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Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi

BACKGROUND: Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the...

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Autores principales: Okagaki, Laura H., Sailsbery, Joshua K., Eyre, Alexander W., Dean, Ralph A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766678/
https://www.ncbi.nlm.nih.gov/pubmed/26911875
http://dx.doi.org/10.1186/s12864-016-2491-y
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author Okagaki, Laura H.
Sailsbery, Joshua K.
Eyre, Alexander W.
Dean, Ralph A.
author_facet Okagaki, Laura H.
Sailsbery, Joshua K.
Eyre, Alexander W.
Dean, Ralph A.
author_sort Okagaki, Laura H.
collection PubMed
description BACKGROUND: Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the sequenced and assembled genomes for these three fungi were reported. Here, the genomes were compared for orthologous genes in order to identified genes that are unique to the Magnaporthaceae family of fungi. In addition, ortholog clustering was used to identify a core proteome for the Magnaporthaceae, which was examined for diversifying and purifying selection and evidence of two-speed genome evolution. RESULTS: A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed. CONCLUSIONS: Taken together, these data show that at the genome level, there is no evidence to suggest multi-speed genome evolution or that proximity to repetitive elements play a role in diversification of genes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2491-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-47666782016-02-26 Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi Okagaki, Laura H. Sailsbery, Joshua K. Eyre, Alexander W. Dean, Ralph A. BMC Genomics Research Article BACKGROUND: Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the sequenced and assembled genomes for these three fungi were reported. Here, the genomes were compared for orthologous genes in order to identified genes that are unique to the Magnaporthaceae family of fungi. In addition, ortholog clustering was used to identify a core proteome for the Magnaporthaceae, which was examined for diversifying and purifying selection and evidence of two-speed genome evolution. RESULTS: A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed. CONCLUSIONS: Taken together, these data show that at the genome level, there is no evidence to suggest multi-speed genome evolution or that proximity to repetitive elements play a role in diversification of genes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2491-y) contains supplementary material, which is available to authorized users. BioMed Central 2016-02-25 /pmc/articles/PMC4766678/ /pubmed/26911875 http://dx.doi.org/10.1186/s12864-016-2491-y Text en © Okagaki et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Okagaki, Laura H.
Sailsbery, Joshua K.
Eyre, Alexander W.
Dean, Ralph A.
Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
title Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
title_full Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
title_fullStr Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
title_full_unstemmed Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
title_short Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
title_sort comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766678/
https://www.ncbi.nlm.nih.gov/pubmed/26911875
http://dx.doi.org/10.1186/s12864-016-2491-y
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