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Early insights into the genome sequence of Uromyces fabae
Uromyces fabae is a major pathogen of broad bean, Vicia faba. U. fabae has served as a model among rust fungi to elucidate the development of infection structures, expression and secretion of cell wall degrading enzymes and gene expression. Using U. fabae, enormous progress was made regarding nutrie...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212606/ https://www.ncbi.nlm.nih.gov/pubmed/25400651 http://dx.doi.org/10.3389/fpls.2014.00587 |
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author | Link, Tobias Seibel, Christian Voegele, Ralf T. |
author_facet | Link, Tobias Seibel, Christian Voegele, Ralf T. |
author_sort | Link, Tobias |
collection | PubMed |
description | Uromyces fabae is a major pathogen of broad bean, Vicia faba. U. fabae has served as a model among rust fungi to elucidate the development of infection structures, expression and secretion of cell wall degrading enzymes and gene expression. Using U. fabae, enormous progress was made regarding nutrient uptake and metabolism and in the search for secreted proteins and effectors. Here, we present results from a genome survey of U. fabae. Paired end Illumina sequencing provided 53 Gb of data. An assembly gave 59,735 scaffolds with a total length of 216 Mb. K-mer analysis estimated the genome size to be 329 Mb. Of a representative set of 23,153 predicted proteins we could annotate 10,209, and predict 599 secreted proteins. Clustering of the protein set indicates families of highly likely effectors. We also found new homologs of RTP1p, a prototype rust effector. The U. fabae genome will be an important resource for comparative analyses with U. appendiculatus and P. pachyrhizi and provide information regarding the phylogenetic relationship of the genus Uromyces with respect to other rust fungi already sequenced, namely Puccinia graminis f. sp. tritici, P. striiformis f. sp. tritici, Melampsora lini, and Melampsora larici-populina. |
format | Online Article Text |
id | pubmed-4212606 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-42126062014-11-14 Early insights into the genome sequence of Uromyces fabae Link, Tobias Seibel, Christian Voegele, Ralf T. Front Plant Sci Plant Science Uromyces fabae is a major pathogen of broad bean, Vicia faba. U. fabae has served as a model among rust fungi to elucidate the development of infection structures, expression and secretion of cell wall degrading enzymes and gene expression. Using U. fabae, enormous progress was made regarding nutrient uptake and metabolism and in the search for secreted proteins and effectors. Here, we present results from a genome survey of U. fabae. Paired end Illumina sequencing provided 53 Gb of data. An assembly gave 59,735 scaffolds with a total length of 216 Mb. K-mer analysis estimated the genome size to be 329 Mb. Of a representative set of 23,153 predicted proteins we could annotate 10,209, and predict 599 secreted proteins. Clustering of the protein set indicates families of highly likely effectors. We also found new homologs of RTP1p, a prototype rust effector. The U. fabae genome will be an important resource for comparative analyses with U. appendiculatus and P. pachyrhizi and provide information regarding the phylogenetic relationship of the genus Uromyces with respect to other rust fungi already sequenced, namely Puccinia graminis f. sp. tritici, P. striiformis f. sp. tritici, Melampsora lini, and Melampsora larici-populina. Frontiers Media S.A. 2014-10-29 /pmc/articles/PMC4212606/ /pubmed/25400651 http://dx.doi.org/10.3389/fpls.2014.00587 Text en Copyright © 2014 Link, Seibel and Voegele. http://creativecommons.org/licenses/by/4.0/ 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) or licensor 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. |
spellingShingle | Plant Science Link, Tobias Seibel, Christian Voegele, Ralf T. Early insights into the genome sequence of Uromyces fabae |
title | Early insights into the genome sequence of Uromyces fabae |
title_full | Early insights into the genome sequence of Uromyces fabae |
title_fullStr | Early insights into the genome sequence of Uromyces fabae |
title_full_unstemmed | Early insights into the genome sequence of Uromyces fabae |
title_short | Early insights into the genome sequence of Uromyces fabae |
title_sort | early insights into the genome sequence of uromyces fabae |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212606/ https://www.ncbi.nlm.nih.gov/pubmed/25400651 http://dx.doi.org/10.3389/fpls.2014.00587 |
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