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Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome ali...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131394/ https://www.ncbi.nlm.nih.gov/pubmed/30202022 http://dx.doi.org/10.1038/s41598-018-30335-7 |
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author | Armitage, Andrew D. Taylor, Andrew Sobczyk, Maria K. Baxter, Laura Greenfield, Bethany P. J. Bates, Helen J. Wilson, Fiona Jackson, Alison C. Ott, Sascha Harrison, Richard J. Clarkson, John P. |
author_facet | Armitage, Andrew D. Taylor, Andrew Sobczyk, Maria K. Baxter, Laura Greenfield, Bethany P. J. Bates, Helen J. Wilson, Fiona Jackson, Alison C. Ott, Sascha Harrison, Richard J. Clarkson, John P. |
author_sort | Armitage, Andrew D. |
collection | PubMed |
description | A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta. |
format | Online Article Text |
id | pubmed-6131394 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-61313942018-09-13 Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae Armitage, Andrew D. Taylor, Andrew Sobczyk, Maria K. Baxter, Laura Greenfield, Bethany P. J. Bates, Helen J. Wilson, Fiona Jackson, Alison C. Ott, Sascha Harrison, Richard J. Clarkson, John P. Sci Rep Article A reference-quality assembly of Fusarium oxysporum f. sp. cepae (Foc), the causative agent of onion basal rot has been generated along with genomes of additional pathogenic and non-pathogenic isolates of onion. Phylogenetic analysis confirmed a single origin of the Foc pathogenic lineage. Genome alignments with other F. oxysporum ff. spp. and non pathogens revealed high levels of syntenic conservation of core chromosomes but little synteny between lineage specific (LS) chromosomes. Four LS contigs in Foc totaling 3.9 Mb were designated as pathogen-specific (PS). A two-fold increase in segmental duplication events was observed between LS regions of the genome compared to within core regions or from LS regions to the core. RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates. FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in planta. Nature Publishing Group UK 2018-09-10 /pmc/articles/PMC6131394/ /pubmed/30202022 http://dx.doi.org/10.1038/s41598-018-30335-7 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Armitage, Andrew D. Taylor, Andrew Sobczyk, Maria K. Baxter, Laura Greenfield, Bethany P. J. Bates, Helen J. Wilson, Fiona Jackson, Alison C. Ott, Sascha Harrison, Richard J. Clarkson, John P. Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae |
title | Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae |
title_full | Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae |
title_fullStr | Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae |
title_full_unstemmed | Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae |
title_short | Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae |
title_sort | characterisation of pathogen-specific regions and novel effector candidates in fusarium oxysporum f. sp. cepae |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131394/ https://www.ncbi.nlm.nih.gov/pubmed/30202022 http://dx.doi.org/10.1038/s41598-018-30335-7 |
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