Dynamic linkage relationships to the mating-type locus in automictic fungi of the genus Microbotryum, Journal of Evolutionary Biology, vol.41, issue.8, pp.1800-1805, 2010. ,
DOI : 10.1111/j.1420-9101.2010.02036.x
INTRATETRAD MATING AND THE EVOLUTION OF LINKAGE RELATIONSHIPS, Evolution, vol.22, issue.4, pp.702-709, 2004. ,
DOI : 10.1016/0040-5809(74)90043-4
Accumulation of Spock and Worf, Two Novel Non-LTR Retrotransposons, on the Neo-Y Chromosome of Drosophila miranda, Molecular Biology and Evolution, vol.20, issue.2, pp.173-181, 2003. ,
DOI : 10.1093/molbev/msg035
Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila, Genome Research, vol.15, issue.10, pp.1393-1401, 2005. ,
DOI : 10.1101/gr.3543605
Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration, Nature Reviews Genetics, vol.70, issue.2, pp.113-124, 2013. ,
DOI : 10.1038/nrg3366
Are all sex chromosomes created equal? Trends Genet, pp.350-357, 2011. ,
Evolution of Amino-Acid Sequences and Codon Usage on the Drosophila miranda Neo-Sex Chromosomes, Genetics, vol.174, issue.4, pp.2033-2044, 2006. ,
DOI : 10.1534/genetics.106.064113
The evolution of restricted recombination in sex chromosomes, Trends in Ecology & Evolution, vol.24, issue.2, pp.94-102, 2009. ,
DOI : 10.1016/j.tree.2008.09.010
Evolutionary Strata on the X Chromosomes of the Dioecious Plant Silene latifolia: Evidence From New Sex-Linked Genes, Genetics, vol.175, issue.4, pp.1945-1954, 2007. ,
DOI : 10.1534/genetics.106.070110
Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types, Biological Reviews, vol.44, issue.2, pp.421-442, 2011. ,
DOI : 10.1111/j.1469-185X.2010.00153.x
URL : https://hal.archives-ouvertes.fr/hal-00609575
Sex Chromosomes in Haploid Dioecy: A Unique Contrast to Muller's Theory for Diploid Dioecy, The American Naturalist, vol.112, issue.983, pp.245-250, 1978. ,
DOI : 10.1086/283267
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1973, 2009. ,
DOI : 10.1093/bioinformatics/btp348
The evolution of sex chromosomes, Science, vol.251, issue.4997, pp.1030-1033, 1991. ,
DOI : 10.1126/science.1998119
URL : https://hal.archives-ouvertes.fr/hal-00427860
Steps in the evolution of heteromorphic sex chromosomes, Heredity, vol.13, issue.10, pp.118-128, 2005. ,
DOI : 10.1038/sj.hdy.6800697
URL : https://hal.archives-ouvertes.fr/hal-00427860
jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, p.772, 2012. ,
DOI : 10.1109/TAC.1974.1100705
Mating Type and Morphogenesis in Ustilago violacea, Botanical Gazette, vol.140, issue.1, pp.94-101, 1979. ,
DOI : 10.1086/337062
Phylogenetic determinants of potential host shifts in fungal pathogens, Journal of Evolutionary Biology, vol.53, issue.12, pp.2532-2541, 2009. ,
DOI : 10.1111/j.1420-9101.2009.01878.x
Ancient Trans-specific Polymorphism at Pheromone Receptor Genes in Basidiomycetes, Genetics, vol.181, issue.1, pp.209-223, 2009. ,
DOI : 10.1534/genetics.108.093708
Population structure of the human pseudoautosomal boundary, Nature, vol.344, issue.6267, pp.663-665, 1990. ,
DOI : 10.1038/344663a0
Massive Changes in Genome Architecture Accompany the Transition to Self-Fertility in the Filamentous Fungus Neurospora tetrasperma, Genetics, vol.189, issue.1, pp.55-69, 2011. ,
DOI : 10.1534/genetics.111.130690
Sex Chromosomal Transposable Element Accumulation and Male-Driven Substitutional Evolution in Humans, Molecular Biology and Evolution, vol.17, issue.5, pp.804-812, 2000. ,
DOI : 10.1093/oxfordjournals.molbev.a026359
Regulation of mating and pathogenic development in Ustilago maydis, Current Opinion in Microbiology, vol.7, issue.6, pp.666-672, 2004. ,
DOI : 10.1016/j.mib.2004.10.006
Substitution Rates in the X- and Y-Linked Genes of the Plants, Silene latifolia and S. dioica, Molecular Biology and Evolution, vol.19, issue.6, pp.898-907, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004147
The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection, Molecular Biology and Evolution, vol.27, issue.10, pp.2257-2267, 2010. ,
DOI : 10.1093/molbev/msq115
Convergent Evolution of Chromosomal Sex-Determining Regions in the Animal and Fungal Kingdoms, PLoS Biology, vol.33, issue.12, pp.2243-2255, 2004. ,
DOI : 10.1371/journal.pbio.0020384.sg003
Genetics of Ustilago violacea. XXXII. Genetic evidence for transposable elements, Theoretical and Applied Genetics, vol.89, issue.7-8, pp.838-846, 1995. ,
DOI : 10.1007/BF00224506
Genetics of Ustilago violacea. XXXIV. Genetic evidence for a transposable element functioning during mitosis and txo transposable elements functioning during meiosis, 1998. ,
Mating System of the Anther Smut Fungus Microbotryum violaceum: Selfing under Heterothallism, Eukaryotic Cell, vol.7, issue.5, pp.765-775, 2008. ,
DOI : 10.1128/EC.00440-07
Maintenance of Fungal Pathogen Species That Are Specialized to Different Hosts: Allopatric Divergence and Introgression through Secondary Contact, Molecular Biology and Evolution, vol.28, issue.1, pp.459-471, 2011. ,
DOI : 10.1093/molbev/msq235
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina, Genetics, vol.197, issue.1, pp.421-432, 2014. ,
DOI : 10.1534/genetics.113.159988
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003. ,
DOI : 10.1080/10635150390235520
Dimorphic mating-type chromosomes in the anthersmut fungus, Genetics, vol.160, pp.457-461, 2002. ,
Repetitive DNA in the automictic fungus Microbotryum violaceum, Genetica, vol.5, issue.1, pp.1-10, 2005. ,
DOI : 10.1007/s10709-004-6615-y
Intratetrad mating, heterozygosity, and the maintenance of deleterious alleles in Microbotryum violaceum (=Ustilago violacea), Heredity, vol.22, issue.3, pp.231-241, 2000. ,
DOI : 10.1086/297470
Shared Forces of Sex Chromosome Evolution in Haploid-Mating and Diploid-Mating Organisms: Microbotryum violaceum and Other Model Organisms, Genetics, vol.168, issue.1, pp.141-146, 2004. ,
DOI : 10.1534/genetics.104.029900
Mating Within the Meiotic Tetrad and the Maintenance of Genomic Heterozygosity, Genetics, vol.166, issue.4, pp.1751-1759, 2004. ,
DOI : 10.1534/genetics.166.4.1751
Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum, Genetics, vol.170, issue.3, pp.1081-1089, 2005. ,
DOI : 10.1534/genetics.105.042564
Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus, Genetics, vol.193, issue.1, pp.309-315, 2013. ,
DOI : 10.1534/genetics.112.146266
THE EVOLUTION OF INTRATETRAD MATING RATES, Evolution, vol.41, issue.4, pp.2525-2532, 2005. ,
DOI : 10.1126/science.288.5469.1211
InterProScan 5: genome-scale protein function classification, Bioinformatics, vol.30, issue.9, pp.1236-1240, 2014. ,
DOI : 10.1093/bioinformatics/btu031
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998142
A normalization strategy for comparing tag count data, Algorithms for Molecular Biology, vol.7, issue.1, p.5, 2012. ,
DOI : 10.1186/gb-2004-5-10-r80
Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota : Urediniomycetes), BMC Evolutionary Biology, vol.6, issue.1, p.35, 2006. ,
DOI : 10.1186/1471-2148-6-35
Four Evolutionary Strata on the Human X Chromosome, Science, vol.286, issue.5441, pp.964-967, 1999. ,
DOI : 10.1126/science.286.5441.964
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, p.25, 2009. ,
DOI : 10.1186/gb-2009-10-3-r25
Optical mapping as a routine tool for bacterial genome sequence finishing, BMC Genomics, vol.8, issue.1, p.6, 2007. ,
DOI : 10.1186/1471-2164-8-321
PHYLOGENETIC EVIDENCE OF HOST-SPECIFIC CRYPTIC SPECIES IN THE ANTHER SMUT FUNGUS, Evolution, vol.18, issue.1, pp.15-26, 2007. ,
DOI : 1010-061X(2005)018[0203:HRDITA]2.0.CO;2
EVOLUTION OF REPRODUCTIVE ISOLATION WITHIN A PARASITIC FUNGAL SPECIES COMPLEX, Evolution, vol.40, issue.7, pp.1781-1787, 2007. ,
DOI : 10.1554/0014-3820(2003)057[0766:ICAMBF]2.0.CO;2
RSEM, BMC Bioinformatics, vol.12, p.323, 2011. ,
DOI : 10.1201/b16589-5
De novo assembly of human genomes with massively parallel short read sequencing, Genome Research, vol.20, issue.2, pp.265-272, 2010. ,
DOI : 10.1101/gr.097261.109
From The Cover: An algorithm for progressive multiple alignment of sequences with insertions, Proceedings of the National Academy of Sciences, vol.102, issue.30, pp.10557-10562, 2005. ,
DOI : 10.1073/pnas.0409137102
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis, Science, vol.320, issue.5883, pp.1632-1635, 2008. ,
DOI : 10.1126/science.1158395
Anther smuts of Caryophyllaceae: Molecular characters indicate host-dependent species delimitation, Mycological Progress, vol.1, issue.2, pp.225-238, 2005. ,
DOI : 10.1007/s11557-006-0126-4
cluster: cluster analysis basics and extensions, 2013. ,
Evidence for Degeneration of the Y Chromosome in the Dioecious Plant Silene latifolia, Current Biology, vol.18, issue.7, pp.545-549, 2008. ,
DOI : 10.1016/j.cub.2008.03.023
URL : https://hal.archives-ouvertes.fr/hal-00412855
High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes, Genome Research, vol.21, issue.6, pp.863-874, 2011. ,
DOI : 10.1101/gr.115949.110
The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes, PLoS Genetics, vol.19, issue.3, p.1000030, 2008. ,
DOI : 10.1371/journal.pgen.1000030.s002
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene, Genetics, vol.148, pp.929-936, 1998. ,
Evolution of uni- and bifactorial sexual compatibility systems in fungi, Heredity, vol.24, issue.6, pp.445-455, 2013. ,
DOI : 10.1016/j.mycres.2008.11.002
URL : https://hal.archives-ouvertes.fr/hal-01110818
T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000. ,
DOI : 10.1006/jmbi.2000.4042
The Distribution of Mating-Type Bias in Natural Populations of the Anther-Smut Ustilago violacea on Silene alba in Virginia, Mycologia, vol.90, issue.3, pp.372-381, 1998. ,
DOI : 10.2307/3761395
Pathovars or Formae speciales of Microbotryum violaceum Differ in Electrophoretic Karyotype, International Journal of Plant Sciences, vol.157, issue.4, pp.447-452, 1996. ,
DOI : 10.1086/297361
: INSIGHTS INTO NONRECOMBINING CHROMOSOMES, Evolution, vol.22, issue.Suppl. 1, pp.3519-3533, 2012. ,
DOI : 10.1111/j.1558-5646.2012.01703.x
jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1256, 2008. ,
DOI : 10.1093/molbev/msn083
High mutation rates have driven extensive structural polymorphism among human Y chromosomes, Nature Genetics, vol.67, issue.4, pp.463-467, 2006. ,
DOI : 10.1038/ng1754
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-140, 2010. ,
DOI : 10.1093/bioinformatics/btp616
Inferring ancient divergences requires genes with strong phylogenetic signals, Nature, vol.27, issue.7449, pp.327-331, 2013. ,
DOI : 10.1038/nature12130
Statistical tests for detecting gene conversion, Mol Biol Evol, vol.6, pp.526-538, 1989. ,
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006. ,
DOI : 10.1093/bioinformatics/btl446
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, vol.21, issue.4, pp.456-463, 2005. ,
DOI : 10.1093/bioinformatics/bti191
Degenerating Y chromosome of Drosophila miranda: a trap for retrotransposons., Proceedings of the National Academy of Sciences, vol.89, issue.16, pp.7591-7595, 1992. ,
DOI : 10.1073/pnas.89.16.7591
from Several Host Species, International Journal of Plant Sciences, vol.164, issue.4, pp.641-647, 2003. ,
DOI : 10.1086/375374
Evolutionary Strata in a Small Mating-Type-Specific Region of the Smut Fungus Microbotryum violaceum, Genetics, vol.182, issue.4, pp.1391-1396, 2009. ,
DOI : 10.1534/genetics.109.103192
Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma, Heredity, vol.155, issue.4, pp.305-314, 2011. ,
DOI : 10.1093/molbev/msm088
Degeneration in Codon Usage within the Region of Suppressed Recombination in the Mating-Type Chromosomes of Neurospora tetrasperma, Eukaryotic Cell, vol.10, issue.4, pp.594-603, 2011. ,
DOI : 10.1128/EC.00284-10
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages, Molecular Biology and Evolution, vol.19, issue.6, pp.908-917, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004148
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection, Molecular Biology and Evolution, vol.22, issue.4, pp.1107-1118, 2005. ,
DOI : 10.1093/molbev/msi097
Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes, BMC Genomics, vol.8, issue.1, p.272, 2007. ,
DOI : 10.1186/1471-2164-8-272
Some principles of the gene localization in eukaryotic chromosomes. Formation of the problem and analysis of nonrandom localization of the mating-type loci in some fungi, Genetika, vol.22, pp.2620-2624, 1986. ,
Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level, Molecular Biology and Evolution, vol.22, issue.12, pp.2472-2479, 2005. ,
DOI : 10.1093/molbev/msi237