Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
<p>Abstract</p> <p>Background</p> <p>Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene g...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-03-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/147 |
| _version_ | 1818514356902559744 |
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| author | Carbone Ignazio Brown Douglas E Conant Gavin C Powell Amy J Dean Ralph A |
| author_facet | Carbone Ignazio Brown Douglas E Conant Gavin C Powell Amy J Dean Ralph A |
| author_sort | Carbone Ignazio |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, despite this phenomenon's known importance in virulence in bacteria and viruses.</p> <p>Results</p> <p>To determine if patterns of gene duplication differed between pathogens and non-pathogens, we identified gene families across nine euascomycete and two basidiomycete species. Gene family size distributions were fit to power laws to compare gene duplication trends in pathogens <it>versus </it>non-pathogens. Fungal phytopathogens showed globally altered patterns of gene duplication, as indicated by differences in gene family size distribution. We also identified sixteen examples of gene family expansion and five instances of gene family contraction in pathogenic lineages. Expanded gene families included those predicted to be important in melanin biosynthesis, host cell wall degradation and transport functions. Contracted families included those encoding genes involved in toxin production, genes with oxidoreductase activity, as well as subunits of the vacuolar ATPase complex. Surveys of the functional distribution of gene duplicates indicated that pathogens show enrichment for gene duplicates associated with receptor and hydrolase activities, while euascomycete pathogens appeared to have not only these differences, but also significantly more duplicates associated with regulatory and carbohydrate binding functions.</p> <p>Conclusion</p> <p>Differences in the overall levels of gene duplication in phytopathogenic species <it>versus </it>non-pathogenic relatives implicate gene inventory flux as an important virulence-associated process in fungi. We hypothesize that the observed patterns of gene duplicate enrichment, gene family expansion and contraction reflect adaptation within pathogenic life histories. These adaptations were likely shaped by ancient, as well as contemporary, intimate associations with monocot hosts.</p> |
| first_indexed | 2024-12-11T00:14:39Z |
| format | Article |
| id | doaj.art-adab1a5997a948c5a76b4ea18f3f38d6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T00:14:39Z |
| publishDate | 2008-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-adab1a5997a948c5a76b4ea18f3f38d62022-12-22T01:28:01ZengBMCBMC Genomics1471-21642008-03-019114710.1186/1471-2164-9-147Altered patterns of gene duplication and differential gene gain and loss in fungal pathogensCarbone IgnazioBrown Douglas EConant Gavin CPowell Amy JDean Ralph A<p>Abstract</p> <p>Background</p> <p>Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, despite this phenomenon's known importance in virulence in bacteria and viruses.</p> <p>Results</p> <p>To determine if patterns of gene duplication differed between pathogens and non-pathogens, we identified gene families across nine euascomycete and two basidiomycete species. Gene family size distributions were fit to power laws to compare gene duplication trends in pathogens <it>versus </it>non-pathogens. Fungal phytopathogens showed globally altered patterns of gene duplication, as indicated by differences in gene family size distribution. We also identified sixteen examples of gene family expansion and five instances of gene family contraction in pathogenic lineages. Expanded gene families included those predicted to be important in melanin biosynthesis, host cell wall degradation and transport functions. Contracted families included those encoding genes involved in toxin production, genes with oxidoreductase activity, as well as subunits of the vacuolar ATPase complex. Surveys of the functional distribution of gene duplicates indicated that pathogens show enrichment for gene duplicates associated with receptor and hydrolase activities, while euascomycete pathogens appeared to have not only these differences, but also significantly more duplicates associated with regulatory and carbohydrate binding functions.</p> <p>Conclusion</p> <p>Differences in the overall levels of gene duplication in phytopathogenic species <it>versus </it>non-pathogenic relatives implicate gene inventory flux as an important virulence-associated process in fungi. We hypothesize that the observed patterns of gene duplicate enrichment, gene family expansion and contraction reflect adaptation within pathogenic life histories. These adaptations were likely shaped by ancient, as well as contemporary, intimate associations with monocot hosts.</p>http://www.biomedcentral.com/1471-2164/9/147 |
| spellingShingle | Carbone Ignazio Brown Douglas E Conant Gavin C Powell Amy J Dean Ralph A Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens BMC Genomics |
| title | Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens |
| title_full | Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens |
| title_fullStr | Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens |
| title_full_unstemmed | Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens |
| title_short | Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens |
| title_sort | altered patterns of gene duplication and differential gene gain and loss in fungal pathogens |
| url | http://www.biomedcentral.com/1471-2164/9/147 |
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