weisberg

doi:10.7717/peerj.2222

Edward W Davis Ii, Jeff H Chang + Show 3 more

Open Access

https://doi.org/10.7717/peerj.2222

Copy DOI

Journal: PeerJ	Publication Date: Jul 19, 2016
Citations: 36	License type: CC BY 4.0

Affiliation: Oregon State University

Abstract

Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.

Highlights

DiagnosticsDetermining the identity of the disease causing pathogen, establishing its source of introduction, and/or understanding the genetic diversity of pathogen populations are critical steps for containment and treatment of disease
We developed Gall-ID to aid in determining the genetic identity of gall-causing members of Agrobacterium, Pseudomonas, Pantoea, and Rhodococcus
Users can download tools that automate the analysis of whole genome sequencing data to infer genetic relatedness based on Multilocus sequence analysis (MLSA), average nucleotide identity (ANI), or single nucleotide polymorphisms (SNPs)

Summary

INTRODUCTION

Determining the identity of the disease causing pathogen, establishing its source of introduction, and/or understanding the genetic diversity of pathogen populations are critical steps for containment and treatment of disease. Expression of the former two genes in the plant leads to an increase in plant hormone levels to cause growth deformation whereas the latter set of genes encode enzymes for the synthesis of modified sugars that only organisms with the corresponding opine catabolism genes can use as an energy source (Bomhoff et al, 1976; Montoya et al, 1977) The latter genes are located outside the T-DNA borders on the Ti plasmid (Zhu et al, 2000). Users can download tools that automate the analysis of whole genome sequencing data to infer genetic relatedness based on MLSA, average nucleotide identity (ANI), or single nucleotide polymorphisms (SNPs)

MATERIAL AND METHODS

RESULTS AND DISCUSSION

CONCLUSIONS