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
THE POTENTIAL FOR SEXUALLY ANTAGONISTIC POLYMORPHISM IN DIFFERENT GENOME REGIONS, Evolution, vol.159, issue.2, pp.505-516, 2012. ,
DOI : 10.1111/j.1558-5646.2011.01448.x
No amicable divorce? Challenging the notion that sexual antagonism drives sex chromosome evolution, BioEssays, vol.182, issue.8, pp.718-726, 2010. ,
DOI : 10.1002/bies.200900124
Four Evolutionary Strata on the Human X Chromosome, Science, vol.286, issue.5441, pp.964-967, 1999. ,
DOI : 10.1126/science.286.5441.964
The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes, Nature, vol.423, issue.6942, pp.825-837, 2003. ,
DOI : 10.1038/nature01722
Footprints of Inversions at Present and Past Pseudoautosomal Boundaries in Human Sex Chromosomes, Genome Biology and Evolution, vol.1, issue.0, pp.56-66, 2009. ,
DOI : 10.1093/gbe/evp006
URL : https://hal.archives-ouvertes.fr/hal-00428362
Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution, Proceedings of the National Academy of Sciences, vol.109, issue.34, pp.13710-13715, 2012. ,
DOI : 10.1073/pnas.1207833109
Evolution of Sex Determining Mechanisms, 1983. ,
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
Are all sex chromosomes created equal?, Trends in Genetics, vol.27, issue.9, pp.350-357, 2011. ,
DOI : 10.1016/j.tig.2011.05.005
Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system, Proceedings of the National Academy of Sciences, vol.104, issue.15, pp.6472-6477, 2007. ,
DOI : 10.1073/pnas.0609054104
Evolution of an Expanded Sex-Determining Locus in Volvox, Science, vol.328, issue.5976, pp.351-354, 2010. ,
DOI : 10.1126/science.1186222
Recent gene-capture on the UV sex chromosome of the moss Ceratodon purpureus, Evolution, vol.15, 2013. ,
(ECTOCARPALES, PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS, Journal of Phycology, vol.40, issue.6, pp.1079-1088, 2004. ,
DOI : 10.1111/j.1529-8817.2004.04058.x
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
The mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma represents a model for early evolution of sex chromosomes Die geschlechtliche Fortpflanzung der eigentlichen Phaeosporeen Algae: An Introduction to Phycology, PLoS Genet Mitt Zool Stat Neapel, vol.4, issue.21, pp.401-413, 1881. ,
A large chromosome in the laminarian nucleus Chromosomes of the brown algae, Nature Phycologia, vol.198, issue.35, pp.19-40, 1963. ,
Sex expression in aneuploid gametophytes of the brown alga Ectocarpus siliculosus (Dillw.) Lyngb, Arch. Protistenk. Bd, vol.117, pp.297-302, 1975. ,
Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae), BMC Molecular Biology, vol.12, issue.1, 2011. ,
DOI : 10.1186/1471-2199-12-2
URL : https://hal.archives-ouvertes.fr/hal-00925432
A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence, New Phytologist, vol.45, issue.Suppl., pp.42-51, 2010. ,
DOI : 10.1111/j.1469-8137.2010.03273.x
Efficient identification of Y chromosome sequences in the human and Drosophila genomes, Genome Research, vol.23, issue.11, pp.1894-1907, 2013. ,
DOI : 10.1101/gr.156034.113
Abundant gene conversion between arms of palindromes in human and ape Y chromosomes, Nature, vol.423, issue.6942, pp.873-876, 2003. ,
DOI : 10.1038/nature01723
Evolution of amino-acid sequences and codon usage on the Drosophila miranda neo-sex chromosomes Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila, Genetics Bachtrog, D. Nat Genet, vol.174, issue.34, pp.2033-2044, 2003. ,
Evidence for Widespread GC-biased Gene Conversion in Eukaryotes, Genome Biology and Evolution, vol.4, issue.7, pp.675-682, 2012. ,
DOI : 10.1093/gbe/evs052
The effect of linkage on limits to artificial selection The degeneration of Y chromosomes The temporal dynamics of processes underlying Y chromosome degeneration, Genet Res Philos Trans R Soc Lond B Biol Sci Bachtrog, D. Genetics, vol.8, issue.179, pp.269-294, 1966. ,
Identification of the sex genes in an early diverged fungus, Nature, vol.95, issue.7175, pp.193-196, 2008. ,
DOI : 10.1038/nature06453
Evolution of sex determination and the Y chromosome: SRY-related sequences in marsupials, Nature, vol.359, issue.6395, pp.531-533, 1992. ,
DOI : 10.1038/359531a0
Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes, Genome Research, vol.18, issue.6, pp.965-973, 2008. ,
DOI : 10.1101/gr.7101908
Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes, PLoS Biology, vol.447, issue.4, p.80, 2008. ,
DOI : 10.1371/journal.pbio.0060080.st005
URL : https://hal.archives-ouvertes.fr/inserm-00521505
Preservation of the Y Transcriptome in a 10-Million-Year-Old Plant Sex Chromosome System, Current Biology, vol.21, issue.17, pp.1470-1474, 2010. ,
DOI : 10.1016/j.cub.2011.07.032
Sex Chromosomes and the Evolution of Sexual Dimorphism, Evolution, vol.38, issue.4, pp.735-742, 1984. ,
DOI : 10.2307/2408385
The evolution of sex-biased genes and sex-biased gene expression, Nature Reviews Genetics, vol.416, issue.9, pp.689-698, 2007. ,
DOI : 10.1038/nrg2167
Sex-Biased Transcriptome Evolution in Drosophila, Genome Biology and Evolution, vol.4, issue.11, pp.1189-1200, 2012. ,
DOI : 10.1093/gbe/evs093
OUROBOROS is a master regulator of the gametophyte to sporophyte life cycle transition in the brown alga Ectocarpus, Proceedings of the National Academy of Sciences, vol.108, issue.28, pp.11518-11523, 2011. ,
DOI : 10.1073/pnas.1102274108
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
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes, Molecular Biology and Evolution, vol.21, issue.5, pp.809-818, 2004. ,
DOI : 10.1093/molbev/msh075
Testing for the Footprint of Sexually Antagonistic Polymorphisms in the Pseudoautosomal Region of a Plant Sex Chromosome Pair, Genetics, vol.194, issue.3, pp.663-672, 2013. ,
DOI : 10.1534/genetics.113.152397
Multiple and independent cessation of recombination between avian sex chromosomes, Genetics, vol.158, pp.325-331, 2001. ,
Ever-Young Sex Chromosomes in European Tree Frogs, PLoS Biology, vol.21, issue.5, 2011. ,
DOI : 10.1371/journal.pbio.1001062.s008
Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution, Proceedings of the National Academy of Sciences, vol.110, issue.16, pp.6453-6458, 2013. ,
DOI : 10.1073/pnas.1217027110
The genetics of bryophytes, The Botanical Review, vol.12, issue.8, pp.269-291, 1935. ,
DOI : 10.1007/BF02869756
How to Cultivate Ectocarpus, Cold Spring Harbor Protocols, vol.2012, issue.2, pp.258-261, 2012. ,
DOI : 10.1101/pdb.prot067934
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
TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, vol.25, issue.9, pp.1105-1111, 2009. ,
DOI : 10.1093/bioinformatics/btp120
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672628
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, vol.7, issue.3, pp.562-578, 2012. ,
DOI : 10.1038/nbt0710-691
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, vol.25, issue.5, pp.511-515, 2010. ,
DOI : 10.1038/nbt.1621
Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010. ,
DOI : 10.1186/gb-2010-11-10-r106
ORCAE: online resource for community annotation of eukaryotes, Nature Methods, vol.9, issue.11, 1041. ,
DOI : 10.1186/gb-2006-7-7-r58
Genome Annotation in Plants and Fungi: EuGene as a Model Platform, Current Bioinformatics, vol.3, issue.2, pp.87-97, 2008. ,
DOI : 10.2174/157489308784340702
SpliceMachine: predicting splice sites from high-dimensional local context representations, Bioinformatics, vol.21, issue.8, pp.1332-1338, 2005. ,
DOI : 10.1093/bioinformatics/bti166
Considering Transposable Element Diversification in De Novo Annotation Approaches, PLoS ONE, vol.25, issue.3, 2011. ,
DOI : 10.1371/journal.pone.0016526.s021
URL : https://hal.archives-ouvertes.fr/hal-00568705
Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes, Genome Biology and Evolution, vol.1, issue.0, pp.205-220, 2009. ,
DOI : 10.1093/gbe/evp023
Sequence mapping by electronic PCR, Genome Res, vol.7, pp.541-550, 1997. ,
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010. ,
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011. ,
DOI : 10.1093/molbev/msr121
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000. ,
DOI : 10.1093/oxfordjournals.molbev.a026334
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
Databases of homologous gene families for comparative genomics An algorithm for progressive multiple alignment of sequences with insertions, BMC Bioinformatics Proc Natl Acad Sci, vol.10, issue.102, pp.10557-10562, 2005. ,
A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages, PLoS ONE, vol.20, issue.9, p.74, 2010. ,
DOI : 10.1371/journal.pone.0012759.s003
Online synonymous codon usage analyses with the ade4 and seqinR packages, Bioinformatics, vol.21, issue.4, pp.545-547, 2005. ,
DOI : 10.1093/bioinformatics/bti037
URL : https://hal.archives-ouvertes.fr/hal-00427727
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Research, vol.15, issue.3, pp.1281-1295, 1987. ,
DOI : 10.1093/nar/15.3.1281