Fungal diversity revisited: 2.2 to 3.8 million species, Microbiol. Spectrum, vol.5, 2017. ,
MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Res, vol.42, pp.699-704, 2014. ,
, Nucleic Acids Research, vol.48, issue.5, p.2329, 2020.
The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species, GigaScience, vol.7, 2018. ,
Tempo and mode of genome evolution in the budding yeast subphylum, Cell, vol.175, pp.1533-1545, 2018. ,
Evolution of pathogenicity and sexual reproduction in eight Candida genomes, Nature, p.657, 2009. ,
Genome evolution in yeasts, Nature, vol.430, pp.35-44, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00104411
Fungal genomes and insights into the evolution of the kingdom, Microbiol. Spectrum, vol.5, 2017. ,
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors, 2007. ,
, Genome Biol, vol.8, p.223
Low-complexity regions within protein sequences have position-dependent roles, BMC Syst. Biol, vol.4, pp.43-43, 2010. ,
Life with 6000 Genes, Science, vol.274, p.546, 1996. ,
Approaches to fungal genome annotation, Mycology, vol.2, pp.118-141, 2011. ,
Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes, Cell, vol.44, pp.283-292, 1986. ,
An analysis of 5 -noncoding sequences from 699 vertebrate messenger RNAs, Nucleic Acids Res, vol.15, pp.8125-8148, 1987. ,
Mechanism and regulation of protein synthesis in Saccharomyces cerevisiae, Genetics, vol.203, pp.65-107, 2016. ,
Deciphering the rules by which 5 -UTR sequences affect protein expression in yeast, Proc. Natl Acad. Sci. U.S.A, vol.110, pp.2792-2801, 2013. ,
Deep learning of the regulatory grammar of yeast 5 untranslated regions from 500,000 random sequences, Genome Res, vol.27, pp.2015-2024, 2017. ,
Inverted translational control of eukaryotic gene expression by ribosome collisions, PLoS Biol, vol.17, p.3000396, 2019. ,
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes, Genome Biol, vol.20, p.162, 2019. ,
Life cycle adapted upstream open reading frames (uORFs) in Trypanosoma congolense: A post-transcriptional approach to accurate gene regulation, PLoS One, vol.13, p.201461, 2018. ,
General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4, Proc. Natl Acad. Sci. U.S.A, vol.115, pp.1829-1838, 2018. ,
A single inhibitory upstream open reading frame (uORF) is sufficient to regulate Candida albicans GCN4 translation in response to amino acid starvation conditions, RNA, vol.20, pp.559-567, 2014. ,
Translation initiation from conserved Non-AUG codons provides additional layers of regulation and coding capacity, mBio, vol.8, pp.844-00817, 2017. ,
Regulation of plant translation by upstream open reading frames, Plant Sci, vol.214, pp.1-12, 2014. ,
Gene expression regulation by upstream open reading frames and human disease, PLos Genet, vol.9, pp.1003529-1003529, 2013. ,
Translational efficiency of a Non-AUG initiation codon is significantly affected by its sequence context in yeast, J. Biol. Chem, vol.283, pp.3173-3180, 2008. ,
Translational control by 5 -untranslated regions of eukaryotic mRNAs, Science, vol.352, pp.1413-1416, 2016. ,
The regulatory potential of upstream open reading frames in eukaryotic gene expression, Wiley Interdiscip. Rev.: RNA, vol.5, pp.765-768, 2014. ,
Conformational differences between open and closed states of the eukaryotic translation initiation complex, Mol. Cell, vol.59, pp.399-412, 2015. ,
Structural insights into the mechanism of scanning and start codon recognition in eukaryotic translation initiation, Trends Biochem. Sci, vol.42, pp.589-611, 2017. ,
Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition, p.39273, 2018. ,
Introns in Cryptococcus, Mem. Inst. Oswaldo Cruz, vol.113, p.170519, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02649397
Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway, PLoS Genet, vol.9, p.1003686, 2013. ,
Stalled spliceosomes are a signal for RNAi-mediated genome defense, Cell, vol.152, pp.957-968, 2013. ,
Introns protect eukaryotic genomes from transcription-Associated genetic instability, Mol. Cell, vol.67, pp.608-621, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01788654
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation, PLos Genet, vol.10, p.1004261, 2014. ,
Intron retention-dependent gene regulation in Cryptococcus neoformans, Sci. Rep, vol.6, p.32252, 2016. ,
Construction of a set of convenient saccharomyces cerevisiae strains that are isogenic to S288C, Yeast, vol.11, pp.53-55, 1995. ,
, Med Mycol, pp.275-304, 2006.
UGE1 and UGE2 regulate the UDP-glucose/UDP-galactose equilibrium in Cryptococcus neoformans, Eukaryot. Cell, vol.7, pp.2069-2077, 2008. ,
Quality control of transcription start site selection by nonsense-mediated-mRNA decay, 2015. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01404014
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol, vol.14, pp.36-36, 2013. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, 2011. ,
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, vol.324, p.218, 2009. ,
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster, p.1179, 2013. ,
riboviz: analysis and visualization of ribosome profiling datasets, BMC Bioinformatics, vol.18, pp.461-461, 2017. ,
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nat. Protoc, vol.11, p.1650, 2016. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-842, 2010. ,
, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2018.
In: ggplot2: Elegant Graphics for Data Analysis, 2016. ,
dplyr: A Grammar of Data Manipulation, 2018. ,
cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2, 2018. ,
2017) ggseqlogo: A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, pp.2947-2948, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00206210
Codon usage influences the local rate of translation elongation to regulate Co-translational protein folding, Mol. Cell, vol.59, pp.744-754, 2015. ,
Ensembl genomes 2018: an integrated omics infrastructure for non-vertebrate species, Nucleic Acids Res, vol.46, pp.802-808, 2018. ,
Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe, Sci. Rep, vol.7, p.10331, 2017. ,
Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans, Genome Res, vol.24, pp.963-973, 2014. ,
The candida genome database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data, Nucleic Acids Res, vol.45, pp.592-596, 2017. ,
Translation inhibitors cause abnormalities in ribosome profiling experiments, Nucleic Acids Res, vol.42, p.134, 2014. ,
Accounting for experimental noise reveals that mRNA Levels, amplified by post-transcriptional processes, largely determine Steady-State protein levels in yeast, PLos Genet, vol.11, p.1005206, 2015. ,
Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation, Cell Rep, vol.14, pp.1787-1799, 2016. ,
Saccharomyces genome database: the genomics resource of budding yeast, Nucleic Acids Res, vol.40, pp.700-705, 2012. ,
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs, Nucleic Acids Res, vol.47, pp.807-811, 2019. ,
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees, Nucleic Acids Res, vol.41, pp.377-386, 2013. ,
FungiDB: an integrated bioinformatic resource for fungi and oomycetes, J. Fungi, vol.4, p.39, 2018. ,
A new system for naming ribosomal proteins, Curr. Opin. Struct. Biol, vol.24, pp.165-169, 2014. ,
Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE, RNA Biol, vol.12, pp.525-537, 2015. ,
Dual modes of natural selection on upstream open reading frames, Mol. Biol. Evol, vol.24, pp.1744-1751, 2007. ,
Translational regulation of GCN4 and the general amino acid control of yeast, Annu. Rev. Microbiol, vol.59, pp.407-450, 2005. ,
General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4, Proc. Natl Acad. Sci. U.S.A, vol.115, p.1829, 2018. ,
rco-3, a gene involved in glucose transport and conidiation in Neurospora crassa, Genetics, vol.146, pp.499-508, 1997. ,
Sucrose-induced translational repression of plant bZIP-type transcription factors, Biochem. Soc. Trans, vol.33, p.272, 2005. ,
Physical evidence for distinct mechanisms of translational control by upstream open reading frames, EMBO J, vol.20, pp.6453-6463, 2001. ,
NMD: a multifaceted response to premature translational termination, Nat. Rev. Mol. Cell Biol, vol.13, pp.703-712, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00776293
Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing, Genome Res, vol.23, pp.977-987, 2013. ,
Evolutionary changes in the fungal carbamoyl-phosphate synthetase small subunit gene and its associated upstream open reading frame, Fungal Genet. Biol, vol.44, pp.93-104, 2007. ,
Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates Nonsense-Mediated mRNA Decay, Mol. Cell, vol.20, pp.449-460, 2005. ,
Control of mRNA stability in fungi by NMD, EJC and CBC factors through 3 UTR introns, Genetics, p.1133, 0200. ,
The stringency of start codon selection in the filamentous fungus Neurospora crassa, J. Biol. Chem, vol.288, pp.9549-9562, 2013. ,
Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data, Genome Res, vol.28, pp.214-222, 2018. ,
How can the products of a single gene be localized to more than one intracellular compartment?, Trends Cell Biol, vol.5, pp.230-238, 1995. ,
One ticket for multiple destinations: dual targeting of proteins to distinct subcellular locations, Curr. Opin. Plant Biol, vol.6, pp.589-595, 2003. ,
The same Arabidopsis gene encodes both cytosolic and mitochondrial alanyl-tRNA synthetases, Plant Cell, vol.8, pp.1027-1039, 1996. ,
URL : https://hal.archives-ouvertes.fr/hal-02687070
Complex organisation of the 5 -end of the human glycine tRNA synthetase gene, Gene, vol.209, pp.45-50, 1998. ,
, Nucleic Acids Research, vol.48, issue.5, p.2331, 2020.
The HTS1 gene encodes both the cytoplasmic and mitochondrial histidine tRNA synthetases of S. cerevisiae, Cell, vol.46, pp.235-243, 1986. ,
Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans, BMC Genomics, vol.15, p.1069, 2014. ,
Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria, Curr. Genet, vol.55, pp.1-18, 2009. ,
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools, Nucleic Acids Res, vol.47, pp.419-426, 2018. ,
Translating organellar glutamine codons: a case by case scenario?, RNA Biol, vol.6, pp.31-34, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00367450
Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin, Nucleic Acids Res, vol.40, pp.314-322, 2012. ,
In vivo selection of lethal mutations reveals two functional domains in arginyl-tRNA synthetase, RNA, vol.6, pp.434-448, 2000. ,
Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae, Genome Biol, vol.10, p.95, 2009. ,
The proteome of Saccharomyces cerevisiae mitochondria, Proc. Natl Acad. Sci. U.S.A, vol.100, pp.13207-13212, 2003. ,
Saccharomyces cerevisiae possesses a stress-inducible glycyl-tRNA synthetase gene, PLoS One, vol.7, p.33363, 2012. ,
Schizosaccharomyces pombe possesses two paralogous Valyl-tRNA synthetase genes of mitochondrial origin, Mol. Biol. Evol, vol.27, pp.1415-1424, 2010. ,
Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1), Proc. Natl Acad. Sci. U.S.A, vol.107, pp.18056-18060, 2010. ,
Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5, Nucleic Acids Res, vol.40, pp.2898-2906, 2012. ,
Functional elements in initiation factors 1, 1A, and 2? discriminate against poor AUG context and non-AUG start codons, Mol. Cell. Biol, vol.31, pp.4814-4831, 2011. ,
Structural changes enable start codon recognition by the eukaryotic translation initiation complex, Cell, vol.159, pp.597-607, 2014. ,
Loop 2 interactions with Met-tRNA(i) control the accuracy of start codon selection by the scanning preinitiation complex, Proc. Natl Acad. Sci. U.S.A, vol.115, pp.4159-4168, 2018. ,
Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo, EMBO J, vol.22, pp.193-204, 2003. ,
The interaction between eukaryotic initiation factor 1A and eIF5 retains eIF1 within scanning preinitiation complexes, Biochemistry, vol.52, pp.9510-9518, 2013. ,
The eIF1A C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo, EMBO J, vol.24, pp.3588-3601, 2005. ,
) mRNA leader length and initiation codon context determine alternative AUG selection for the yeast gene MOD5, Proc. Natl Acad. Sci. U.S.A, vol.88, p.9789, 1991. ,
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans, Proc. Natl Acad. Sci. U.S.A, vol.106, pp.7507-7512, 2009. ,
Pervasive, coordinated protein-Level changes driven by transcript isoform switching during meiosis, Cell, vol.172, pp.910-923, 2018. ,
Global proteome remodeling during ER stress involves Hac1-Driven expression of long undecoded transcript isoforms, Dev. Cell, vol.46, pp.219-235, 2018. ,
Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins, Nucleic Acids Res, vol.47, pp.5777-5791, 2019. ,
Beyond the triplet code: Context cues transform translation, Cell, vol.167, pp.1681-1692, 2016. ,
Daily magnesium fluxes regulate cellular timekeeping and energy balance, Nature, vol.532, pp.375-379, 2016. ,
Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins, 2019. ,
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes, Nucleic Acids Res, vol.36, pp.861-871, 2008. ,
A transcript-specific eIF3 complex mediates global translational control of energy metabolism, Cell Rep, vol.16, pp.1891-1902, 2016. ,
The S. cerevisiae CLU1 and D. discoideum cluA genes are functional homologues that influence mitochondrial morphology and distribution, J. Cell Sci, vol.111, p.1717, 1998. ,
URL : https://hal.archives-ouvertes.fr/in2p3-01447887
CLUH regulates mitochondrial biogenesis by binding mRNAs of nuclear-encoded mitochondrial proteins, J. Cell Biol, vol.207, pp.213-223, 2014. ,
CLUH regulates mitochondrial metabolism by controlling translation and decay of target mRNAs, J. Cell Biol, vol.216, pp.675-693, 2017. ,
Human-Like eukaryotic translation initiation factor 3 from neurospora crassa, PLoS One, vol.8, p.78715, 2013. ,
The frustrated gene: origins of eukaryotic gene expression, Cell, vol.155, pp.744-749, 2013. ,