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

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 ofmore » 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.« less
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [3] ;  [2] ;  [6] ;  [7]
  1. Univ. of Florida, Gainesville, FL (United States). Plant Molecular and Cellular Biology Program
  2. US Dept. of Agriculture (USDA)., Saucier, MS (United States). Southern Research Station, Southern Inst. of Forest Genetics
  3. Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Forest Sciences
  4. Univ. de Lorraine, Champenoux (France). Interactions Arbres/Microorganismes, Lab. d'Excellence ARBRE, INRA-Nancy, UMR Inst. National de la Recherche Agronomique
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. 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.
  7. 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
Publication Date:
Report Number(s):
LBNL-178026
Journal ID: ISSN 1664-462X; ir:178026
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 5; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; effectors; rustpathogens; secretome; genome evolution; comparative genomics
OSTI Identifier:
1469147

Pendleton, Amanda L., Smith, Katherine E., Feau, Nicolas, Martin, Francis M., Grigoriev, Igor V., Hamelin, Richard, Nelson, C. Dana, Burleigh, J. Gordon, and Davis, John M.. Duplications and losses in gene families of rust pathogens highlight putative effectors. United States: N. p., Web. doi:10.3389/fpls.2014.00299.
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.. Duplications and losses in gene families of rust pathogens highlight putative effectors. United States. doi:10.3389/fpls.2014.00299.
Pendleton, Amanda L., Smith, Katherine E., Feau, Nicolas, Martin, Francis M., Grigoriev, Igor V., Hamelin, Richard, Nelson, C. Dana, Burleigh, J. Gordon, and Davis, John M.. 2014. "Duplications and losses in gene families of rust pathogens highlight putative effectors". United States. doi:10.3389/fpls.2014.00299. https://www.osti.gov/servlets/purl/1469147.
@article{osti_1469147,
title = {Duplications and losses in gene families of rust pathogens highlight putative effectors},
author = {Pendleton, Amanda L. and Smith, Katherine E. and Feau, Nicolas and Martin, Francis M. and Grigoriev, Igor V. and Hamelin, Richard and Nelson, C. Dana and Burleigh, J. Gordon and Davis, John M.},
abstractNote = {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.},
doi = {10.3389/fpls.2014.00299},
journal = {Frontiers in Plant Science},
number = ,
volume = 5,
place = {United States},
year = {2014},
month = {6}
}