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Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence
Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538342/ https://www.ncbi.nlm.nih.gov/pubmed/23316438 http://dx.doi.org/10.1534/g3.112.004044 |
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author | Manning, Viola A. Pandelova, Iovanna Dhillon, Braham Wilhelm, Larry J. Goodwin, Stephen B. Berlin, Aaron M. Figueroa, Melania Freitag, Michael Hane, James K. Henrissat, Bernard Holman, Wade H. Kodira, Chinnappa D. Martin, Joel Oliver, Richard P. Robbertse, Barbara Schackwitz, Wendy Schwartz, David C. Spatafora, Joseph W. Turgeon, B. Gillian Yandava, Chandri Young, Sarah Zhou, Shiguo Zeng, Qiandong Grigoriev, Igor V. Ma, Li-Jun Ciuffetti, Lynda M. |
author_facet | Manning, Viola A. Pandelova, Iovanna Dhillon, Braham Wilhelm, Larry J. Goodwin, Stephen B. Berlin, Aaron M. Figueroa, Melania Freitag, Michael Hane, James K. Henrissat, Bernard Holman, Wade H. Kodira, Chinnappa D. Martin, Joel Oliver, Richard P. Robbertse, Barbara Schackwitz, Wendy Schwartz, David C. Spatafora, Joseph W. Turgeon, B. Gillian Yandava, Chandri Young, Sarah Zhou, Shiguo Zeng, Qiandong Grigoriev, Igor V. Ma, Li-Jun Ciuffetti, Lynda M. |
author_sort | Manning, Viola A. |
collection | PubMed |
description | Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes. |
format | Online Article Text |
id | pubmed-3538342 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-35383422013-01-11 Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence Manning, Viola A. Pandelova, Iovanna Dhillon, Braham Wilhelm, Larry J. Goodwin, Stephen B. Berlin, Aaron M. Figueroa, Melania Freitag, Michael Hane, James K. Henrissat, Bernard Holman, Wade H. Kodira, Chinnappa D. Martin, Joel Oliver, Richard P. Robbertse, Barbara Schackwitz, Wendy Schwartz, David C. Spatafora, Joseph W. Turgeon, B. Gillian Yandava, Chandri Young, Sarah Zhou, Shiguo Zeng, Qiandong Grigoriev, Igor V. Ma, Li-Jun Ciuffetti, Lynda M. G3 (Bethesda) Investigations Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes. Genetics Society of America 2013-01-01 /pmc/articles/PMC3538342/ /pubmed/23316438 http://dx.doi.org/10.1534/g3.112.004044 Text en Copyright © 2013 Manning et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Manning, Viola A. Pandelova, Iovanna Dhillon, Braham Wilhelm, Larry J. Goodwin, Stephen B. Berlin, Aaron M. Figueroa, Melania Freitag, Michael Hane, James K. Henrissat, Bernard Holman, Wade H. Kodira, Chinnappa D. Martin, Joel Oliver, Richard P. Robbertse, Barbara Schackwitz, Wendy Schwartz, David C. Spatafora, Joseph W. Turgeon, B. Gillian Yandava, Chandri Young, Sarah Zhou, Shiguo Zeng, Qiandong Grigoriev, Igor V. Ma, Li-Jun Ciuffetti, Lynda M. Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence |
title | Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence |
title_full | Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence |
title_fullStr | Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence |
title_full_unstemmed | Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence |
title_short | Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence |
title_sort | comparative genomics of a plant-pathogenic fungus, pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538342/ https://www.ncbi.nlm.nih.gov/pubmed/23316438 http://dx.doi.org/10.1534/g3.112.004044 |
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