The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome, BMC Genomics, vol.9, issue.1, p.327, 2008. ,
DOI : 10.1186/1471-2164-9-327
Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties, BMC Genomics, vol.11, issue.1, p.441, 2010. ,
DOI : 10.1186/1471-2164-11-441
Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing, Proceedings of the National Academy of Sciences, vol.72, issue.3, pp.16151-16157, 2009. ,
DOI : 10.1128/AEM.72.3.2126-2133.2006
Strains, Industrial Biotechnology, vol.9, issue.6, pp.352-67, 2013. ,
DOI : 10.1089/ind.2013.0015
Single nucleotide polymorphism analysis of a Trichoderma reesei hyper?cellulolytic mutant developed in Japan, Biosci Biotechnol Biochem, vol.77, pp.534-577, 2013. ,
A new Zn(II)2Cys6-type transcription factor BglR regulates ??-glucosidase expression in Trichoderma reesei, Fungal Genetics and Biology, vol.49, issue.5, pp.388-97, 2012. ,
DOI : 10.1016/j.fgb.2012.02.009
Mind the gap; seven reasons to close fragmented genome assemblies, Fungal Genetics and Biology, vol.90, pp.24-30, 2016. ,
DOI : 10.1016/j.fgb.2015.08.010
Centromeres of filamentous fungi, Chromosome Research, vol.472, issue.5, pp.635-56, 2012. ,
DOI : 10.1038/nature09854
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409310
Capturing Chromosome Conformation, Science, vol.295, issue.5558, pp.1306-1317, 2002. ,
DOI : 10.1126/science.1067799
High-quality genome (re)assembly using chromosomal contact data, Nature Communications, vol.5, p.5695, 2014. ,
DOI : 10.1080/01621459.2000.10473908
URL : https://hal.archives-ouvertes.fr/hal-01138788
Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures, FEBS Letters, vol.111, issue.20PartA, pp.2966-74, 2015. ,
DOI : 10.1073/pnas.1416014111
URL : https://hal.archives-ouvertes.fr/pasteur-01419996
Filling annotation gaps in yeast genomes using genome-wide contact maps, Bioinformatics, vol.30, issue.15, pp.2105-2118, 2014. ,
DOI : 10.1093/bioinformatics/btu162
URL : https://hal.archives-ouvertes.fr/pasteur-01488132
A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness, Biotechnology for Biofuels, vol.7, issue.Web Server issu, p.75, 2016. ,
DOI : 10.1186/1471-2105-7-474
A three-dimensional model of the yeast genome, Nature, vol.465, issue.7296, pp.363-370, 2010. ,
DOI : 10.1073/pnas.0402766101
Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain, Biotechnology for Biofuels, vol.32, issue.suppl 2, p.173, 2014. ,
DOI : 10.1093/nar/gkh894
URL : https://hal.archives-ouvertes.fr/hal-01112360
Repression of harmful meiotic recombination in centromeric regions, Seminars in Cell & Developmental Biology, vol.54, pp.188-97, 2016. ,
DOI : 10.1016/j.semcdb.2016.01.042
The genome sequence of Schizosaccharomyces pombe, Nature, vol.415, issue.6874, pp.871-80, 2002. ,
DOI : 10.1038/nature724
Major Evolutionary Transitions in Centromere Complexity, Cell, vol.138, issue.6, pp.1067-82, 2009. ,
DOI : 10.1016/j.cell.2009.08.036
URL : http://doi.org/10.1016/j.cell.2009.08.036
Chromosome walking shows a highly homologous repetitive sequence present in all the centromere regions of fission yeast, EMBO J, vol.5, pp.1011-1032, 1986. ,
Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe., Molecular and Cellular Biology, vol.8, issue.2, pp.754-63, 1988. ,
DOI : 10.1128/MCB.8.2.754
Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique, Proceedings of the National Academy of Sciences, vol.79, issue.5, pp.11374-11383, 2004. ,
DOI : 10.1016/0092-8674(94)90075-2
Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis, PLOS Genetics, vol.6, issue.1, p.1005839, 2016. ,
DOI : 10.1371/journal.pgen.1005839.s014
Have a Simple Inverted-Repeat Structure, Genome Biology and Evolution, vol.8, issue.8, pp.2482-92, 2016. ,
DOI : 10.1093/gbe/evw178
URL : http://doi.org/10.1093/gbe/evw178
Mutation of ribosomal protein RPS24 in Diamond-Blackfan anemia results in a ribosome biogenesis disorder, Human Molecular Genetics, vol.17, issue.9, pp.1253-63, 2008. ,
DOI : 10.1093/hmg/ddn015
URL : https://hal.archives-ouvertes.fr/hal-00308960
Aberrant mitosis in fission yeast mutants defective in fatty acid synthetase and acetyl CoA carboxylase, The Journal of Cell Biology, vol.134, issue.4, pp.949-61, 1996. ,
DOI : 10.1083/jcb.134.4.949
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2120970/pdf
Functional profiling of the Saccharomyces cerevisiae genome, Nature, vol.95, issue.6896, pp.387-91, 2002. ,
DOI : 10.1073/pnas.95.25.14863
The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum, BMC Genomics, vol.16, issue.1, p.544, 2015. ,
DOI : 10.1093/bioinformatics/btp352
Making contacts on a nucleic acid polymer, Trends in Biochemical Sciences, vol.26, issue.12, pp.733-773, 2001. ,
DOI : 10.1016/S0968-0004(01)01978-8
0, on the JGI Genome Portal, 2016. ,
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology, BMC Genomics, vol.11, issue.1, p.81, 2010. ,
DOI : 10.1186/1471-2164-11-81
A meta-approach for improving the prediction and the functional annotation of ortholog groups, BMC Genomics, vol.15, issue.Suppl 6, p.16, 2014. ,
DOI : 10.1186/1471-2105-12-11
URL : https://hal.archives-ouvertes.fr/inserm-01229454
The Pathway Tools software, Bioinformatics, vol.18, issue.Suppl 1, pp.225-257, 2002. ,
DOI : 10.1093/bioinformatics/18.suppl_1.S225