Duplications and losses in gene families of rust pathogens highlight putative effectors
Abstract
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 »
- Authors:
-
- 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
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1469147
- Report Number(s):
- LBNL-178026
Journal ID: ISSN 1664-462X; ir:178026
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Plant Science
- Additional Journal Information:
- Journal Volume: 5; Journal ID: ISSN 1664-462X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; effectors; rustpathogens; secretome; genome evolution; comparative genomics
Citation Formats
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., 2014.
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. https://doi.org/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. Thu .
"Duplications and losses in gene families of rust pathogens highlight putative effectors". United States. https://doi.org/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 = {Thu Jun 26 00:00:00 EDT 2014},
month = {Thu Jun 26 00:00:00 EDT 2014}
}
Web of Science
Works referenced in this record:
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
journal, January 1997
- Nielsen, H.; Engelbrecht, J.; Brunak, S.
- Protein Engineering Design and Selection, Vol. 10, Issue 1, p. 1-6
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
journal, March 2008
- Martin, F.; Aerts, A.; Ahrén, D.
- Nature, Vol. 452, Issue 7183
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
journal, May 2011
- Duplessis, S.; Cuomo, C. A.; Lin, Y. -C.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 22
Fruiting body production in basidiomycetes
journal, August 2000
- Kües, U.; Liu, Y.
- Applied Microbiology and Biotechnology, Vol. 54, Issue 2
Challenges and progress towards understanding the role of effectors in plant–fungal interactions
journal, August 2012
- Rafiqi, Maryam; Ellis, Jeffrey G.; Ludowici, Victoria A.
- Current Opinion in Plant Biology, Vol. 15, Issue 4
The genome sequence of the rice blast fungus Magnaporthe grisea
journal, April 2005
- Dean, Ralph A.; Talbot, Nicholas J.; Ebbole, Daniel J.
- Nature, Vol. 434, Issue 7036
Host-Parasite Coevolutionary Conflict Between Arabidopsis and Downy Mildew
journal, December 2004
- Allen, R. L.
- Science, Vol. 306, Issue 5703
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
journal, September 2006
- Tyler, B. M.
- Science, Vol. 313, Issue 5791
Prediction of Potential GPI-modification Sites in Proprotein Sequences
journal, September 1999
- Eisenhaber, Birgit; Bork, Peer; Eisenhaber, Frank
- Journal of Molecular Biology, Vol. 292, Issue 3
TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
journal, November 2012
- Wu, Yi-Chieh; Rasmussen, Matthew D.; Bansal, Mukul S.
- Systematic Biology, Vol. 62, Issue 1
Lignin-modifying enzymes in filamentous basidiomycetes - ecological, functional and phylogenetic review
journal, February 2010
- Lundell, Taina K.; Mäkelä, Miia R.; Hildén, Kristiina
- Journal of Basic Microbiology, Vol. 50, Issue 1
URec: a system for unrooted reconciliation
journal, December 2006
- Gorecki, P.; Tiuryn, J.
- Bioinformatics, Vol. 23, Issue 4
Fungal Effector Proteins
journal, September 2009
- Stergiopoulos, Ioannis; de Wit, Pierre J. G. M.
- Annual Review of Phytopathology, Vol. 47, Issue 1
Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini
journal, July 2009
- Barrett, L. G.; Thrall, P. H.; Dodds, P. N.
- Molecular Biology and Evolution, Vol. 26, Issue 11
Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi
journal, January 2012
- Saunders, Diane G. O.; Win, Joe; Cano, Liliana M.
- PLoS ONE, Vol. 7, Issue 1
Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens
journal, November 2007
- Xu, J.; Saunders, C. W.; Hu, P.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 47
The structure and function of fungal laccases
journal, January 1994
- Thurston, C. F.
- Microbiology, Vol. 140, Issue 1
Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust
journal, August 2011
- Cantu, Dario; Govindarajulu, Manjula; Kozik, Alex
- PLoS ONE, Vol. 6, Issue 8
SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011
- Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
- Nature Methods, Vol. 8, Issue 10
The Genomics of Obligate (and Nonobligate) Biotrophs
journal, September 2012
- Spanu, Pietro D.
- Annual Review of Phytopathology, Vol. 50, Issue 1
Effectors of biotrophic fungi and oomycetes: pathogenicity factors and triggers of host resistance
journal, September 2009
- Dodds, Peter N.; Rafiqi, Maryam; Gan, Pamela H. P.
- New Phytologist, Vol. 183, Issue 4
InterPro in 2011: new developments in the family and domain prediction database
journal, November 2011
- Hunter, S.; Jones, P.; Mitchell, A.
- Nucleic Acids Research, Vol. 40, Issue D1
Small proteins of plant-pathogenic fungi secreted during host colonization
journal, December 2005
- Rep, Martijn
- FEMS Microbiology Letters, Vol. 253, Issue 1
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
journal, October 2012
- Morin, E.; Kohler, A.; Baker, A. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 43
The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi
journal, July 2011
- Eastwood, D. C.; Floudas, D.; Binder, M.
- Science, Vol. 333, Issue 6043, p. 762-765
A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
journal, July 2010
- Rasmussen, M. D.; Kellis, M.
- Molecular Biology and Evolution, Vol. 28, Issue 1
Multiple Multi-Copper Oxidase Gene Families in Basidiomycetes – What for?
journal, April 2011
- Kues, Ursula; Ruhl, Martin
- Current Genomics, Vol. 12, Issue 2
The plant immune system
journal, November 2006
- Jones, Jonathan D. G.; Dangl, Jeffery L.
- Nature, Vol. 444, Issue 7117
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
journal, November 2006
- Kämper, Jörg; Kahmann, Regine; Bölker, Michael
- Nature, Vol. 444, Issue 7115
Role of laccase in the biology and virulence of
journal, October 2004
- Zhu, X.; Williamson, P.
- FEMS Yeast Research, Vol. 5, Issue 1
Large-Scale Gene Disruption in Magnaporthe oryzae Identifies MC69, a Secreted Protein Required for Infection by Monocot and Dicot Fungal Pathogens
journal, May 2012
- Saitoh, Hiromasa; Fujisawa, Shizuko; Mitsuoka, Chikako
- PLoS Pathogens, Vol. 8, Issue 5
Rapid genetic change underpins antagonistic coevolution in a natural host-pathogen metapopulation: Coevolution in a wild host-pathogen system
journal, February 2012
- Thrall, Peter H.; Laine, Anna-Liisa; Ravensdale, Michael
- Ecology Letters, Vol. 15, Issue 5
Life with 6000 Genes
journal, October 1996
- Goffeau, A.; Barrell, B. G.; Bussey, H.
- Science, Vol. 274, Issue 5287
Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen
journal, March 2012
- Olson, Åke; Aerts, Andrea; Asiegbu, Fred
- New Phytologist, Vol. 194, Issue 4
Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae
journal, December 2013
- Toome, Merje; Ohm, Robin A.; Riley, Robert W.
- New Phytologist, Vol. 202, Issue 2
Genome Evolution in Plant Pathogenic and Symbiotic Fungi
book, January 2009
- Aguileta, Gabriela; Hood, Michael E.; Refrégier, Guislaine
- Advances in Botanical Research
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
journal, December 2004
- Stamatakis, A.; Ludwig, T.; Meier, H.
- Bioinformatics, Vol. 21, Issue 4
An ultrastructural comparison of monokaryotic and dikaryotic haustoria formed by the fusiform rust fungus Cronartium quercuum f.sp. fusiforme
journal, December 1982
- Gray, D. J.; Amerson, H. V.; Dyke, C. G. Van
- Canadian Journal of Botany, Vol. 60, Issue 12
Recent progress in discovery and functional analysis of effector proteins of fungal and oomycete plant pathogens
journal, August 2009
- Ellis, Jeffrey G.; Rafiqi, Maryam; Gan, Pamela
- Current Opinion in Plant Biology, Vol. 12, Issue 4
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001
- Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 305, Issue 3
Genome size variation in the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme as determined by flow cytometry
journal, November 2010
- Anderson, Claire L.; Kubisiak, Thomas L.; Nelson, C. Dana
- Mycologia, Vol. 102, Issue 6
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
journal, August 2004
- Edgar, Robert C.
- BMC Bioinformatics, Vol. 5, Issue 1, p. 113
A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme
journal, March 2011
- Kubisiak, Thomas L.; Anderson, Claire L.; Amerson, Henry V.
- Fungal Genetics and Biology, Vol. 48, Issue 3
Filamentous plant pathogen effectors in action
journal, October 2013
- Giraldo, Martha C.; Valent, Barbara
- Nature Reviews Microbiology, Vol. 11, Issue 11
Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence
journal, July 2000
- Emanuelsson, Olof; Nielsen, Henrik; Brunak, Søren
- Journal of Molecular Biology, Vol. 300, Issue 4
Some biological features of Candida albicans mutants for genes coding fungal proteins containing the CFEM domain: Candida albicans mutants for CFEM domain-containing proteins
journal, January 2011
- Pérez, Ana; Ramage, Gordon; Blanes, Rosario
- FEMS Yeast Research, Vol. 11, Issue 3
Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat
journal, January 2014
- Bruce, Myron; Neugebauer, Kerri A.; Joly, David L.
- Frontiers in Plant Science, Vol. 4
The adenylate cyclase gene MAC1 of Magnaporthe grisea controls appressorium formation and other aspects of growth and development.
journal, November 1997
- Choi, W.; Dean, R. A.
- The Plant Cell, Vol. 9, Issue 11
Nutrient uptake in rust fungi: how sweet is parasitic life?
journal, February 2011
- Voegele, Ralf T.; Mendgen, Kurt W.
- Euphytica, Vol. 179, Issue 1
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
journal, April 2011
- Letunic, I.; Bork, P.
- Nucleic Acids Research, Vol. 39, Issue suppl
Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.)
journal, January 2010
- Joly, David L.; Feau, Nicolas; Tanguay, Philippe
- BMC Genomics, Vol. 11, Issue 1
Phylogenetic Relationships among the Pine Stem Rust Fungi (Cronartium and Peridermium spp.)
journal, March 1998
- Vogler, Detlev R.; Bruns, Thomas D.
- Mycologia, Vol. 90, Issue 2
MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013
- Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
- Nucleic Acids Research, Vol. 42, Issue D1
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
journal, May 2004
- Martinez, Diego; Larrondo, Luis F.; Putnam, Nik
- Nature Biotechnology, Vol. 22, Issue 6
Magnaporthe grisea Pth11p Is a Novel Plasma Membrane Protein That Mediates Appressorium Differentiation in Response to Inductive Substrate Cues
journal, October 1999
- DeZwaan, Todd M.; Carroll, Anne M.; Valent, Barbara
- The Plant Cell, Vol. 11, Issue 10
A sand fly salivary protein acts as a neutrophil chemoattractant
journal, May 2021
- Guimaraes-Costa, Anderson B.; Shannon, John P.; Waclawiak, Ingrid
- Nature Communications, Vol. 12, Issue 1
Phylogenetic relationships among the pine stem rust fungi ( Cronartium and Peridermium spp.)
journal, March 1998
- Vogler, Detlev R.; Bruns, Thomas D.
- Mycologia, Vol. 90, Issue 2
Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp.)
text, January 2010
- Joly, David L.; Feau, Nicolas; Tanguay, Philippe
- BioMed Central
Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha
text, January 2021
- Liebal, Ulf Winfried; Fabry, Brigida A.; Ravikrishnan, Aarthi
- RWTH Aachen University
The Adenylate Cyclase Gene MAC1 of Magnaporthe grisea Controls Appressorium Formation and Other Aspects of Growth and Development
journal, November 1997
- Choi, Woobong; Dean, Ralph A.
- The Plant Cell, Vol. 9, Issue 11
Magnaporthe grisea Pth11p Is a Novel Plasma Membrane Protein That Mediates Appressorium Differentiation in Response to Inductive Substrate Cues
journal, October 1999
- DeZwaan, Todd M.; Carroll, Anne M.; Valent, Barbara
- The Plant Cell, Vol. 11, Issue 10
InterPro in 2011: new developments in the family and domain prediction database
journal, May 2012
- Hunter, S.; Jones, P.; Mitchell, A.
- Nucleic Acids Research, Vol. 40, Issue 10
Prediction of Potential GPI-modification Sites in Proprotein Sequences
journal, September 1999
- Eisenhaber, Birgit; Bork, Peer; Eisenhaber, Frank
- Journal of Molecular Biology, Vol. 292, Issue 3
Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence
journal, July 2000
- Emanuelsson, Olof; Nielsen, Henrik; Brunak, Søren
- Journal of Molecular Biology, Vol. 300, Issue 4
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001
- Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 305, Issue 3
Fruiting body production in basidiomycetes
journal, August 2000
- Kües, U.; Liu, Y.
- Applied Microbiology and Biotechnology, Vol. 54, Issue 2
Nutrient uptake in rust fungi: how sweet is parasitic life?
journal, February 2011
- Voegele, Ralf T.; Mendgen, Kurt W.
- Euphytica, Vol. 179, Issue 1
Small proteins of plant-pathogenic fungi secreted during host colonization
journal, December 2005
- Rep, Martijn
- FEMS Microbiology Letters, Vol. 253, Issue 1
Role of laccase in the biology and virulence of
journal, October 2004
- Zhu, X.; Williamson, P.
- FEMS Yeast Research, Vol. 5, Issue 1
A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme
journal, March 2011
- Kubisiak, Thomas L.; Anderson, Claire L.; Amerson, Henry V.
- Fungal Genetics and Biology, Vol. 48, Issue 3
Improved Prediction of Signal Peptides: SignalP 3.0
journal, July 2004
- Dyrløv Bendtsen, Jannick; Nielsen, Henrik; von Heijne, Gunnar
- Journal of Molecular Biology, Vol. 340, Issue 4, p. 783-795
Recent progress in discovery and functional analysis of effector proteins of fungal and oomycete plant pathogens
journal, August 2009
- Ellis, Jeffrey G.; Rafiqi, Maryam; Gan, Pamela
- Current Opinion in Plant Biology, Vol. 12, Issue 4
Challenges and progress towards understanding the role of effectors in plant–fungal interactions
journal, August 2012
- Rafiqi, Maryam; Ellis, Jeffrey G.; Ludowici, Victoria A.
- Current Opinion in Plant Biology, Vol. 15, Issue 4
Biosynthesis of fungal melanins and their importance for human pathogenic fungi
journal, March 2003
- Langfelder, Kim; Streibel, Martin; Jahn, Bernhard
- Fungal Genetics and Biology, Vol. 38, Issue 2
The genome sequence of the rice blast fungus Magnaporthe grisea
journal, April 2005
- Dean, Ralph A.; Talbot, Nicholas J.; Ebbole, Daniel J.
- Nature, Vol. 434, Issue 7036
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis
journal, November 2006
- Kämper, Jörg; Kahmann, Regine; Bölker, Michael
- Nature, Vol. 444, Issue 7115
The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
journal, March 2008
- Martin, F.; Aerts, A.; Ahrén, D.
- Nature, Vol. 452, Issue 7183
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78
journal, May 2004
- Martinez, Diego; Larrondo, Luis F.; Putnam, Nik
- Nature Biotechnology, Vol. 22, Issue 6
SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011
- Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
- Nature Methods, Vol. 8, Issue 10
Filamentous plant pathogen effectors in action
journal, October 2013
- Giraldo, Martha C.; Valent, Barbara
- Nature Reviews Microbiology, Vol. 11, Issue 11
Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture
journal, November 2022
- Woo, Sheridan L.; Hermosa, Rosa; Lorito, Matteo
- Nature Reviews Microbiology, Vol. 21, Issue 5
Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens
journal, November 2007
- Xu, J.; Saunders, C. W.; Hu, P.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 47
Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
journal, October 2012
- Morin, E.; Kohler, A.; Baker, A. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 43
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
journal, December 2004
- Stamatakis, A.; Ludwig, T.; Meier, H.
- Bioinformatics, Vol. 21, Issue 4
Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini
journal, July 2009
- Barrett, L. G.; Thrall, P. H.; Dodds, P. N.
- Molecular Biology and Evolution, Vol. 26, Issue 11
A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
journal, July 2010
- Rasmussen, M. D.; Kellis, M.
- Molecular Biology and Evolution, Vol. 28, Issue 1
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
journal, April 2011
- Letunic, I.; Bork, P.
- Nucleic Acids Research, Vol. 39, Issue suppl
InterPro in 2011: new developments in the family and domain prediction database
journal, May 2012
- Hunter, S.; Jones, P.; Mitchell, A.
- Nucleic Acids Research, Vol. 40, Issue 10
MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013
- Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
- Nucleic Acids Research, Vol. 42, Issue D1
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
journal, January 1997
- Nielsen, H.; Engelbrecht, J.; Brunak, S.
- Protein Engineering Design and Selection, Vol. 10, Issue 1, p. 1-6
TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
journal, November 2012
- Wu, Yi-Chieh; Rasmussen, Matthew D.; Bansal, Mukul S.
- Systematic Biology, Vol. 62, Issue 1
Melampsora larici-populina Transcript Profiling During Germination and Timecourse Infection of Poplar Leaves Reveals Dynamic Expression Patterns Associated with Virulence and Biotrophy
journal, July 2011
- Duplessis, Sébastien; Hacquard, Stéphane; Delaruelle, Christine
- Molecular Plant-Microbe Interactions, Vol. 24, Issue 7
A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors in Melampsora larici-populina (Poplar Leaf Rust)
journal, March 2012
- Hacquard, Stéphane; Joly, David L.; Lin, Yao-Cheng
- Molecular Plant-Microbe Interactions, Vol. 25, Issue 3
The structure and function of fungal laccases
journal, January 1994
- Thurston, C. F.
- Microbiology, Vol. 140, Issue 1
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003
- Li, L.
- Genome Research, Vol. 13, Issue 9
Magnaporthe grisea Pth11p Is a Novel Plasma Membrane Protein That Mediates Appressorium Differentiation in Response to Inductive Substrate Cues
journal, October 1999
- DeZwaan, Todd M.; Carroll, Anne M.; Valent, Barbara
- The Plant Cell, Vol. 11, Issue 10
Rapid genetic change underpins antagonistic coevolution in a natural host-pathogen metapopulation: Coevolution in a wild host-pathogen system
journal, February 2012
- Thrall, Peter H.; Laine, Anna-Liisa; Ravensdale, Michael
- Ecology Letters, Vol. 15, Issue 5
Effectors of biotrophic fungi and oomycetes: pathogenicity factors and triggers of host resistance
journal, September 2009
- Dodds, Peter N.; Rafiqi, Maryam; Gan, Pamela H. P.
- New Phytologist, Vol. 183, Issue 4
Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen
journal, March 2012
- Olson, Åke; Aerts, Andrea; Asiegbu, Fred
- New Phytologist, Vol. 194, Issue 4
Some biological features of Candida albicans mutants for genes coding fungal proteins containing the CFEM domain: Candida albicans mutants for CFEM domain-containing proteins
journal, January 2011
- Pérez, Ana; Ramage, Gordon; Blanes, Rosario
- FEMS Yeast Research, Vol. 11, Issue 3
Genome sequencing provides insight into the reproductive biology, nutritional mode and ploidy of the fern pathogen Mixia osmundae
journal, December 2013
- Toome, Merje; Ohm, Robin A.; Riley, Robert W.
- New Phytologist, Vol. 202, Issue 2
Host-Parasite Coevolutionary Conflict Between Arabidopsis and Downy Mildew
journal, December 2004
- Allen, R. L.
- Science, Vol. 306, Issue 5703
Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
journal, September 2006
- Tyler, B. M.
- Science, Vol. 313, Issue 5791
The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi
journal, July 2011
- Eastwood, D. C.; Floudas, D.; Binder, M.
- Science, Vol. 333, Issue 6043, p. 762-765
Funding Sequencing Efforts
journal, February 1997
- Bond, Enriqueta; Austin, M. J. Finley
- Science, Vol. 275, Issue 5303
An ultrastructural comparison of monokaryotic and dikaryotic haustoria formed by the fusiform rust fungus Cronartium quercuum f.sp. fusiforme
journal, December 1982
- Gray, D. J.; Amerson, H. V.; Dyke, C. G. Van
- Canadian Journal of Botany, Vol. 60, Issue 12
The Genomics of Obligate (and Nonobligate) Biotrophs
journal, September 2012
- Spanu, Pietro D.
- Annual Review of Phytopathology, Vol. 50, Issue 1
Fungal Effector Proteins
journal, September 2009
- Stergiopoulos, Ioannis; de Wit, Pierre J. G. M.
- Annual Review of Phytopathology, Vol. 47, Issue 1
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
journal, August 2004
- Edgar, Robert C.
- BMC Bioinformatics, Vol. 5, Issue 1, p. 113
Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust
journal, August 2011
- Cantu, Dario; Govindarajulu, Manjula; Kozik, Alex
- PLoS ONE, Vol. 6, Issue 8
Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi
journal, January 2012
- Saunders, Diane G. O.; Win, Joe; Cano, Liliana M.
- PLoS ONE, Vol. 7, Issue 1
Large-Scale Gene Disruption in Magnaporthe oryzae Identifies MC69, a Secreted Protein Required for Infection by Monocot and Dicot Fungal Pathogens
journal, May 2012
- Saitoh, Hiromasa; Fujisawa, Shizuko; Mitsuoka, Chikako
- PLoS Pathogens, Vol. 8, Issue 5
Multiple Multi-Copper Oxidase Gene Families in Basidiomycetes – What for?
journal, April 2011
- Kues, Ursula; Ruhl, Martin
- Current Genomics, Vol. 12, Issue 2
The Adenylate Cyclase Gene MAC1 of Magnaporthe grisea Controls Appressorium Formation and Other Aspects of Growth and Development
journal, November 1997
- Choi, Woobong; Dean, Ralph A.
- The Plant Cell, Vol. 9, Issue 11
Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat
journal, January 2014
- Bruce, Myron; Neugebauer, Kerri A.; Joly, David L.
- Frontiers in Plant Science, Vol. 4
Genome size variation in the pine fusiform rust pathogen Cronartium quercuum f.sp. fusiforme as determined by flow cytometry
journal, November 2010
- Anderson, Claire L.; Kubisiak, Thomas L.; Nelson, C. Dana
- Mycologia, Vol. 102, Issue 6
Works referencing / citing this record:
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements
journal, January 2017
- Hartmann, Fanny E.; Sánchez-Vallet, Andrea; McDonald, Bruce A.
- The ISME Journal, Vol. 11, Issue 5
Plant Innate Immune Response: Qualitative and Quantitative Resistance
journal, January 2016
- Kushalappa, Ajjamada C.; Yogendra, Kalenahalli N.; Karre, Shailesh
- Critical Reviews in Plant Sciences, Vol. 35, Issue 1
The emergence of the multi‐species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses
journal, April 2019
- Mohd‐Assaad, Norfarhan; McDonald, Bruce A.; Croll, Daniel
- Environmental Microbiology, Vol. 21, Issue 8
Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism
journal, January 2015
- Kemen, Ariane C.; Agler, Matthew T.; Kemen, Eric
- New Phytologist, Vol. 206, Issue 4
Advances in understanding obligate biotrophy in rust fungi
journal, February 2019
- Lorrain, Cécile; Gonçalves dos Santos, Karen Cristine; Germain, Hugo
- New Phytologist, Vol. 222, Issue 3
Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
journal, October 2017
- Menardo, Fabrizio; Praz, Coraline R.; Wicker, Thomas
- BMC Evolutionary Biology, Vol. 17, Issue 1
Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors
journal, September 2015
- Liu, Jun-Jun; Sturrock, Rona N.; Sniezko, Richard A.
- BMC Genomics, Vol. 16, Issue 1
Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi
journal, February 2016
- Okagaki, Laura H.; Sailsbery, Joshua K.; Eyre, Alexander W.
- BMC Genomics, Vol. 17, Issue 1
Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle
journal, October 2019
- Tao, Si-Qi; Cao, Bin; Morin, Emmanuelle
- BMC Genomics, Vol. 20, Issue 1
Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens
journal, December 2019
- Pandaranayaka, Eswari PJ; Frenkel, Omer; Elad, Yigal
- BMC Genomics, Vol. 20, Issue 1
BcCFEM1, a CFEM Domain-Containing Protein with Putative GPI-Anchored Site, Is Involved in Pathogenicity, Conidial Production, and Stress Tolerance in Botrytis cinerea
journal, September 2017
- Zhu, Wenjun; Wei, Wei; Wu, Yayun
- Frontiers in Microbiology, Vol. 8
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1
journal, September 2015
- Firrincieli, Andrea; Otillar, Robert; Salamov, Asaf
- Frontiers in Microbiology, Vol. 6
Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle
preprint, October 2019
- Tao, Si-Qi; Cao, Bin; Morin, Emmanuelle
Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
text, January 2017
- Menardo, Fabrizio; Praz, Coraline R.; Wicker, Thomas
- BioMed Central
Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle
posted_content, October 2019
- Tao, Si-Qi; Cao, Bin; Morin, Emmanuelle
- Research Square [preprint]
Phylogenomic analyses of non-Dikarya fungi supports horizontal gene transfer driving diversification of secondary metabolism in the amphibian gastrointestinal symbiont, Basidiobolus
journal, April 2020
- Tabima, Javier F.; Trautman, Ian A.; Chang, Ying
Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
journal, October 2017
- Menardo, Fabrizio; Praz, Coraline R.; Wicker, Thomas
- BMC Evolutionary Biology, Vol. 17, Issue 1
Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors
journal, September 2015
- Liu, Jun-Jun; Sturrock, Rona N.; Sniezko, Richard A.
- BMC Genomics, Vol. 16, Issue 1
Network analysis exposes core functions in major lifestyles of fungal and oomycete plant pathogens
journal, December 2019
- Pandaranayaka, Eswari PJ; Frenkel, Omer; Elad, Yigal
- BMC Genomics, Vol. 20, Issue 1
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1
journal, September 2015
- Firrincieli, Andrea; Otillar, Robert; Salamov, Asaf
- Frontiers in Microbiology, Vol. 6
BcCFEM1, a CFEM Domain-Containing Protein with Putative GPI-Anchored Site, Is Involved in Pathogenicity, Conidial Production, and Stress Tolerance in Botrytis cinerea
journal, September 2017
- Zhu, Wenjun; Wei, Wei; Wu, Yayun
- Frontiers in Microbiology, Vol. 8
Genomic Patterns Of Positive Selection At The Origin Of Rust Fungi
text, January 2015
- Silva, Dn; Duplessis, S.; Talhinhas, P.
- Zenodo