Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Statist. Soc. B, vol.57, pp.289-300, 2005. ,
Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment, Evolution, vol.46, pp.16-30, 1992. ,
Trimmomatic: a flexible trimmer for illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014. ,
Genetic dissection of transcriptional regulation in budding yeast, Science, vol.296, pp.752-755, 2002. ,
Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty, Q. Rev. Biol, vol.46, pp.111-138, 1971. ,
Temperature-related reaction norms of gene expression: regulatory architecture and functional implications, Mol. Biol. Evol, vol.32, pp.2393-2402, 2015. ,
The genetic basis of adaptation following plastic changes in coloration in a novel environment, Curr. Biol, vol.28, pp.2970-2977, 2018. ,
The accessory genome as a cradle for adaptive evolution in pathogens, PLoS Patho, vol.8, p.1002608, 2012. ,
Evolution of evolvability and phenotypic plasticity in virtual cells, BMC Evol. Biol, vol.17, p.60, 2017. ,
A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat. Genet, vol.43, pp.491-498, 2011. ,
Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation, Mol. Biol. Evol, vol.30, pp.573-588, 2013. ,
The two-speed genomes of filamentous pathogens: waltz with plants, Curr. Opin. Genet. Dev, vol.35, pp.57-65, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02637383
Intraand interspecific variation in primate gene expression patterns, Science, vol.296, pp.340-343, 2002. ,
Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae, Genome Biol, vol.5, p.26, 2004. ,
Links between transcription, environmental adaptation and gene variability in Escherichia coli: correlations between gene expression and gene variability reflect growth efficiencies, Mol. Biol. Evol, vol.33, pp.2515-2529, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-02641264
Anthropogenic contribution to global occurrence of heavy-precipitation and high-temperature extremes, Nat. Clim. Chang, vol.46, pp.560-564, 2015. ,
Experimental evolution in fungi: an untapped resource, Fungal Genet. Biol, vol.94, pp.88-94, 2016. ,
The impact of Septoria tritici Blotch disease on wheat: an EU perspective, Fungal Genet Biol, vol.79, pp.3-7, 2015. ,
Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change, Phil. Trans. R. Soc. B, vol.374, 2019. ,
Morphological changes in response to environmental stresses in the fungal plant pathogen Zymoseptoria tritici, Sci. Rep, vol.9, p.9642, 2019. ,
The need for speed: compartmentalized genome evolution in filamentous phytopathogens, Mol. Plant Pathol, vol.20, pp.3-7, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02623576
Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments, 2009. ,
Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature, vol.525, pp.372-375, 2015. ,
Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments, Funct. Ecol, vol.21, pp.394-407, 2007. ,
Functional characterization of adaptive variation within a cis-regulatory element influencing Drosophila melanogaster growth, PLoS Biol, vol.16, pp.1-28, 2018. ,
Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis, PLoS Genet, vol.7, p.1002070, 2011. ,
RNA-seq-based gene annotation and comparative genomics of four fungal grass pathogens in the genus Zymoseptoria identify novel orphan genes and species-specific invasions of transposable elements, G3, vol.5, pp.1323-1333, 2015. ,
Genome-wide evidence for divergent selection between populations of a major agricultural pathogen, Mol. Ecol, vol.27, pp.2725-2741, 2018. ,
A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements, ISME J, vol.11, pp.1189-1204, 2017. ,
Highly flexible infection programs in a specialized wheat pathogen, Ecol. Evol, vol.9, pp.275-294, 2019. ,
The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis Genus, Mol. Biol. Evol, vol.33, pp.2088-2101, 2016. ,
Evolutionary adaptations to new environments generally reverse plastic phenotypic changes, Nat. Comm, vol.9, p.350, 2018. ,
Genetic basis of transcriptome diversity in Drosophila melanogaster, PNAS, vol.112, pp.6010-6019, 2015. ,
Experimental evolution of gene expression and plasticity in alternative selective regimes, PLoS Genet, vol.12, p.1006336, 2016. ,
An experimental evolutionary study on adaptation to temporally fluctuating pH in Escherichia coli, Physiol. Biochem. Zool, vol.80, pp.406-421, 2007. ,
Evolution and plasticity of the transcriptome under temperature fluctuations in the fungal plant pathogen Zymoseptoria tritici, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02983043
Temporal dynamics of gene expression in heat-stressed Caenorhabditis elegans, PLoS ONE, vol.12, p.189445, 2017. ,
Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs, Genome Biol. Evol, vol.6, pp.1353-1365, 2014. ,
Wee1-dependent mechanisms required for coordination of cell growth and cell division, J. Cell Sci, vol.116, pp.4883-4890, 2003. ,
Gene expression plasticity as a mechanism of coral adaptation to a variable environment, Nat. Ecol. Evol, vol.7, p.14, 2016. ,
Evolution at two levels in humans and chimpanzees, Science, vol.188, pp.107-116, 1975. ,
Redundancy, feedback, and robustness in the Arabidopsis thaliana BZR/BEH gene family, Front. Genet, vol.9, p.3389, 2018. ,
Adaptation to an extraordinary environment by evolution of phenotypic plasticity and assimilation, J. Evol. Biol, vol.22, pp.1435-1446, 2009. ,
, , 2006.
, Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes, Gene, vol.366, pp.343-351
WGCNA: An R package for weighted correlation network analysis, BMC Bioinform, vol.9, p.559, 2008. ,
The evolution of canalization and evolvability in stable and fluctuating environments, Evol. Biol, vol.40, pp.317-340, 2013. ,
Evolutionary potential of hidden genetic variation, Trends Ecol. Evol, vol.23, pp.33-37, 2008. ,
The evolution and adaptive potential of transcriptional variation in sticklebacks-signatures of selection and widespread heritability, Mol. Biol. Evol, vol.32, pp.674-689, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02631858
QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici, Heredity, vol.116, pp.384-394, 2016. ,
Evolutionary adaptation to temperature. III. Adaptation of Escherichia coli to a temporally varying environment, Evolution, vol.48, pp.1222-1229, 1994. ,
Evaluating "plasticity-first" evolution in nature:key criteria and empirical approaches, Trends Ecol. Evol, vol.31, pp.563-574, 2016. ,
The cellular robustness by genetic redundancy in budding yeast, PLoS Genet, vol.6, p.1001187, 2010. ,
Mapping determinants of gene expression plasticity by genetical genomics in C. elegans, PLoS Genet, vol.2, pp.2155-2161, 2006. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
RNA-seq:technical variability and sampling, BMC Genomics, vol.12, p.293, 2011. ,
A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch, New Phytol, vol.219, pp.1048-1061, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02420450
Extraordinary genome instability and widespread chromosome rearrangements during vegetative growth, Genetics, vol.210, pp.517-529, 2018. ,
Adaptive evolution of gene expression in Drosophila, Cell Rep, vol.20, pp.1385-1395, 2017. ,
The wheat -Septoria conflict: a new front opening up?, Trends Plant Sci, vol.19, pp.602-610, 2014. ,
Variation in gene expression within and among natural populations, Nat. Genet, vol.32, pp.261-266, 2002. ,
Cis-and trans-regulatory effects on gene expression, Genetics, vol.206, pp.2139-2148, 2017. ,
Comparative transcriptome analyses in Zymoseptoria tritici reveal significant differences in gene expression among strains during plant infection, MPMI, vol.30, pp.231-244, 2017. ,
The causes of evolvability and their evolution, Nat. Rev. Genet, vol.20, pp.24-38, 2019. ,
Transcriptlevel expression analysis of RNA-seq experiments with HISAT. StringTie and Ballgown, Nat Protoc, vol.11, pp.1650-1667, 2016. ,
Phenotypic plasticity and evolution by genetic assimilation, J. Exp. Biol, vol.209, pp.2362-2367, 2006. ,
Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus, J. Exp. Biol, vol.207, pp.2237-2254, 2004. ,
Abundant raw material for cisregulatory evolution in humans, Mol. Biol. Evol, vol.19, 1991. ,
Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition, Plant Physiol, vol.167, pp.1158-1185, 2015. ,
Genetics of gene expression surveyed in maize, mouse and man, Nature, vol.422, pp.292-297, 2003. ,
Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes, Epigenetics Chromatin, vol.8, p.41, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02637052
The impact of transposable elements in adaptive evolution, Mol. Ecol, vol.28, pp.1537-1549, 2019. ,
Waddington's canalization revisited: Developmental stability and evolution, PNAS, vol.99, pp.10528-10532, 2002. ,
Environmental and evolutionary drivers of the modular gene regulatory network underlying ophenotypic plasticity for stress resistance in the nematode Caenorhabditis remanei, vol.3, pp.969-982, 2019. ,
Gene-environment interaction in yeast gene expression, PLoS Biol, vol.6, p.83, 2008. ,
Thermal fluctuations affect the transcriptome through mechanisms independent of average temperature, Sci Rep, vol.6, p.30975, 2016. ,
Cell biology of Zymoseptoria tritici: Pathogen cell organization and wheat infection, Fungal Genet. Biol, vol.79, pp.17-23, 2015. ,
Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici, Mol Plant Pathol, vol.9, pp.201-216, 2018. ,
Neutral and adaptive variation in gene expression, PNAS, vol.103, pp.5425-5430, 2006. ,
Evolutionary changes in cis and trans gene regulation, Nature, vol.430, pp.85-88, 2004. ,
Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol, vol.11, 2010. ,
Genetic regulation of transcriptional variation in natural Arabidopsis thaliana accessions, G3, vol.6, pp.2319-2328, 2016. ,
Pervasive gene expression responses to a fluctuating diet in Drosophila melanogaster: the importance of measuring multiple traits to decouple potential mediators of life span and reproduction, Evolution, vol.71, pp.2572-2583, 2017. ,
Thermal adaptation in the fungal pathogen Mycosphaerella graminicola, Mol. Ecol, vol.20, pp.1689-1701, 2011. ,
A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene, New Phytol, vol.214, pp.619-631, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01530826
Phenotypic plasticity of the Drosophila transcriptome, PLoS Genet, vol.8, p.1002593, 2012. ,