Duplications and losses in gene families of rust pathogens highlight putative effectors

Pendleton, Amanda L.; Smith, Katherine E.; Feau, Nicolas; Martin, Francis M.; Grigoriev, Igor V.; Hamelin, Richard; Nelson, C. Dana; Burleigh, J. Gordon; Davis, John M.

doi:10.3389/fpls.2014.00299

Duplications and losses in gene families of rust pathogens highlight putative effectors

Journal Article · Thu Jun 26 00:00:00 EDT 2014 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2014.00299· OSTI ID:1469147

Pendleton, Amanda L. ^[1]; Smith, Katherine E. ^[2]; Feau, Nicolas ^[3]; Martin, Francis M. ^[4]; Grigoriev, Igor V. ^[5]; Hamelin, Richard ^[3]; Nelson, C. Dana ^[2]; Burleigh, J. Gordon ^[6]; Davis, John M. ^[7]

Univ. of Florida, Gainesville, FL (United States). Plant Molecular and Cellular Biology Program
US Dept. of Agriculture (USDA)., Saucier, MS (United States). Southern Research Station, Southern Inst. of Forest Genetics
Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Forest Sciences
Univ. de Lorraine, Champenoux (France). Interactions Arbres/Microorganismes, Lab. d'Excellence ARBRE, INRA-Nancy, UMR Inst. National de la Recherche Agronomique
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Florida, Gainesville, FL (United States). Plant Molecular and Cellular Biology Program; Univ. of Florida, Gainesville, FL (United States). Biology Dept.; Univ. of Florida, Gainesville, FL (United States). Genetics Inst.
Univ. of Florida, Gainesville, FL (United States). Plant Molecular and Cellular Biology Program; Univ. of Florida, Gainesville, FL (United States). Genetics Inst.; Univ. of Florida, Gainesville, FL (United States). School of Forest Resources and Conservation

Rust fungi are a group of fungal pathogens that cause some of the world's most destructive diseases of trees and crops. A shared characteristic among rust fungi is obligate biotrophy, the inability to complete a lifecycle without a host. This dependence on a host species likely affects patterns of gene expansion, contraction, and innovation within rust pathogen genomes. The establishment of disease by biotrophic pathogens is reliant upon effector proteins that are encoded in the fungal genome and secreted from the pathogen into the host's cell apoplast or within the cells. This study uses a comparative genomic approach to elucidate putative effectors and determine their evolutionary histories. We used OrthoMCL to identify nearly 20,000 gene families in proteomes of 16 diverse fungal species, which include 15 basidiomycetes and one ascomycete. We inferred patterns of duplication and loss for each gene family and identified families with distinctive patterns of expansion/contraction associated with the evolution of rust fungal genomes. To recognize potential contributors for the unique features of rust pathogens, we identified families harboring secreted proteins that: (i) arose or expanded in rust pathogens relative to other fungi, or (ii) contracted or were lost in rust fungal genomes. While the origin of rust fungi appears to be associated with considerable gene loss, there are many gene duplications associated with each sampled rust fungal genome. We also highlight two putative effector gene families that have expanded in Cqf that we hypothesize have roles in pathogenicity.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1469147

Report Number(s):: LBNL--178026; ir:178026

Journal Information:: Frontiers in Plant Science, Journal Name: Frontiers in Plant Science Vol. 5; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Duplications and losses in gene families of rust pathogens highlight putative effectors

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