The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

Autor: Eves-van den Akker, S, Laetsch, DR, Thorpe, P, Lilley, CJ, Danchin, EGJ, Da Rocha, M, Rancurel, C, Holroyd, NE, Cotton, JA, Szitenberg, A, Grenier, E, Montarry, J, Mimee, B, Duceppe, MO, Boyes, I, Marvin, JMC, Jones, LM, Yusup, HB, Lafond-Lapalme, J, Esquibet, M, Sabeh, M, Rott, M, Overmars, H, Finkers-Tomczak, A, Smant, G, Koutsovoulos, G, Blok, V, Mantelin, S, Cock, PJA, Phillips, W, Henrissat, B, Urwin, PE, Blaxter, M, Jones, JT
Přispěvatelé: Eves-Van Den Akker, Sebastian [0000-0002-8833-9679], Apollo - University of Cambridge Repository, Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), BB/F000642/1, Biotechnology and Biological Sciences Research Council, grant 098051, Wellcome Trust, FA 1208, European Cooperation in Science and Technology, CRTI09_462RD, Canadian Safety and Security Program, Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), University of St Andrews. School of Medicine, University of St Andrews. School of Biology, University of St Andrews. Biomedical Sciences Research Complex
Jazyk: angličtina
Rok vydání: 2016
Předmět:
Gene Transfer
Horizontal
Genomic Islands
QH301 Biology
RNA Splicing
globodera rostochiensis
transfert horizontal de gène
QH301
pomme de terre
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Animals
Position-Specific Scoring Matrices
[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Tylenchoidea
Nucleotide Motifs
Laboratorium voor Nematologie
R2C
Plant Diseases
Solanum tuberosum
Life Cycle Stages
Virulence
Gene Expression Profiling
Research
~DC~
High-Throughput Nucleotide Sequencing
Genomics
Horizontal gene transfer
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Effectors
[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
séquence du génome
Enhancer Elements
Genetic
effector
Genome sequence
potato
RNA Splice Sites
EPS
Laboratory of Nematology
BDC
Transcriptome
Genome
Protozoan
Plant-parasitic nematode
Zdroj: Genome Biology 17 (2016) 1
Genome Biology
Genome Biology, 2016, 17 (1), pp.1-23. ⟨10.1186/s13059-016-0985-1⟩
Genome Biology, BioMed Central, 2016, 17 (1), pp.1-23. ⟨10.1186/s13059-016-0985-1⟩
Genome Biology, 17(1)
ISSN: 1474-7596
1474-760X
1465-6906
DOI: 10.1186/s13059-016-0985-1⟩
Popis: SE-vdA is supported by BBSRC grant BB/M014207/1. Sequencing was funded by BBSRC grant BB/F000642/1 to the University of Leeds and grant BB/F00334X/1 to the Wellcome Trust Sanger Institute). DRL was supported by a fellowship from The James Hutton Institute and the School of Biological Sciences, University of Edinburgh. GK was supported by a BBSRC PhD studentship. The James Hutton Institute receives funding from the Scottish Government. JAC and NEH are supported by the Wellcome Trust through its core funding of the Wellcome Trust Sanger Institute (grant 098051). This work was also supported by funding from the Canadian Safety and Security Program, project number CRTI09_462RD. Background. The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results. We generate a high quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5 % of the predicted genes, of which approximately 8.5 % are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative ‘effector islands’ in the genome. We identify a dorsal gland promoter element motif (termed DOG Box) present upstream in representatives from 26 out of 28 dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. Conclusions. These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action. Publisher PDF
Databáze: OpenAIRE
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