title: Characterization of the Xanthomonas translucens Complex Using Draft Genomes, Comparative Genomics, Phylogenetic Analysis, and Diagnostic LAMP Assays.
abstract: Prevalence of Xanthomonas translucens, which causes cereal leaf streak (CLS) in cereal crops and bacterial wilt in forage and turfgrass species, has increased in many regions in recent years. Because the pathogen is seedborne in economically important cereals, it is a concern for international and interstate germplasm exchange and, thus, reliable and robust protocols for its detection in seed are needed. However, historical confusion surrounding the taxonomy within the species has complicated the development of accurate and reliable diagnostic tools for X. translucens. Therefore, we sequenced genomes of 15 X. translucens strains representing six different pathovars and compared them with additional publicly available X. translucens genome sequences to obtain a genome-based phylogeny for robust classification of this species. Our results reveal three main clusters: one consisting of pv. cerealis, one consisting of pvs. undulosa and translucens, and a third consisting of pvs. arrhenatheri, graminis, phlei, and poae. Based on genomic differences, diagnostic loop-mediated isothermal amplification (LAMP) primers were developed that clearly distinguish strains that cause disease on cereals, such as pvs. undulosa, translucens, hordei, and secalis, from strains that cause disease on noncereal hosts, such as pvs. arrhenatheri, cerealis, graminis, phlei, and poae. Additional LAMP assays were developed that selectively amplify strains belonging to pvs. cerealis and poae, distinguishing them from other pathovars. These primers will be instrumental in diagnostics when implementing quarantine regulations to limit further geographic spread of X. translucens pathovars.
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Langlois
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Jacob
authors.initials: J
authors.lastname: Snelling
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: John P
authors.initials: JP
authors.lastname: Hamilton
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Claude
authors.initials: C
authors.lastname: Bragard
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Valérie
authors.initials: V
authors.lastname: Verdier
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Lindsay R
authors.initials: LR
authors.lastname: Triplett
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Ned A
authors.initials: NA
authors.lastname: Tisserat
authors.affiliation: First, second, sixth, seventh, ninth, and tenth authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins 80523-1177; second author: Department of Horticulture, Oregon State University, Corvallis 97331; third author: Department of Plant Biology, Michigan State University, East Lansing 48824; fourth author: Université catholique de Louvain, Earth and Life Institute, B1348 Louvain-la-Neuve, Belgium; fifth and sixth authors: IRD, CIRAD, University Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France; seventh author: Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven; and eighth author: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Jan E
authors.initials: JE
authors.lastname: Leach
mesh_terms: D017931:DNA Primers / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology*; D012680:Sensitivity and Specificity; D013045:Species Specificity; D014974:Xanthomonas / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D017931:DNA Primers