Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
Abstract
Background: 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. Results: To determine if patterns of gene duplication differed between pathogens and nonpathogens, 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 versus 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,more »
- Authors:
-
- Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Dept. of Computational Systems Biology
- Univ. of Dublin (Ireland). Trinity College. Smurfit Inst. of Genetics
- North Carolina State Univ., Raleigh, NC (United States). Center for Integrated Fungal Research. Dept. of Plant Pathology
- Publication Date:
- Research Org.:
- Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1626461
- Grant/Contract Number:
- NA0003525
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Genomics
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1471-2164
- Publisher:
- Springer
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity
Citation Formats
Powell, Amy J., Conant, Gavin C., Brown, Douglas E., Carbone, Ignazio, and Dean, Ralph A. Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. United States: N. p., 2008.
Web. doi:10.1186/1471-2164-9-147.
Powell, Amy J., Conant, Gavin C., Brown, Douglas E., Carbone, Ignazio, & Dean, Ralph A. Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. United States. https://doi.org/10.1186/1471-2164-9-147
Powell, Amy J., Conant, Gavin C., Brown, Douglas E., Carbone, Ignazio, and Dean, Ralph A. Fri .
"Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens". United States. https://doi.org/10.1186/1471-2164-9-147. https://www.osti.gov/servlets/purl/1626461.
@article{osti_1626461,
title = {Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens},
author = {Powell, Amy J. and Conant, Gavin C. and Brown, Douglas E. and Carbone, Ignazio and Dean, Ralph A.},
abstractNote = {Background: 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. Results: To determine if patterns of gene duplication differed between pathogens and nonpathogens, 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 versus 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. Conclusion: Differences in the overall levels of gene duplication in phytopathogenic species versus 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.},
doi = {10.1186/1471-2164-9-147},
journal = {BMC Genomics},
number = 1,
volume = 9,
place = {United States},
year = {Fri Mar 28 00:00:00 EDT 2008},
month = {Fri Mar 28 00:00:00 EDT 2008}
}
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Molecular evolution meets the genomics revolution
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Comparative genomics and genome evolution in yeasts
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Adaptation of proteases and carbohydrases of saprophytic, phytopathogenic and entomopathogenic fungi to the requirements of their ecological niches
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The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
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Genomics of the fungal kingdom: Insights into eukaryotic biology
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