Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high-throughput sequencing. From outer Oslofjorden, S Norway, nano- and picoplanktonic samples were collected monthly for 2years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta-specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA-sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September-October (autumn) and lowest in April-May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP-3-5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in-depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters. See also the Perspective by Massana
ISSN: 0962-1083

hal-01545321
https://hal.archives-ouvertes.fr/hal-01545321
DOI : 10.1111/mec.13160

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Holoprosencephaly (HPE) is the most common congenital cerebral malformation, characterized by impaired forebrain cleavage and midline facial anomalies. Heterozygous mutations in 14 genes have been associated with HPE, and are often inherited from an unaffected parent underlying complex genetic bases. It is now emerging that HPE may result from a combination of multiple genetic events, rather than from a single heterozygous mutation. To explore this hypothesis, we undertook whole exome sequencing (WES) and targeted high-throughput sequencing approaches to identify mutations in HPE subjects. We report here two HPE families in which two mutations are implicated in the disease. In the first family presenting two fetuses with alobar and semi-lobar HPE, we found mutations in two genes involved in HPE, SHH and DISP1, inherited respectively from the father and the mother. The second reported case is a family with a 9-year old girl presenting lobar HPE, harbouring two compound heterozygous mutations in DISP1. Together, these cases of digenic inheritance SHH/DISP1 and autosomal recessive HPE suggest that in some families, several genetic events are necessary to cause HPE. This study highlights the complexity of HPE inheritance and has to be taken into account by clinicians to improve HPE genetic counseling.
ISSN: 0009-9163

hal-01259228
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259228
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259228/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01259228/file/Complex%20mode%20of%20inheritance%20in%20holoprosencephaly_accepted.pdf
DOI : 10.1111/cge.12722

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD
Résumé : Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.
Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale.
https://tel.archives-ouvertes.fr/tel-01405400

NNT : 2015YANE0005
tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400/document
https://tel.archives-ouvertes.fr/tel-01405400/file/these_-_tinaut.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Genetics and molecular biology have been instrumental for a better understanding of heritable defects causing human infertility over the past decades. More recently, the field of reproductive biology has harnessed genome biological approaches to gain insight into molecular processes underlying normal and pathological gametogenesis and gamete function. We are currently witnessing yet another quantum leap in our ability to monitor the flow of information from the genome via the transcriptome to the proteome: tiling arrays that cover both strands of a given target genome and RNA-Seq, a method based on ultra-high throughput DNA sequencing, enable us to study noncoding and protein-coding transcripts with unprecedented precision and depth at a reasonable cost. These technologies have spawned a thriving discipline within the bioinformatics field that employs information technology for managing and interpreting biological high-throughput data. This review outlines database projects and online analysis tools useful for life scientists in general and discusses in detail selected projects that have specifically been developed for researchers and clinicians in the field of reproductive biology. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.
ISSN: 0006-3002

hal-00877444
https://hal.archives-ouvertes.fr/hal-00877444
DOI : 10.1016/j.bbadis.2012.05.018
PUBMED : 22687534

Éditeur(s) : Nature Publishing Group
Résumé : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
Isme Journal (1751-7362) (Nature Publishing Group), 2013-10 , Vol. 7 , N. 10 , P. 1985-1996

Droits : 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13
http://archimer.ifremer.fr/doc/00160/27117/28369.pdf
DOI:10.1038/ismej.2013.90
http://archimer.ifremer.fr/doc/00160/27117/

Éditeur(s) : HAL CCSD American Society for Biochemistry and Molecular Biology
Résumé : International audience
The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.
ISSN: 1535-9476

hal-00682837
https://hal.archives-ouvertes.fr/hal-00682837
DOI : 10.1074/mcp.M111.012682
PUBMED : 21997732

Éditeur(s) : HAL CCSD
Résumé : The bacterial microbiota of ants (Hymenoptera: Formicidae) is known to have a defensive role in social insects, particularly for leaf-cutting ants (Formicidae: Attini) due to the use of antimicrobial molecules produced by cuticular actinobacteria. In this thesis, we studied the bacterial microbiota of ants in French Guyana using different approaches based on natural products chemistry and molecular ecology. The first chapter describes the isolation, identification, culture and biological evaluations of 43 cuticular actinobacteria. Antagonism bioassays of isolated strains and antibiotic activities of the culture extracts against human pathogens are presented as well as the identification of an antimicrobial cyclic dipeptide (Cyclo (LPro-LPhe)) isolated from a strain close to Streptomyces thioluteus. Moreover, the implementation of molecular networks applied to UPLC/MS/MS analysis of actinobacterial cocultures allowed us to explore the diversity of metabolites produced under these conditions. The second chapter presents a methodological study to evaluate the capacity of four DNA extraction methods, in terms of richness and composition of the cuticular bacterial microbiota, in high-throughput sequencing from Atta cephalotes and Pseudomyrmex penetrator. The results of metabarcoding highlight two methods of extraction and reveal inter- and intraspecific differences in the composition of cuticular bacterial communities. Finally, chapter three describes the composition of the cuticular bacterial microbiota of Camponotus femoratus and Crematogaster levior in ant garden and the results reveal the acquisition in the environment of a part of the microbiota. In parallel, metabolomic analyses of ant’s cuticle show, on the contrary, a greater specificity related to the ant species. Future researches focusing on statistical analysis strategies combining metabarcoding and metabolomics data are discussed.
Le microbiote bactérien cuticulaire des fourmis (Hymenoptera : Formicidae) est connu pour avoir un rôle défensif chez ces insectes sociaux, notamment chez les fourmis attines (Formicidae : Attini) grâce l’utilisation de molécules antimicrobiennes produites par des actinobactéries cuticulaires. Dans le cadre de cette thèse, nous avons étudié le microbiote bactérien des fourmis de Guyane en utilisant différentes approches en chimie des produits naturels et en écologie moléculaire. Le premier chapitre décrit l’isolement, l’identification, la culture et l’évaluation biologique de 43 actinobactéries cuticulaires de fourmis de Guyane. Les tests d’antagonismes des souches isolées et l’activité antibiotique des extraits de culture contre des micro-organismes pathogènes humains sont présentés ainsi que l’identification d’un dipeptide cyclique (Cyclo(LPro-LPhe)) antimicrobien qui a été isolé à partir d’une souche proche de Streptomyces thioluteus. Par ailleurs, la mise en œuvre de réseaux moléculaires appliqués à une analyse par UPLC/MS/MS de cocultures d’actinobactéries a permis d’explorer la diversité des métabolites produits dans ces conditions. Le deuxième chapitre présente une étude méthodologique pour comparer quatre méthodes d’extraction d’ADN, en termes de richesse et de composition du microbiote bactérien cuticulaire, par séquençage haut débit à partir des espèces Atta cephalotes et Pseudomyrmex penetrator. Les résultats du métabarcoding ADN mettent en lumière deux méthodes d’extraction et révèlent des différences inter- et intraspécifiques dans la composition des communautés bactériennes cuticulaires. Enfin, le chapitre trois décrit la composition du microbiote bactérien cuticulaire des espèces Camponotus femoratus et Crematogaster levior dans les jardins de fourmis. Les résultats soulignent l’acquisition d’une partie du microbiote dans l’environnement. En parallèle l’analyse métabolomique des cuticules montre à contrario une plus grande spécificité liée à l’espèce de fourmi. Les recherches futures axées sur les stratégies d’analyses statistiques combinant le métabarcoding et la métabolomique sont discutées.
https://tel.archives-ouvertes.fr/tel-01537793

NNT : 2017YANE0003
tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793
https://tel.archives-ouvertes.fr/tel-01537793/document
https://tel.archives-ouvertes.fr/tel-01537793/file/thesecarolinebirer.pdf

Éditeur(s) : HAL CCSD BioScientifica
Résumé : International audience
Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testis-specific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation during spermatogenesis by comparing the testicular transcriptome and proteome. We also discuss the recent development and use of new transcriptomic approaches that provide a better proxy for the proteome, from both qualitative and quantitative perspectives. Finally, we provide illustrations of how testis-derived transcriptomic and proteomic data can be integrated to address new questions and how the 'proteomics informed by transcriptomics' technique, by combining RNA-seq and MS-based proteomics, can contribute significantly to the discovery of new protein-coding genes or new protein isoforms expressed during spermatogenesis.
ISSN: 1470-1626

hal-01214005
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005/file/Linking%20transcriptomics%20and%20proteomics%20in%20spermatogenesis.pdf
DOI : 10.1530/REP-15-0073

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.
ISSN: 1932-6203

hal-01190578
https://hal.archives-ouvertes.fr/hal-01190578
PRODINRA : 209109
PUBMED : 23560107
DOI : 10.1371/journal.pone.0060799