Éditeur(s) : HAL CCSD
Résumé : International audience
Motivation: Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports. Availability and Implementation: Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www.outils.genomique.biologie.ens.fr/aozan/. Aozan source code is available on GitHub: https://github.com/GenomicParisCentre/aozan.
Bioinformatics

hal-01545317
https://hal.archives-ouvertes.fr/hal-01545317
DOI : 10.1093/bioinformatics/btx154

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The distribution of the lagoon cockle Cerastoderma glaucum is strongly fragmented and usually restricted to isolated, shallow and nontidal lagoons. A high level of genetic structuring was found among the European populations of this species based on mtDNA (COI) sequences, as well as allozymic and microsatellite markers. However, the strengths and geographic locations of the major divisions differed among markers. In the present study we characterized the diversity of a new, potentially universal exon-primed intron-crossing marker, i34, for 17 C. glaucum populations. Allele frequency data at the i34 locus were informative and relevant with respect to geography. Multivariate analyses of new data together with previously published microsatellites confirmed the divergent character of the Ionian Sea and the Aegean-Ponto-Caspian populations, but also revealed the existence of a genetic cline from the Bay of Biscay to the Baltic Sea. Some noncongruent patterns among loci were detected, which may reflect either differential introgression along the genome at the hypothetical contact zone, or selective sweeps. This strong genetic differentiation, and the occurrence of private alleles, may hint at the presence of cryptic species within C. glaucum.
ISSN: 0260-1230

hal-01444646
https://hal.archives-ouvertes.fr/hal-01444646
DOI : 10.1093/mollus/eyw019

Éditeur(s) : HAL CCSD American Academy of Pediatrics
Résumé : International audience
Vitamin D is an essential hormone for calcium gut absorption. It is also involved in child growth, cancer prevention, immune system responses, and tooth formation. Due to inadequate vitamin D intake and/or decreased sunlight exposure, vitamin D deficiency has resurfaced in developed countries despite known inexpensive and effective preventive methods. Vitamin D deficiency is a common cause of rickets, a condition that affects bone development in children and that can have serious dental complications. Deficiency during pregnancy can cause enamel hypoplasia of primary teeth. Enamel regeneration is currently impossible; hypoplasia is therefore irreversible, and once affected, teeth are prone to fast caries development. Deficiency during early childhood can affect permanent teeth and ensuing caries can sometimes lead to tooth loss at a young age. Oral manifestations of rickets should be diagnosed early by both physicians and dentists to prevent severe dental complications. This case study presents 2 young girls with rickets in early childhood who suffered from subsequent serious tooth decay.
ISSN: 0031-4005

hal-01545477
https://hal.archives-ouvertes.fr/hal-01545477
DOI : 10.1542/peds.2013-0733

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Over the last few decades, sessile benthic organisms from the Mediterranean Sea have suffered from the global warming of the world's oceans, and several mass mortality events were observed during warm summers. It has been hypothesized that mortality could have been due to a nutrient (food) shortage following the stratification of the water column. However, the symbiotic gorgonian Eunicella singularis has also presented a locally exceptional mortality, despite its autotrophic capacities through the photosynthesis of its dinoflagellate symbionts. Thus, this study has experimentally investigated the response of E. singularis to a thermal stress (temperature increase from 18 to 26 degrees C), with colonies maintained more than 2 months under four nutritional diets: autotrophy only (AO), autotrophy and inorganic nitrogen addition (AN), autotrophy and heterotrophy (AH), heterotrophy only (HO). At 18 degrees C, and contrary to many other anthozoans, supplementation of autotrophy with either inorganic nitrogen or food (heterotrophy) had no effect on the rates of respiration, photosynthesis, as well as in the chlorophyll, lipid and protein content. In the dark, heterotrophy maintained the gorgonian's metabolism, except a bleaching (loss of pigments), which did not affect the rates of photosynthesis. At 24 degrees C, rates of respiration, and photosynthesis significantly decreased in all treatments. At 26 degrees C, in addition to a decrease in the lipid content of all treatments, a bleaching was observed after 1 week in the AO treatment, while the AH and AN treatments resisted three weeks before bleaching. These last results suggest that, temperatures above 24 degrees C impair the energetic reserves of this species and might explain the mortality events in the Mediterranean.
ISSN: 1932-6203

hal-01546169
https://hal.archives-ouvertes.fr/hal-01546169
DOI : 10.1371/journal.pone.0064370

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.
ISSN: 2041-1723

hal-01545322
https://hal.archives-ouvertes.fr/hal-01545322
DOI : 10.1038/ncomms3091

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Beggiatoaceae, giant sulphur-oxidizing bacteria, are well known to occur in cold and temperatewaters, as well as hydrothermal vents, where they form dense mats on the floor.However, they have never been described in tropical marine mangroves. Here, we describetwo new species of benthic Beggiatoaceae colonizing a marine mangrove adjacent to mangroveroots. We combined phylogenetic and lipid analysis with electron microscopy in orderto describe these organisms. Furthermore, oxygen and sulphide measurements in and exsitu were performed in a mesocosm to characterize their environment. Based on this, two new species, Candidatus Maribeggiatoa sp. and Candidatus Isobeggiatoa sp. inhabiting tropical marine mangroves in Guadeloupe were identified. The species identified as CandidatusMaribeggiatoa group suggests that this genus could harbour a third cluster with organisms ranging from 60 to 120 μm in diameter. This is also the first description of an Isobeggiatoa species outside of Arctic and temperate waters. The multiphasic approach also gives information about the environment and indications for the metabolism of these bacteria. Our study shows the widespread occurrence of members of Beggiatoaceae family and provides new insight in their potential role in shallow-water marine sulphide-rich environments such as mangroves.
ISSN: 1932-6203

hal-01205641
https://hal.univ-antilles.fr/hal-01205641
https://hal.univ-antilles.fr/hal-01205641/document
https://hal.univ-antilles.fr/hal-01205641/file/Beggiatoa%20Plosone2015.pdf
DOI : 10.1371/journal.pone.0117832

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Associations between marine invertebrates and chemoautotrophic bacteria constitute a wide field for the study of symbiotic associations. In these interactions, symbiont transmission must represent the cornerstone allowing the persistence of the association throughout generations. Within Bivalvia, in families such as Solemyidae or Vesicomyidae, symbiont transmission is undoubtedly vertical. However, in Lucinidae, symbiont transmission is described in the literature as 'environmental', symbionts being acquired from the environment by the new host generations. Hence, if there is transmission, symbionts should be transmitted from adults to juveniles via the environment. Consequently, we should observe a release of the symbiont by adults. We attempted to detect such a release within two Lucinidae species of the genus Codakia. We sampled 10 Codakia orbicularis and 20 Codakia orbiculata distributed in 10 crystallizing dishes containing filtered seawater. During 1 month of investigation, we analyzed water of the dishes in order to detect any release of a symbiont using catalyzed report deposition-FISH techniques. For 140 observations realized during this period, we did not observe any release of symbionts. This suggests that the idea of host-to-host passage in Lucinidae is inaccurate. We could therefore consider that the transmission mode from generation to generation does not occur within Lucinidae, symbiosis appearing to be advantageous in this case only for the host, and constitutes an evolutionary dead-end for the bacteria.
ISSN: 0168-6496

hal-00751560
https://hal.univ-antilles.fr/hal-00751560
DOI : 10.1111/j.1574-6941.2008.00626.x

Éditeur(s) : HAL CCSD Magnolia Press
Résumé : International audience
The species belonging to the trechine genus Adriaphaenops Noesske, 1928 are studied. As a result, seven currently known and five newly described species are recognized. Morphological characters of the habitus (especially the shape of head and pronotum) as well as male genitalia are widely used to delimit the species. The following new species are described: A. albanicus sp. nov. (Albania, Shkoder, Boga, Thate Mts.), A. jasminkoi sp. nov. (Bosnia & Hercegovina, Nevesinje, Novakova pecina cave), A. mlejneki sp. nov. (Montenegro, Gornje Stravce, Kucke planine Mts.), A. njegosiensis sp. nov. (Montenegro, Cetinje, Cetinjska pecina cave) and A. rumijaensis sp. nov. (Montenegro, Virpazar, Rumija Mts.). Lectotype for A. stirni (Pretner, 1959) is designated. Data on the distribution and ecology of new taxa, complemented with descriptions of the type localities are provided. Key to the identification of all twelve Adriaphaenops species, as well as a key of all hitherto known aphaenopsoid Trechini genera from Dinarides are also given.
ISSN: 1175-5326

hal-01544473
https://hal.archives-ouvertes.fr/hal-01544473
DOI : 10.11646/zootaxa.4205.6.1

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Genetic approaches have shown that several genes could modify caries susceptibility; AmelogeninX (AMELX) has been repeatedly designated. Here, we hypothesized that AMELX mutations resulting in discrete changes of enamel microstructure may be found in children with a severe caries phenotype. In parallel, possible AMELX mutations that could explain resistance to caries may be found in caries-free patients. In this study, coding exons of AMELX and exon-intron boundaries were sequenced in 399 individuals with extensive caries (250) or caries-free (149) individuals from nine French hospital groups. No mutation responsible for a direct change of amelogenin function was identified. Seven single-nucleotide polymorphisms (SNPs) were found, 3 presenting a high allele frequency, and 1 being detected for the first time. Three SNPs were located in coding regions, 2 of them being non-synonymous. Both evolutionary and statistical analyses showed that none of these SNPs was associated with caries susceptibility, suggesting that AMELX is not a gene candidate in our studied population.
ISSN: 0022-0345

hal-01545481
https://hal.archives-ouvertes.fr/hal-01545481
DOI : 10.1177/0022034513482941

Éditeur(s) : HAL CCSD Station Biologique
Résumé : International audience
This study deals with temporal variations in eel diet Anguilla anguilla sampled at each of the four seasons in the Languedocian Prévost lagoon (Gulf of Lion) from Autumn 1998 to Summer 1999. The following feeding indices were calculated based on observations of 12 categories of prey found in the contents of full stomachs: coefficient of vacuity CV, degree of fullness DR, occurrence frequency PP, relative abundance N (in %) and relative weight P (in %). The interpretation of results is also based on the Costello's method (1990) which combines PP and N. Anguilla anguilla mainly feeds on benthic organisms, primarily Gammarus gr. locusta, Polychaeta, insect larvae, small fish. Based on variations in eel diet, seasonal influence is illustrated by a decrease in feeding activity in summer which gradually increases during the following seasons. The good trophic quality available to eels in the Prévost lagoon depends on its hydrodynamics which is directly related to the movement of water entering and leaving lagoon by a short communication with the sea. This water movement accelerates the enrichment and production processes of this ecosystem. Changes observed during the four seasons illustrate an opportunistic type of feeding behaviour. Eels consume the most available benthic prey. They favour the importance of the prey at a given moment without using a particular feeding strategy like specialisation or generalisation. Thus, eel adapts its diet in adjusting available energy resources in the ecosystem. Because of this, the lagoon-resident species Anguilla anguilla is an obvious indirect bioindicator of the trophic capacity and present level of confinement in the brackish water lagoon ecosystem of Prévost.
ISSN: 0007-9723

hal-00753021
https://hal.univ-antilles.fr/hal-00753021

Éditeur(s) : HAL CCSD Magnolia Press
Résumé : International audience
Hydroporus galloprovincialis sp. n. is described from Jouques, north-east of Aix-en-Provence in south-eastern France (Provence). The new species belongs to the Hydroporus memnonius-group, within which it is the only ascertained normandi-complex species of the French fauna. The habitat (small springs) and morphological features of the species suggest a semi-subterranean life style. It can be separated from the other species of the complex notably by its more elongated and parallel-sided habitus, by its wider pronotum and flatter dorsal surface, and furthermore differs from H. normandi Regimbart, 1903 by a different shape of the gonocoxa. Illustrations are provided for other described normandi-complex species and subspecies for comparison. Analyses of partial cox1 sequences indicate that the three sampled H. normandi-complex species (H. galloprovincialis sp. n., H. normandi and H. lluci Fery, 1999) diverged recently; their relationships are unresolved. H. galloprovincialis sp. n. is for the moment the only species of the genus Hydroporus Clairville, 1806 endemic to continental France.
ISSN: 1175-5326

hal-01544484
https://hal.archives-ouvertes.fr/hal-01544484
DOI : 10.11646/zootaxa.3652.4.4

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the ``germ-line multipotency program'' and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.
ISSN: 0027-8424

hal-01544480
https://hal.archives-ouvertes.fr/hal-01544480
DOI : 10.1073/pnas.1514789112

Éditeur(s) : HAL CCSD Nakanishi Printing Co
Résumé : International audience
In Vibrio cholerae, the etiological agent of cholera, most of the virulence genes are located in two pathogenicity islands, named TCP (Toxin-Co-regulated Pilus) and CTX (Cholera ToXins). For each V. cholerae pathogenicity gene, we retrieved every primer published since 1990 and every known allele in order to perform a complete in silico survey and assess the quality of the PCR primers used for amplification of these genes. Primers with a melting temperature in the range 55-60 degrees C against any target sequence were considered valid. Our survey clearly revealed that two thirds of the published primers are not able to properly detect every genetic variant of the target genes. Moreover, the quality of primers did not improve with time. Their lifetime, i.e. the number of times they were cited in the literature, is also not a factor allowing the selection of valid primers. We were able to improve some primers or design new primers for the few cases where no valid primer was found. In conclusion, many published primers should be avoided or improved for use in molecular detection tests, in order to improve and perfect specificity and coverage. This study suggests that bioinformatic analyses are important to validate the choice of primers.
ISSN: 1342-6311

hal-01546178
https://hal.archives-ouvertes.fr/hal-01546178
DOI : 10.1264/jsme2.ME11317

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
We review current knowledge of axial skeleton biology in Acipenseriformes with the aim to know whether available data can help in understanding axial anomalies (anomalies of the vertebral column) in reared sturgeons or if further investigations are needed prior to undertake such analysis. In particular, accurate data on axial skeleton development, structure and mineralization are required to understand these pathologies. We show that such knowledge is fragmented and incomplete when compared to the information available in teleost fish. In Acipenseriformes, we only know that (i) the axial skeleton morphology is highly distinctive, as mostly cartilaginous, (ii) the vertebrae are composed of several elements organized around a persistent and unconstricted notochord, and (iii) mineralization only concerns a few of these elements and occurs late in ontogeny, but virtually no descriptions demonstrating the presence of bone (perichondral, membranous...) or mineralized cartilage is available in the literature. In addition, few studies concern axial anomalies in the wild or in rearing conditions, and the determinism of these pathologies is largely unknown. This is in contrast with the numerous studies dealing with the axial skeleton and its anomalies in many farmed teleost species, in which axial anomalies can result from numerous factors, such as unfavourable abiotic conditions, inappropriate nutrition and genetic factors. However, even if some parallels can be established between teleosts and sturgeons, it appears that current knowledge of the axial skeleton in teleosts may not help much in the study of axial anomalies in sturgeons. Knowledge of axial skeleton biology in sturgeon has to be therefore deeply improved prior to undertake investigations focusing on these pathologies.
ISSN: 0175-8659

hal-01545478
https://hal.archives-ouvertes.fr/hal-01545478
DOI : 10.1111/jai.12525

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely ``processually equivalent'' entities, ``processually versatile'' entities, and ``stabilized'' entities.
ISSN: 0169-3867

hal-01544796
https://hal.archives-ouvertes.fr/hal-01544796
DOI : 10.1007/s10539-012-9350-2

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Grande Terre of New Caledonia is enclosed by one of the longest barrier reefs in the world. For the first time, the fore-reef slopes of this barrier reef have been sampled by dredging, from 40 to 320 m deep, in order to analyze their sedimentological and biological characteristics. The rocks and sediments can be divided into seven sedimentary facies: bindstones dominated by coralline algal crusts, bindstones dominated by foraminiferal crusts, bindstones dominated by bryozoan crusts, coral framestones, bindstones and interstratified packstones rich in skeletal debris, packstones/wackestones and grainstones rich in rock gravels. Radiocarbon dating performed on encrusting organisms (coralline algae and acervulinids) and corals provide ages relatively young. These ages confirm that the encrusting organisms are modern and the corals mainly dated of Holocene are reworked due to the instability of the fore-reef slopes, especially during storms. Because the biological assemblages are distributed according to a bathymetric range depending on light intensity, a model of distribution of modern encrusting calcareous organisms can be proposed from our observations and analyses. From the upper reef slopes to approximately 90 m, thick coralline algal crusts are dominant and distributed in three groups. Group C, the shallowest parts of the fore slopes, is mainly characterized by mastophorids (Hydrolithon reinboldii, H. cf. munitum, Lithoporella melobesoides, Aethesolithon cf. problematicum, Neogoniolithon sp. and undetermined species) and lithophylloids (Lithophyllum sp., L. pustulatum). Group B, composed of lithophylloids (Lithophyllum sp., L. cf. kotschyanum, L. cf. moluccence, L. pustulatum), Mesophyllum sp. and Peyssonnelia sp. occurs from 15 to 40 m. Group A, rich in Mesophyllum sp., M. cf. mesomorphum, Peyssonnelia sp. and Sporolithon sp. is characteristic of deep reef slopes up to 90 m. Below approximately 90 m, when the light intensity decreases, the encrusting foraminifera acervulinids progressively replace the coralline algal crusts. Such a model is particularly useful to interpret and reconstruct the past Quaternary reef environments rich in crusts of coralline algae and/or foraminifera.
ISSN: 0025-3227

hal-00393705
https://hal.archives-ouvertes.fr/hal-00393705
DOI : 10.1016/j.margeo.2007.12.002

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal-bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur-oxidizing g-Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide-rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur-oxidizing ability of the bacteria has been assessed by genetic investigation on alpha-subunit of the adenosine-5_- phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur-oxidizing g-Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota.
ISSN: 1462-2912

hal-00715219
https://hal.univ-antilles.fr/hal-00715219
DOI : 10.1111/j.1462-2920.2010.02309.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The temperate symbiotic sea anemone Anemonia viridis, a member of the Cnidaria phylum, is a relevant experimental model to investigate the molecular and cellular events involved in the preservation or in the rupture of the symbiosis between the animal cells and their symbiotic microalgae, commonly named zooxanthellae. In order to increase research tools for this model, we developed a primary culture from A. viridis animal cells. By adapting enzymatic dissociation protocols, we isolated animal host cells from a whole tentacle in regeneration state. Each plating resulted in a heterogeneous primary culture consisted of free zooxanthellae and many regular, small rounded and adherent cells (of 3-5 mu m diameter). Molecular analyses conducted on primary cultures, maintained for 2 weeks, confirmed a specific signature of A. viridis cells. Further serial dilutions and micromanipulation allowed us to obtain homogenous primary cultures of the small rounded cells, corresponding to A. viridis ``epithelial-like cells''. The maintenance and the propagation over a 4 weeks period of primary cells provide, for in vitro cnidarian studies, a preliminary step for further investigations on cnidarian cellular pathways notably in regard to symbiosis interactions.
ISSN: 0920-9069

hal-01546173
https://hal.archives-ouvertes.fr/hal-01546173
DOI : 10.1007/s10616-013-9566-2

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
The main familial focal epilepsies are autosomal dominant nocturnal frontal lobe epilepsy, familial temporal lobe epilepsy and familial focal epilepsy with variable foci. A frameshift mutation in the DEPDC5 gene (encoding DEP domain-containing protein 5) was identified in a family with focal epilepsy with variable foci by linkage analysis and exome sequencing. Subsequent pyrosequencing of DEPDC5 in a cohort of 15 additional families with focal epilepsies identified 4 nonsense mutations and 1 missense mutation. Our findings provided evidence of frequent (37%) loss-of-function mutations in DEPDC5 associated with a broad spectrum of focal epilepsies. The implication of a DEP (Dishevelled, Egl-10 and Pleckstrin) domain-containing protein that may be involved in membrane trafficking and/or G protein signaling opens new avenues for research.
ISSN: 1061-4036

hal-01544763
https://hal.archives-ouvertes.fr/hal-01544763
DOI : 10.1038/ng.2601

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Background: Researchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability. Methodology/Principal Findings: We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets. Conclusions/Significance: This approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.
ISSN: 1932-6203

hal-01544766
https://hal.archives-ouvertes.fr/hal-01544766
DOI : 10.1371/journal.pone.0051263