The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

Handle URI:
http://hdl.handle.net/10754/325273
Title:
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode
Authors:
Cotton, James A; Lilley, Catherine J; Jones, Laura M; Kikuchi, Taisei; Reid, Adam J; Thorpe, Peter; Tsai, Isheng J; Beasley, Helen; Blok, Vivian; Cock, Peter J A; den Akker, Sebastian Eves-van; Holroyd, Nancy; Hunt, Martin; Mantelin, Sophie; Naghra, Hardeep; Pain, Arnab ( 0000-0002-1755-2819 ) ; Palomares-Rius, Juan E; Zarowiecki, Magdalena; Berriman, Matthew; Jones, John T; Urwin, Peter E
Abstract:
Background: Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. Results: We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. Conclusions: The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens. 2014 Cotton et al.; licensee BioMed Central Ltd.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Computational Bioscience Research Center (CBRC)
Citation:
Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, et al. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology 15: R43. doi:10.1186/gb-2014-15-3-r43.
Publisher:
BioMed Central
Journal:
Genome Biology
Issue Date:
3-Mar-2014
DOI:
10.1186/gb-2014-15-3-r43
PubMed ID:
24580726
PubMed Central ID:
PMC4054857
Type:
Article
ISSN:
1474760X
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorCotton, James Aen
dc.contributor.authorLilley, Catherine Jen
dc.contributor.authorJones, Laura Men
dc.contributor.authorKikuchi, Taiseien
dc.contributor.authorReid, Adam Jen
dc.contributor.authorThorpe, Peteren
dc.contributor.authorTsai, Isheng Jen
dc.contributor.authorBeasley, Helenen
dc.contributor.authorBlok, Vivianen
dc.contributor.authorCock, Peter J Aen
dc.contributor.authorden Akker, Sebastian Eves-vanen
dc.contributor.authorHolroyd, Nancyen
dc.contributor.authorHunt, Martinen
dc.contributor.authorMantelin, Sophieen
dc.contributor.authorNaghra, Hardeepen
dc.contributor.authorPain, Arnaben
dc.contributor.authorPalomares-Rius, Juan Een
dc.contributor.authorZarowiecki, Magdalenaen
dc.contributor.authorBerriman, Matthewen
dc.contributor.authorJones, John Ten
dc.contributor.authorUrwin, Peter Een
dc.date.accessioned2014-08-27T09:44:14Z-
dc.date.available2014-08-27T09:44:14Z-
dc.date.issued2014-03-03en
dc.identifier.citationCotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, et al. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology 15: R43. doi:10.1186/gb-2014-15-3-r43.en
dc.identifier.issn1474760Xen
dc.identifier.pmid24580726en
dc.identifier.doi10.1186/gb-2014-15-3-r43en
dc.identifier.urihttp://hdl.handle.net/10754/325273en
dc.description.abstractBackground: Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. Results: We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. Conclusions: The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens. 2014 Cotton et al.; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectglutathione synthaseen
dc.subjectsprouty proteinen
dc.subjecttranscriptomeen
dc.subjectadulten
dc.subjectgene expressionen
dc.subjectgene sequenceen
dc.subjectgenetic codeen
dc.subjectgenetic conservationen
dc.subjectgenome analysisen
dc.subjectGlobodera pallidaen
dc.subjectglutathione synthetase geneen
dc.subjectmolecular dynamicsen
dc.subjectmolecular phylogenyen
dc.subjectnematode life cycle stageen
dc.subjectnucleotide sequenceen
dc.subjectplant rooten
dc.subjectRNA interferenceen
dc.subjectsignal transductionen
dc.subjectspecies invasionen
dc.titleThe genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematodeen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalGenome Biologyen
dc.identifier.pmcidPMC4054857en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionWellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdomen
dc.contributor.institutionCentre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdomen
dc.contributor.institutionThe James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdomen
dc.contributor.institutionForestry and Forest Products Research Institute, Tsukuba, Japanen
dc.contributor.institutionDivision of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japanen
dc.contributor.institutionBiodiversity Research Center, Academia Sinica, Taipei 11529, Taiwanen
dc.contributor.institutionSchool of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdomen
dc.contributor.institutionInstitute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n Apdo 4084, 14080 Crdoba, Spainen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorPain, Arnaben

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