Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences

Simple item page
dc.contributor.authorMechan Llontop, Marco Enriqueen
dc.contributor.authorSharma, Parulen
dc.contributor.authorAguilera Flores, Marcelaen
dc.contributor.authorYang, Shuen
dc.contributor.authorPollock, Jillen
dc.contributor.authorTian, Longen
dc.contributor.authorHuang, Chengjieen
dc.contributor.authorRideout, Steven L.en
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorLi, Songen
dc.contributor.authorVinatzer, Boris A.en
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.contributor.departmentVirginia Agricultural Experiment Stationen
dc.date.accessioned2019-12-30T19:15:19Zen
dc.date.available2019-12-30T19:15:19Zen
dc.date.issued2019-12-12en
dc.date.updated2019-12-30T19:15:16Zen
dc.description.abstractRoutine strain-level identification of plant pathogens directly from symptomatic tissue could significantly improve plant disease control and prevention. Here we tested the Oxford Nanopore Technologies (ONT) MinIONTM sequencer for metagenomic sequencing of tomato plants either artificially inoculated with a known strain of the bacterial speck pathogen Pseudomonas syringae pv. tomato (Pto), or collected in the field and showing bacterial spot symptoms caused by either one of four Xanthomonas species. After species-level identification using ONT's WIMP software and the third party tools Sourmash and MetaMaps, we used Sourmash and MetaMaps with a custom database of representative genomes of bacterial tomato pathogens to attempt strain-level identification. In parallel, each metagenome was assembled and the longest contigs were used as query with the genome-based microbial identification Web service LINbase. Both the read-based and assembly-based approaches correctly identified Pto strain T1 in the artificially inoculated samples. The pathogen strain in most field samples was identified as a member of Xanthomonas perforans group 2. This result was confirmed by whole genome sequencing of colonies isolated from one of the samples. Although in our case, metagenome-based pathogen identification at the strain-level was achieved, caution still needs to be exerted when interpreting strain-level results because of the challenges inherent to assigning reads to specific strains and the error rate of nanopore sequencing.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifierPHYTO-09-19-0351-R (Article number)en
dc.identifier.doihttps://doi.org/10.1094/phyto-09-19-0351-ren
dc.identifier.eissn1943-7684en
dc.identifier.issn0031-949Xen
dc.identifier.orcidHeath, Lenwood [0000-0003-1608-431X]en
dc.identifier.orcidVinatzer, Boris [0000-0003-4612-225X]en
dc.identifier.orcidLi, Song [0000-0002-8133-3944]en
dc.identifier.pmid31829116en
dc.identifier.urihttp://hdl.handle.net/10919/96237en
dc.language.isoenen
dc.publisherScientific Societiesen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/31829116en
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectBacteriologyen
dc.subjectDisease control and pest managementen
dc.subjectTechniquesen
dc.subject0607 Plant Biologyen
dc.subject0605 Microbiologyen
dc.subject0703 Crop and Pasture Productionen
dc.subjectPlant Biology & Botanyen
dc.titleStrain-level identification of bacterial tomato pathogens directly from metagenomic sequencesen
dc.title.serialPhytopathologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherJournal Articleen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/School of Plant and Environmental Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Durelle Scotten
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutesen

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Revised_Proof_PHYTO-09-19-0351-R.R1.pdf
Size:
2.02 MB
Format:
Adobe Portable Document Format
Download

Collections

All Faculty Deposits
Scholarly Works, School of Plant and Environmental Sciences
Scholarly Works, Virginia Agricultural Experiment Station