“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?
Identifieur interne : 000000 ( Pmc/Checkpoint ); suivant : 000001“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?
Auteurs : James K. Hane [Australie] ; Jonathan Paxman [Australie] ; Darcy A. B. Jones [Australie] ; Richard P. Oliver [Australie] ; Pierre De Wit [Pays-Bas]Source :
- Frontiers in Microbiology [ 1664-302X ] ; 2020.
Abstract
The traditional classification of fungal and oomycete phytopathogens into three classes – biotrophs, hemibiotrophs, or necrotrophs – is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at
Url:
DOI: 10.3389/fmicb.2019.03088
PubMed: 32038539
PubMed Central: 6986263
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:6986263Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?</title><author><name sortKey="Hane, James K" sort="Hane, James K" uniqKey="Hane J" first="James K." last="Hane">James K. Hane</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Curtin Institute for Computation, Faculty of Science and Engineering, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Paxman, Jonathan" sort="Paxman, Jonathan" uniqKey="Paxman J" first="Jonathan" last="Paxman">Jonathan Paxman</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Mechanical Engineering, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Jones, Darcy A B" sort="Jones, Darcy A B" uniqKey="Jones D" first="Darcy A. B." last="Jones">Darcy A. B. Jones</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Oliver, Richard P" sort="Oliver, Richard P" uniqKey="Oliver R" first="Richard P." last="Oliver">Richard P. Oliver</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="De Wit, Pierre" sort="De Wit, Pierre" uniqKey="De Wit P" first="Pierre" last="De Wit">Pierre De Wit</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University & Research</institution>,<addr-line>Wageningen</addr-line>,<country>Netherlands</country></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32038539</idno><idno type="pmc">6986263</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986263</idno><idno type="RBID">PMC:6986263</idno><idno type="doi">10.3389/fmicb.2019.03088</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000802</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000802</idno><idno type="wicri:Area/Pmc/Curation">000802</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000802</idno><idno type="wicri:Area/Pmc/Checkpoint">000000</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000000</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?</title><author><name sortKey="Hane, James K" sort="Hane, James K" uniqKey="Hane J" first="James K." last="Hane">James K. Hane</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Curtin Institute for Computation, Faculty of Science and Engineering, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Paxman, Jonathan" sort="Paxman, Jonathan" uniqKey="Paxman J" first="Jonathan" last="Paxman">Jonathan Paxman</name><affiliation wicri:level="1"><nlm:aff id="aff3"><institution>Department of Mechanical Engineering, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Jones, Darcy A B" sort="Jones, Darcy A B" uniqKey="Jones D" first="Darcy A. B." last="Jones">Darcy A. B. Jones</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Oliver, Richard P" sort="Oliver, Richard P" uniqKey="Oliver R" first="Richard P." last="Oliver">Richard P. Oliver</name><affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="De Wit, Pierre" sort="De Wit, Pierre" uniqKey="De Wit P" first="Pierre" last="De Wit">Pierre De Wit</name><affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University & Research</institution>,<addr-line>Wageningen</addr-line>,<country>Netherlands</country></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Frontiers in Microbiology</title><idno type="eISSN">1664-302X</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The traditional classification of fungal and oomycete phytopathogens into three classes – biotrophs, hemibiotrophs, or necrotrophs – is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at <ext-link ext-link-type="uri" xlink:href="https://github.com/ccdmb/catastrophy">https://github.com/ccdmb/catastrophy</ext-link>. We present the CATAStrophy method for the prediction of trophic phenotypes based on CAZyme gene content, as a complementary method to the traditional tripartite “biotroph–hemibiotroph–necrotroph” classifications that may encourage renewed investigation and revision within the fungal biology community.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Andrew, M" uniqKey="Andrew M">M. Andrew</name></author><author><name sortKey="Barua, R" uniqKey="Barua R">R. Barua</name></author><author><name sortKey="Short, S M" uniqKey="Short S">S. M. Short</name></author><author><name sortKey="Kohn, L M" uniqKey="Kohn L">L. M. Kohn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baroncelli, R" uniqKey="Baroncelli R">R. Baroncelli</name></author><author><name sortKey="Amby, D B" uniqKey="Amby D">D. B. Amby</name></author><author><name sortKey="Zapparata, A" uniqKey="Zapparata A">A. Zapparata</name></author><author><name sortKey="Sarrocco, S" uniqKey="Sarrocco S">S. Sarrocco</name></author><author><name sortKey="Vannacci, G" uniqKey="Vannacci G">G. Vannacci</name></author><author><name sortKey="Le Floch, G" uniqKey="Le Floch G">G. Le Floch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bebber, D P" uniqKey="Bebber D">D. P. Bebber</name></author><author><name sortKey="Gurr, S J" uniqKey="Gurr S">S. J. Gurr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Burdon, J J" uniqKey="Burdon J">J. J. Burdon</name></author><author><name sortKey="Barrett, L G" uniqKey="Barrett L">L. G. Barrett</name></author><author><name sortKey="Rebetzke, G" uniqKey="Rebetzke G">G. Rebetzke</name></author><author><name sortKey="Thrall, P H" uniqKey="Thrall P">P. H. Thrall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cantarel, B L" uniqKey="Cantarel B">B. L. Cantarel</name></author><author><name sortKey="Coutinho, P M" uniqKey="Coutinho P">P. M. Coutinho</name></author><author><name sortKey="Rancurel, C" uniqKey="Rancurel C">C. Rancurel</name></author><author><name sortKey="Bernard, T" uniqKey="Bernard T">T. Bernard</name></author><author><name sortKey="Lombard, V" uniqKey="Lombard V">V. Lombard</name></author><author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B. Henrissat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Choquer, M" uniqKey="Choquer M">M. Choquer</name></author><author><name sortKey="Fournier, E" uniqKey="Fournier E">E. Fournier</name></author><author><name sortKey="Kunz, C" uniqKey="Kunz C">C. Kunz</name></author><author><name sortKey="Levis, C" uniqKey="Levis C">C. Levis</name></author><author><name sortKey="Pradier, J M" uniqKey="Pradier J">J. M. Pradier</name></author><author><name sortKey="Simon, A" uniqKey="Simon A">A. Simon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Bary, A" uniqKey="De Bary A">A. de Bary</name></author><author><name sortKey="Garnsey, H E F" uniqKey="Garnsey H">H. E. F. Garnsey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Wit, P J" uniqKey="De Wit P">P. J. de Wit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Eddy, S" uniqKey="Eddy S">S. Eddy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fisher, M C" uniqKey="Fisher M">M. C. Fisher</name></author><author><name sortKey="Hawkins, N J" uniqKey="Hawkins N">N. J. Hawkins</name></author><author><name sortKey="Sanglard, D" uniqKey="Sanglard D">D. Sanglard</name></author><author><name sortKey="Gurr, S J" uniqKey="Gurr S">S. J. Gurr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fisher, M C" uniqKey="Fisher M">M. C. Fisher</name></author><author><name sortKey="Henk, D A" uniqKey="Henk D">D. A. Henk</name></author><author><name sortKey="Briggs, C J" uniqKey="Briggs C">C. J. Briggs</name></author><author><name sortKey="Brownstein, J S" uniqKey="Brownstein J">J. S. Brownstein</name></author><author><name sortKey="Madoff, L C" uniqKey="Madoff L">L. C. Madoff</name></author><author><name sortKey="Mccraw, S L" uniqKey="Mccraw S">S. L. McCraw</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gay, J L" uniqKey="Gay J">J. L. Gay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Glazebrook, J" uniqKey="Glazebrook J">J. Glazebrook</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goffeau, A" uniqKey="Goffeau A">A. Goffeau</name></author><author><name sortKey="Barrell, B G" uniqKey="Barrell B">B. G. Barrell</name></author><author><name sortKey="Bussey, H" uniqKey="Bussey H">H. Bussey</name></author><author><name sortKey="Davis, R W" uniqKey="Davis R">R. W. Davis</name></author><author><name sortKey="Dujon, B" uniqKey="Dujon B">B. Dujon</name></author><author><name sortKey="Feldmann, H" uniqKey="Feldmann H">H. Feldmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gurr, G M" uniqKey="Gurr G">G. M. Gurr</name></author><author><name sortKey="Zhu, Z R" uniqKey="Zhu Z">Z.-R. Zhu</name></author><author><name sortKey="You, M" uniqKey="You M">M. You</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hahn, M" uniqKey="Hahn M">M. Hahn</name></author><author><name sortKey="Mendgen, K" uniqKey="Mendgen K">K. Mendgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hahn, M" uniqKey="Hahn M">M. Hahn</name></author><author><name sortKey="Mendgen, K" uniqKey="Mendgen K">K. Mendgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hammond Kosack, K E" uniqKey="Hammond Kosack K">K. E. Hammond-Kosack</name></author><author><name sortKey="Parker, J E" uniqKey="Parker J">J. E. Parker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Horbach, R" uniqKey="Horbach R">R. Horbach</name></author><author><name sortKey="Navarro, A R" uniqKey="Navarro A">A. R. Navarro</name></author><author><name sortKey="Quesada Knogge" uniqKey="Quesada Knogge">Quesada Knogge</name></author><author><name sortKey="Deising, H B" uniqKey="Deising H">H. B. Deising</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klosterman, S J" uniqKey="Klosterman S">S. J. Klosterman</name></author><author><name sortKey="Subbarao, K V" uniqKey="Subbarao K">K. V. Subbarao</name></author><author><name sortKey="Kang, S" uniqKey="Kang S">S. Kang</name></author><author><name sortKey="Veronese, P" uniqKey="Veronese P">P. Veronese</name></author><author><name sortKey="Gold, S E" uniqKey="Gold S">S. E. Gold</name></author><author><name sortKey="Thomma, B P" uniqKey="Thomma B">B. P. Thomma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Koeck, M" uniqKey="Koeck M">M. Koeck</name></author><author><name sortKey="Hardham, A R" uniqKey="Hardham A">A. R. Hardham</name></author><author><name sortKey="Dodds, P N" uniqKey="Dodds P">P. N. Dodds</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kuo, H C" uniqKey="Kuo H">H. C. Kuo</name></author><author><name sortKey="Hui, S" uniqKey="Hui S">S. Hui</name></author><author><name sortKey="Choi, J" uniqKey="Choi J">J. Choi</name></author><author><name sortKey="Asiegbu, F O" uniqKey="Asiegbu F">F. O. Asiegbu</name></author><author><name sortKey="Valkonen, J P" uniqKey="Valkonen J">J. P. Valkonen</name></author><author><name sortKey="Lee, Y H" uniqKey="Lee Y">Y. H. Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Laluk, K" uniqKey="Laluk K">K. Laluk</name></author><author><name sortKey="Mengiste, T" uniqKey="Mengiste T">T. Mengiste</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lewis, D" uniqKey="Lewis D">D. Lewis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lombard, V" uniqKey="Lombard V">V. Lombard</name></author><author><name sortKey="Golaconda Ramulu, H" uniqKey="Golaconda Ramulu H">H. Golaconda Ramulu</name></author><author><name sortKey="Drula, E" uniqKey="Drula E">E. Drula</name></author><author><name sortKey="Coutinho, P M" uniqKey="Coutinho P">P. M. Coutinho</name></author><author><name sortKey="Henrissat, B" uniqKey="Henrissat B">B. Henrissat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lucas, J A" uniqKey="Lucas J">J. A. Lucas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mendgen, K" uniqKey="Mendgen K">K. Mendgen</name></author><author><name sortKey="Struck, C" uniqKey="Struck C">C. Struck</name></author><author><name sortKey="Voegele, R T" uniqKey="Voegele R">R. T. Voegele</name></author><author><name sortKey="Hahn, M" uniqKey="Hahn M">M. Hahn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oliver, R" uniqKey="Oliver R">R. Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oliver, R P" uniqKey="Oliver R">R. P. Oliver</name></author><author><name sortKey="Ip Cho, S V" uniqKey="Ip Cho S">S. V. Ip-Cho</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parbery, D G" uniqKey="Parbery D">D. G. Parbery</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pedregosa, F" uniqKey="Pedregosa F">F. Pedregosa</name></author><author><name sortKey="Varoquaux, G" uniqKey="Varoquaux G">G. Varoquaux</name></author><author><name sortKey="Gramfort, A" uniqKey="Gramfort A">A. Gramfort</name></author><author><name sortKey="Michel, V" uniqKey="Michel V">V. Michel</name></author><author><name sortKey="Thirion, B" uniqKey="Thirion B">B. Thirion</name></author><author><name sortKey="Grisel, O" uniqKey="Grisel O">O. Grisel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pedro, H" uniqKey="Pedro H">H. Pedro</name></author><author><name sortKey="Maheswari, U" uniqKey="Maheswari U">U. Maheswari</name></author><author><name sortKey="Urban, M" uniqKey="Urban M">M. Urban</name></author><author><name sortKey="Irvine, A G" uniqKey="Irvine A">A. G. Irvine</name></author><author><name sortKey="Cuzick, A" uniqKey="Cuzick A">A. Cuzick</name></author><author><name sortKey="Mcdowall, M D" uniqKey="Mcdowall M">M. D. McDowall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perfect, S E" uniqKey="Perfect S">S. E. Perfect</name></author><author><name sortKey="Hughes, H B" uniqKey="Hughes H">H. B. Hughes</name></author><author><name sortKey="O Onnell, R J" uniqKey="O Onnell R">R. J. O’Connell</name></author><author><name sortKey="Green, J R" uniqKey="Green J">J. R. Green</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Poland, J A" uniqKey="Poland J">J. A. Poland</name></author><author><name sortKey="Balint Kurti, P J" uniqKey="Balint Kurti P">P. J. Balint-Kurti</name></author><author><name sortKey="Wisser, R J" uniqKey="Wisser R">R. J. Wisser</name></author><author><name sortKey="Pratt, R C" uniqKey="Pratt R">R. C. Pratt</name></author><author><name sortKey="Nelson, R J" uniqKey="Nelson R">R. J. Nelson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Richards, T A" uniqKey="Richards T">T. A. Richards</name></author><author><name sortKey="Talbot, N J" uniqKey="Talbot N">N. J. Talbot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rodrigues, F" uniqKey="Rodrigues F">F. Rodrigues</name></author><author><name sortKey="Ludovico, P" uniqKey="Ludovico P">P. Ludovico</name></author><author><name sortKey="Leao, C" uniqKey="Leao C">C. Leão</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanchez Vallet, A" uniqKey="Sanchez Vallet A">A. Sánchez-Vallet</name></author><author><name sortKey="Mcdonald, M C" uniqKey="Mcdonald M">M. C. McDonald</name></author><author><name sortKey="Solomon, P S" uniqKey="Solomon P">P. S. Solomon</name></author><author><name sortKey="Mcdonald, B A" uniqKey="Mcdonald B">B. A. McDonald</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Saunders, D" uniqKey="Saunders D">D. Saunders</name></author><author><name sortKey="Yoshida, K" uniqKey="Yoshida K">K. Yoshida</name></author><author><name sortKey="Sambles, C" uniqKey="Sambles C">C. Sambles</name></author><author><name sortKey="Glover, R" uniqKey="Glover R">R. Glover</name></author><author><name sortKey="Clavijo, B" uniqKey="Clavijo B">B. Clavijo</name></author><author><name sortKey="Corpas, M" uniqKey="Corpas M">M. Corpas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Savary, S" uniqKey="Savary S">S. Savary</name></author><author><name sortKey="Willocquet, L" uniqKey="Willocquet L">L. Willocquet</name></author><author><name sortKey="Pethybridge, S J" uniqKey="Pethybridge S">S. J. Pethybridge</name></author><author><name sortKey="Esker, P" uniqKey="Esker P">P. Esker</name></author><author><name sortKey="Mcroberts, N" uniqKey="Mcroberts N">N. McRoberts</name></author><author><name sortKey="Nelson, A" uniqKey="Nelson A">A. Nelson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Scott, K J" uniqKey="Scott K">K. J. Scott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soanes, D M" uniqKey="Soanes D">D. M. Soanes</name></author><author><name sortKey="Alam, I" uniqKey="Alam I">I. Alam</name></author><author><name sortKey="Cornell, M" uniqKey="Cornell M">M. Cornell</name></author><author><name sortKey="Wong, H M" uniqKey="Wong H">H. M. Wong</name></author><author><name sortKey="Hedeler, C" uniqKey="Hedeler C">C. Hedeler</name></author><author><name sortKey="Paton, N W" uniqKey="Paton N">N. W. Paton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Solomon, P S" uniqKey="Solomon P">P. S. Solomon</name></author><author><name sortKey="Wilson, T J G" uniqKey="Wilson T">T. J. G. Wilson</name></author><author><name sortKey="Rybak, K" uniqKey="Rybak K">K. Rybak</name></author><author><name sortKey="Parker, K" uniqKey="Parker K">K. Parker</name></author><author><name sortKey="Lowe, R G T" uniqKey="Lowe R">R. G. T. Lowe</name></author><author><name sortKey="Oliver, R P" uniqKey="Oliver R">R. P. Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stam, R" uniqKey="Stam R">R. Stam</name></author><author><name sortKey="Munsterkotter, M" uniqKey="Munsterkotter M">M. Munsterkotter</name></author><author><name sortKey="Pophaly, S D" uniqKey="Pophaly S">S. D. Pophaly</name></author><author><name sortKey="Fokkens, L" uniqKey="Fokkens L">L. Fokkens</name></author><author><name sortKey="Sghyer, H" uniqKey="Sghyer H">H. Sghyer</name></author><author><name sortKey="Guldener, U" uniqKey="Guldener U">U. Guldener</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Staples, R C" uniqKey="Staples R">R. C. Staples</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stergiopoulos, I" uniqKey="Stergiopoulos I">I. Stergiopoulos</name></author><author><name sortKey="De Wit, P J" uniqKey="De Wit P">P. J. de Wit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stotz, H U" uniqKey="Stotz H">H. U. Stotz</name></author><author><name sortKey="Mitrousia, G K P J" uniqKey="Mitrousia G">G. K. P. J. Mitrousia</name></author><author><name sortKey="De, G M" uniqKey="De G">G. M. de</name></author><author><name sortKey="Wit Fitt, B D" uniqKey="Wit Fitt B">B. D. Wit Fitt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tan, K C" uniqKey="Tan K">K. C. Tan</name></author><author><name sortKey="Oliver, R P" uniqKey="Oliver R">R. P. Oliver</name></author><author><name sortKey="Solomon, P S" uniqKey="Solomon P">P. S. Solomon</name></author><author><name sortKey="Moffat, C S" uniqKey="Moffat C">C. S. Moffat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tanaka, S" uniqKey="Tanaka S">S. Tanaka</name></author><author><name sortKey="Han, X" uniqKey="Han X">X. Han</name></author><author><name sortKey="Kahmann, R" uniqKey="Kahmann R">R. Kahmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thrower, L B" uniqKey="Thrower L">L. B. Thrower</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Videira, S" uniqKey="Videira S">S. Videira</name></author><author><name sortKey="Groenewald, J" uniqKey="Groenewald J">J. Groenewald</name></author><author><name sortKey="Nakashima, C" uniqKey="Nakashima C">C. Nakashima</name></author><author><name sortKey="Braun, U" uniqKey="Braun U">U. Braun</name></author><author><name sortKey="Barreto, R W" uniqKey="Barreto R">R. W. Barreto</name></author><author><name sortKey="De Wit, P J" uniqKey="De Wit P">P. J. de Wit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Voegele, R T" uniqKey="Voegele R">R. T. Voegele</name></author><author><name sortKey="Struck, C" uniqKey="Struck C">C. Struck</name></author><author><name sortKey="Hahn, M" uniqKey="Hahn M">M. Hahn</name></author><author><name sortKey="Mendgen, K" uniqKey="Mendgen K">K. Mendgen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, X" uniqKey="Wang X">X. Wang</name></author><author><name sortKey="Jiang, N" uniqKey="Jiang N">N. Jiang</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J. Liu</name></author><author><name sortKey="Liu, W" uniqKey="Liu W">W. Liu</name></author><author><name sortKey="Wang, G L" uniqKey="Wang G">G.-L. Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yin, Y" uniqKey="Yin Y">Y. Yin</name></author><author><name sortKey="Mao, X" uniqKey="Mao X">X. Mao</name></author><author><name sortKey="Yang, J" uniqKey="Yang J">J. Yang</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author><author><name sortKey="Mao, F" uniqKey="Mao F">F. Mao</name></author><author><name sortKey="Xu, Y" uniqKey="Xu Y">Y. Xu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zeilinger, S" uniqKey="Zeilinger S">S. Zeilinger</name></author><author><name sortKey="Gupta, V K" uniqKey="Gupta V">V. K. Gupta</name></author><author><name sortKey="Dahms, T E" uniqKey="Dahms T">T. E. Dahms</name></author><author><name sortKey="Silva, R N" uniqKey="Silva R">R. N. Silva</name></author><author><name sortKey="Singh, H B" uniqKey="Singh H">H. B. Singh</name></author><author><name sortKey="Upadhyay, R S" uniqKey="Upadhyay R">R. S. Upadhyay</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">Front Microbiol</journal-id><journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id><journal-title-group><journal-title>Frontiers in Microbiology</journal-title></journal-title-group><issn pub-type="epub">1664-302X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32038539</article-id><article-id pub-id-type="pmc">6986263</article-id><article-id pub-id-type="doi">10.3389/fmicb.2019.03088</article-id><article-categories><subj-group subj-group-type="heading"><subject>Microbiology</subject><subj-group><subject>Methods</subject></subj-group></subj-group></article-categories><title-group><article-title>“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Hane</surname><given-names>James K.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="aff" rid="aff2"><sup>2</sup></xref><xref ref-type="corresp" rid="c001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/241698/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Paxman</surname><given-names>Jonathan</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jones</surname><given-names>Darcy A. B.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/821823/overview"></uri></contrib><contrib contrib-type="author"><name><surname>Oliver</surname><given-names>Richard P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="c002"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/165597/overview"></uri></contrib><contrib contrib-type="author"><name><surname>de Wit</surname><given-names>Pierre</given-names></name><xref ref-type="aff" rid="aff4"><sup>4</sup></xref><uri xlink:type="simple" xlink:href="http://loop.frontiersin.org/people/199158/overview"></uri></contrib></contrib-group><aff id="aff1"><sup>1</sup><institution>Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></aff><aff id="aff2"><sup>2</sup><institution>Curtin Institute for Computation, Faculty of Science and Engineering, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></aff><aff id="aff3"><sup>3</sup><institution>Department of Mechanical Engineering, Curtin University</institution>,<addr-line>Perth, WA</addr-line>,<country>Australia</country></aff><aff id="aff4"><sup>4</sup><institution>Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University & Research</institution>,<addr-line>Wageningen</addr-line>,<country>Netherlands</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Baolei Jia, Chung-Ang University, South Korea</p></fn><fn fn-type="edited-by"><p>Reviewed by: Brett Merrick Tyler, Oregon State University, United States; Krishna V. Subbarao, University of California, Davis, United States; Remco Stam, Technical University of Munich, Germany; Jinliang Liu, Jilin University, China</p></fn><corresp id="c001">*Correspondence: James K. Hane, <email>James.Hane@curtin.edu.au</email></corresp><corresp id="c002"> Richard P. Oliver, <email>Richard.Oliver@curtin.edu.au</email></corresp><fn fn-type="other" id="fn004"><p>This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology</p></fn></author-notes><pub-date pub-type="epub"><day>21</day><month>1</month><year>2020</year></pub-date><pub-date pub-type="collection"><year>2019</year></pub-date><volume>10</volume><elocation-id>3088</elocation-id><history><date date-type="received"><day>29</day><month>8</month><year>2019</year></date><date date-type="accepted"><day>20</day><month>12</month><year>2019</year></date></history><permissions><copyright-statement>Copyright © 2020 Hane, Paxman, Jones, Oliver and de Wit.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>Hane, Paxman, Jones, Oliver and de Wit</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>The traditional classification of fungal and oomycete phytopathogens into three classes – biotrophs, hemibiotrophs, or necrotrophs – is unsustainable. This study highlights multiple phytopathogen species for which these labels have been inappropriately applied. We propose a novel and reproducible classification based solely on genome-derived analysis of carbohydrate-active enzyme (CAZyme) gene content called CAZyme-Assisted Training And Sorting of -trophy (CATAStrophy). CATAStrophy defines four major divisions for species associated with living plants. These are monomertrophs (Mo) (corresponding to biotrophs), polymertrophs (P) (corresponding to necrotrophs), mesotrophs (Me) (corresponding to hemibiotrophs), and vasculartrophs (including species commonly described as wilts, rots, or anthracnoses). The Mo class encompasses symbiont, haustorial, and non-haustorial species. Me are divided into the subclasses intracellular and extracellular Me, and the P into broad and narrow host sub-classes. This gives a total of seven discrete plant-pathogenic classes. The classification provides insight into the properties of these species and offers a facile route to develop control measures for newly recognized diseases. Software for CATAStrophy is available online at <ext-link ext-link-type="uri" xlink:href="https://github.com/ccdmb/catastrophy">https://github.com/ccdmb/catastrophy</ext-link>. We present the CATAStrophy method for the prediction of trophic phenotypes based on CAZyme gene content, as a complementary method to the traditional tripartite “biotroph–hemibiotroph–necrotroph” classifications that may encourage renewed investigation and revision within the fungal biology community.</p></abstract><kwd-group><kwd>fungi</kwd><kwd>plant pathogen</kwd><kwd>biotroph</kwd><kwd>necrotroph</kwd><kwd>hemibiotroph</kwd><kwd>CAZymes</kwd><kwd>metabolism</kwd></kwd-group><counts><fig-count count="3"></fig-count><table-count count="2"></table-count><equation-count count="0"></equation-count><ref-count count="54"></ref-count><page-count count="12"></page-count><word-count count="0"></word-count></counts></article-meta></front></pmc><affiliations><list><country><li>Australie</li><li>Pays-Bas</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Hane, James K" sort="Hane, James K" uniqKey="Hane J" first="James K." last="Hane">James K. Hane</name></noRegion><name sortKey="Hane, James K" sort="Hane, James K" uniqKey="Hane J" first="James K." last="Hane">James K. Hane</name><name sortKey="Jones, Darcy A B" sort="Jones, Darcy A B" uniqKey="Jones D" first="Darcy A. B." last="Jones">Darcy A. B. Jones</name><name sortKey="Oliver, Richard P" sort="Oliver, Richard P" uniqKey="Oliver R" first="Richard P." last="Oliver">Richard P. Oliver</name><name sortKey="Paxman, Jonathan" sort="Paxman, Jonathan" uniqKey="Paxman J" first="Jonathan" last="Paxman">Jonathan Paxman</name></country><country name="Pays-Bas"><noRegion><name sortKey="De Wit, Pierre" sort="De Wit, Pierre" uniqKey="De Wit P" first="Pierre" last="De Wit">Pierre De Wit</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/MelampsoraV2/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000000 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000000 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= MelampsoraV2
|flux= Pmc
|étape= Checkpoint
|type= RBID
|clé= PMC:6986263
|texte= “CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:32038539" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MelampsoraV2
| This area was generated with Dilib version V0.6.38. |  |