The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications

We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic ‘p-distance tree’ using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

International audienceReconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements , and protein divergence into a single evolutionary framework

Light-driven processes: key players of the functional biodiversity in microalgae

International audienc

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities

INGENIERIE DES ACIDES NUCLEIQUES SUR ORDINATEUR PAR UN ALGORITHME NOVATEUR PERMETTANT L'OPTIMISATION DE LA SEQUENCE DES BASES

CETTE THESE S'INSCRIT DANS L'ETUDE DE L'INFLUENCE DE LA SEQUENCE DE L'ADN SUR SA STRUCTURE ET SES INTERACTIONS AVEC D'AUTRES MOLECULES. LE NOMBRE DE SEQUENCES POSSIBLES POUR UN FRAGMENT D'ADN DONNE CROIT EXPONENTIELLEMENT AVEC SA TAILLE ET IL DEVIENT VITE IMPOSSIBLE D'ETUDIER EXHAUSTIVEMENT UN TEL ENSEMBLE. L'OBJECTIF DE CE TRAVAIL EST DE CONTOURNER L'OBSTACLE COMBINATOIRE GRACE A L'INTRODUCTION D'UNE SEQUENCE EVOLUTIVE ET DE DETERMINER AINSI LES SEQUENCES LES PLUS APTES A SUBIR UNE DEFORMATION DONNEE OU FAVORISANT UNE INTERACTION DONNEE. CETTE TECHNIQUE, BASEE SUR DES CALCULS DE PROPRIETES PHYSIQUES, A PERMIS DE RETROUVER PLUSIEURS RESULTATS EXPERIMENTAUX SUR LA STRUCTURE DE L'ADN. PREMIEREMENT, LES SEQUENCES DE TYPE (RY) N SONT LES PLUS APTES A SUBIR LA TRANSITION ALLOMORPHE DE LA FORME B VERS LA FORME Z. DEUXIEMEMENT, LES SEQUENCES LES PLUS APTES A SE COURBER SONT DES SEQUENCES DU TYPE (A NT NCG) N. ENFIN, LES SEQUENCES LES PLUS APTES A FORMER UN COMPLEXE AVEC LA NETROPSINE COMPORTENT DES PAIRES DE BASES A.T AU NIVEAU DU SITE DE FIXATION DE LA NETROPSINE. CETTE METHODE PERMET EGALEMENT L'EXPLORATION DE GENOMES ENTIERS POUR DETERMINER LES SITES FAVORABLES A LA FIXATION DE PROTEINES JOUANT UN ROLE DANS LA REGULATION DE L'EXPRESSION GENETIQUE. NOUS AVONS AINSI EXPLORE DES SEQUENCES GENOMIQUES, POUR DETERMINER LES SITES FAVORABLES A LA FIXATION DE LA TATA-BOX BINDING PROTEIN (TBP). NOUS AVONS RETROUVE DES PROMOTEURS IDENTIFIES EXPERIMENTALEMENT, AINSI QUE LA POSITION DU SITE DE FIXATION DE LA TBP DANS DES SEQUENCES OU LA POSITION DU CODON D'INITIATION DE LA TRANSCRIPTION EST CONNUE. NOUS AVONS AUSSI ESQUISSE UN TRAVAIL SUR LE POSITIONNEMENT DES NUCLEOSOMES ET SUR LA CAPACITE DE COURBURE DANS LES SEQUENCES GENOMIQUES. L'ENSEMBLE DES RESULTATS OBTENUS EST TRES PROMETTEUR ET EN BON ACCORD AVEC LES RESULTATS EXPERIMENTAUX. LA METHODE DEVELOPPEE ICI PEUT DONC CONSTITUER UN APPORT PRECIEUX AUX ALGORITHMES DE DETECTIONS DE REGIONS PROMOTRICES DANS LES GENOMES.PARIS7-Bibliothèque centrale (751132105) / SudocSudocFranceF

Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis

Abstract Background Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only the genome of the S. cerevisiae reference strain has been analyzed so far for pseudogenes. Results We present here the first comparative analysis of pseudogenes within the fully sequenced and annotated genomes of eight yeast species, spanning the entire phylogenetic range of Hemiascomycetes. A total of 871 pseudogenes were found, out of which mutational degradation patterns and consequences on the genetic repertoire of each species could be identified. We found that most pseudogenes in yeasts originate from mutational degradation of gene copies formed after species-specific duplications but duplications of pseudogenes themselves are also encountered. In all yeasts, except in Y. lipolytica, pseudogenes tend to cluster in subtelomeric regions where they can outnumber the number of functional genes from 3 to 16 times. Pseudogenes are generally not conserved between the yeast species studied (except in two cases), consistent with their large evolutionary distances, but tend to be conserved among S. cerevisiae strains. Reiterated pseudogenization of some genes is often observed in different lineages and may affect functions essential in S. cerevisiae, which are, therefore, lost in other species. Although a variety of functions are affected by pseudogenization, there is a bias towards functions involved in the adaptation of the yeasts to their environment, and towards genes of unknown functions. Conclusions Our work illustrates for the first time the formation of pseudogenes in different branches of hemiascomycetous yeasts, showing their limited conservation and how they testify for the adaptation of the yeasts functional repertoires.</p

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries

International audienceMotivation: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. Results: Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes