publication . Review . Article . Other literature type . 2014

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes.

Jeanne Ropars; Jeanne Ropars; Gabriela Aguileta; Hélène Badouin; Hélène Badouin; Pierre Gladieux; Pierre Gladieux; Pierre Gladieux; Sara Branco; Ricardo C. Rodríguez de la Vega; ...
Open Access English
  • Published: 28 Feb 2014 Journal: MOLECULAR ECOLOGY (issn: 0962-1083, Copyright policy)
  • Publisher: WILEY-BLACKWELL
  • Country: France
Abstract
International audience; Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well-identified ecological niches and tend to have short generation times, and many are amenable to experimental approaches. Fungi also display diverse lifestyles , from saprotrophs to pathogens or mutualists, and they play extremely important roles in both ecosystems and human activities, as wood decayers, mycorrhizal fungi, lichens, endophytes, plant and animal pathogens, and in fermentation or drug production. We review here recent insights into the patterns and mech...
Subjects
free text keywords: Neurospora, local adaptation, Penicillium, Coccidioides, competition, geno-mic islands, genetic incompatibilities, gene regulation, effector, yeast, positive selection, Saccharomyces, [SDV]Life Sciences [q-bio], Genetics, Ecology, Evolution, Behavior and Systematics, Evolutionary biology, Introgression, Genome, Gene duplication, Reproductive isolation, Biology, Gene, Model organism, ved/biology.organism_classification_rank.species, ved/biology, Pleiotropy
Funded by
EC| GEDINDIS
Project
GEDINDIS
Genomics of Ecological Divergence in the fungal species Neurospora discreta
  • Funder: European Commission (EC)
  • Project Code: 273086
  • Funding stream: FP7 | SP3 | PEOPLE
,
EC| FUNGI-PATHNCODE
Project
FUNGI-PATHNCODE
The genomic basis of emerging fungal pathogenicity
  • Funder: European Commission (EC)
  • Project Code: 274223
  • Funding stream: FP7 | SP3 | PEOPLE
,
EC| RBUCE-UP
Project
RBUCE-UP
Research Based University Chairs of Excellence- Universities of Paris
  • Funder: European Commission (EC)
  • Project Code: 246556
  • Funding stream: FP7 | SP3 | PEOPLE
,
EC| GENOMEFUN
Project
GENOMEFUN
Genomics of adaptive divergence in Fungi
  • Funder: European Commission (EC)
  • Project Code: 309403
  • Funding stream: FP7 | SP2 | ERC
,
NSF| Dimensions: Collaborative Research: Deconstructing diversity and ecosystem function at multiple spatial and genetic scales in a keystone plant-microbe symbiosis
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1046115
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
233 references, page 1 of 16

Adams J, Puskas-Rozsa S, Simlar J, Wilke C (1992) Adaptation and major chromosomal changes in populations of Saccharomyces cerevisiae. Current Genetics, 22, 13-19.

Aguileta G, Refregier G, Yockteng Y, Fournier E, Giraud T (2009) Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protozoa. Infection, Genetics and Evolution, 9, 656-670. [OpenAIRE]

Aguileta G, Lengelle J, Marthey S et al. (2010) Finding candidate genes under positive Selection in non-model species: examples of genes involved in host specialization in pathogens. Molecular Ecology, 19, 292-306.

Aguileta G, Lengelle J, Chiapello H et al. (2012) Genes under positive selection in a model plant pathogenic fungus, Botrytis. Infection Genetics and Evolution, 12, 987-996.

Ajouz S, Nicot PC, Bardin M (2010) Adaptation to pyrrolnitrin in Botrytis cinerea and cost of resistance. Plant Pathology, 59, 556-566. [OpenAIRE]

Akagi Y, Akamatsu H, Otani H, Kodama M (2009) Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus. Eukaryotic Cell, 8, 1732-1738.

Alfoeldi J, Lindblad-Toh K (2013) Comparative genomics as a tool to understand evolution and disease. Genome Research, 23, 1063-1068. [OpenAIRE]

Altelaar AFM, Munoz J, Heck AJR (2013) Next-generation proteomics: towards an integrative view of proteome dynamics. Nature Reviews Genetics, 14, 35-48.

Ames R, Money D, Ghatge V, Whelan S, Lovell S (2012) Determining the evolutionary history of gene families. Bioinformatics, 28, 48-55.

Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P (2004) Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends in Ecology & Evolution 19, 535-544.

Anderson JB, Funt J, Thompson DA et al. (2010) Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Current Biology, 20, 1383- 1388. [OpenAIRE]

Barrick JE, Lenski RE (2013) Genome dynamics during experimental evolution. Nature Reviews Genetics, 14, 827-839. [OpenAIRE]

Barsoum E, Martinez P, Astrom SU (2013) Alpha 3, a transposable element that promotes host sexual reproduction. Genes & Development, 24, 33-44.

Bergot M, Cloppet E, Perarnaud V, Deque M, Marcais B, Desprez-Loustau ML (2004) Simulation of potential range expansion of oak disease caused by Phytophthora cinnamomi under climate change. Global Change Biology, 10, 1539-1552. [OpenAIRE]

Bezerra A, Simoes J, Lee WP et al. (2013) Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proceedings of the National Academy of Sciences USA, 110, 11079-11084. [OpenAIRE]

233 references, page 1 of 16
Abstract
International audience; Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well-identified ecological niches and tend to have short generation times, and many are amenable to experimental approaches. Fungi also display diverse lifestyles , from saprotrophs to pathogens or mutualists, and they play extremely important roles in both ecosystems and human activities, as wood decayers, mycorrhizal fungi, lichens, endophytes, plant and animal pathogens, and in fermentation or drug production. We review here recent insights into the patterns and mech...
Subjects
free text keywords: Neurospora, local adaptation, Penicillium, Coccidioides, competition, geno-mic islands, genetic incompatibilities, gene regulation, effector, yeast, positive selection, Saccharomyces, [SDV]Life Sciences [q-bio], Genetics, Ecology, Evolution, Behavior and Systematics, Evolutionary biology, Introgression, Genome, Gene duplication, Reproductive isolation, Biology, Gene, Model organism, ved/biology.organism_classification_rank.species, ved/biology, Pleiotropy
Funded by
EC| GEDINDIS
Project
GEDINDIS
Genomics of Ecological Divergence in the fungal species Neurospora discreta
  • Funder: European Commission (EC)
  • Project Code: 273086
  • Funding stream: FP7 | SP3 | PEOPLE
,
EC| FUNGI-PATHNCODE
Project
FUNGI-PATHNCODE
The genomic basis of emerging fungal pathogenicity
  • Funder: European Commission (EC)
  • Project Code: 274223
  • Funding stream: FP7 | SP3 | PEOPLE
,
EC| RBUCE-UP
Project
RBUCE-UP
Research Based University Chairs of Excellence- Universities of Paris
  • Funder: European Commission (EC)
  • Project Code: 246556
  • Funding stream: FP7 | SP3 | PEOPLE
,
EC| GENOMEFUN
Project
GENOMEFUN
Genomics of adaptive divergence in Fungi
  • Funder: European Commission (EC)
  • Project Code: 309403
  • Funding stream: FP7 | SP2 | ERC
,
NSF| Dimensions: Collaborative Research: Deconstructing diversity and ecosystem function at multiple spatial and genetic scales in a keystone plant-microbe symbiosis
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1046115
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
233 references, page 1 of 16

Adams J, Puskas-Rozsa S, Simlar J, Wilke C (1992) Adaptation and major chromosomal changes in populations of Saccharomyces cerevisiae. Current Genetics, 22, 13-19.

Aguileta G, Refregier G, Yockteng Y, Fournier E, Giraud T (2009) Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protozoa. Infection, Genetics and Evolution, 9, 656-670. [OpenAIRE]

Aguileta G, Lengelle J, Marthey S et al. (2010) Finding candidate genes under positive Selection in non-model species: examples of genes involved in host specialization in pathogens. Molecular Ecology, 19, 292-306.

Aguileta G, Lengelle J, Chiapello H et al. (2012) Genes under positive selection in a model plant pathogenic fungus, Botrytis. Infection Genetics and Evolution, 12, 987-996.

Ajouz S, Nicot PC, Bardin M (2010) Adaptation to pyrrolnitrin in Botrytis cinerea and cost of resistance. Plant Pathology, 59, 556-566. [OpenAIRE]

Akagi Y, Akamatsu H, Otani H, Kodama M (2009) Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus. Eukaryotic Cell, 8, 1732-1738.

Alfoeldi J, Lindblad-Toh K (2013) Comparative genomics as a tool to understand evolution and disease. Genome Research, 23, 1063-1068. [OpenAIRE]

Altelaar AFM, Munoz J, Heck AJR (2013) Next-generation proteomics: towards an integrative view of proteome dynamics. Nature Reviews Genetics, 14, 35-48.

Ames R, Money D, Ghatge V, Whelan S, Lovell S (2012) Determining the evolutionary history of gene families. Bioinformatics, 28, 48-55.

Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P (2004) Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends in Ecology & Evolution 19, 535-544.

Anderson JB, Funt J, Thompson DA et al. (2010) Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Current Biology, 20, 1383- 1388. [OpenAIRE]

Barrick JE, Lenski RE (2013) Genome dynamics during experimental evolution. Nature Reviews Genetics, 14, 827-839. [OpenAIRE]

Barsoum E, Martinez P, Astrom SU (2013) Alpha 3, a transposable element that promotes host sexual reproduction. Genes & Development, 24, 33-44.

Bergot M, Cloppet E, Perarnaud V, Deque M, Marcais B, Desprez-Loustau ML (2004) Simulation of potential range expansion of oak disease caused by Phytophthora cinnamomi under climate change. Global Change Biology, 10, 1539-1552. [OpenAIRE]

Bezerra A, Simoes J, Lee WP et al. (2013) Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proceedings of the National Academy of Sciences USA, 110, 11079-11084. [OpenAIRE]

233 references, page 1 of 16
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