Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

Powell, Amy J.; Conant, Gavin C.; Brown, Douglas E.; Carbone, Ignazio; Dean, Ralph A.

doi:10.1186/1471-2164-9-147

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

Journal Article · Fri Mar 28 00:00:00 EDT 2008 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-9-147· OSTI ID:1626461

Powell, Amy J. ^[1]; Conant, Gavin C. ^[2]; Brown, Douglas E. ^[3]; Carbone, Ignazio ^[3]; Dean, Ralph A. ^[3]

Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Dept. of Computational Systems Biology; DOE/OSTI
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

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.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: NA0003525

OSTI ID:: 1626461

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 9; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome Wolff, Sara M.; Ellison, Melinda J.; Hao, Yue Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0274-6	journal	June 2017
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Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas ETH Zurich https://doi.org/10.3929/ethz-b-000318752	text	January 2018
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas Nature Publishing Group https://doi.org/10.5167/uzh-162417	text	January 2019

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Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

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