Genoscope Center National Of Sequencage

Évry, France

Genoscope Center National Of Sequencage

Évry, France
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Marin J.,French Natural History Museum | Donnellan S.C.,South Australian Museum | Donnellan S.C.,University of Adelaide | Blair Hedges S.,Pennsylvania State University | And 4 more authors.
Journal of Biogeography | Year: 2013

Aim: We investigated the biogeographical history of Australian blindsnakes (Ramphotyphlops) with reference to Australia's palaeoclimatic history over the past 20 Myr, particularly the development of an extensive arid zone over this period. Terrestrial vertebrate lineages dating back to the Miocene or earlier are predicted to display some or all of the following patterns: (1) for taxa including mesic, arid and monsoonal representatives, a mesic distribution should be phylogenetically ancestral; (2) mesic and monsoon tropical lineages should have diverged before the onset of aridification (with arid lineages appearing later); and (3) refuges may have allowed local persistence and diversification of lineages in the monsoon tropical and mesic zones since the mid-Miocene. Location: Continental Australia. Methods: We compiled a molecular data set comprising one mitochondrial and three nuclear genes for 107 individuals belonging to 28 blindsnake species. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference with RAxML and MrBayes, respectively. Divergence times were assessed using multidivtime. Ancestral habitat states (arid and non arid) were reconstructed using the maximum likelihood method implemented in Mesquite. Results: The age of the Australian Ramphotyphlops radiation was estimated at 21.9 Ma (95% credibility interval: 30.2-15.1 Ma). Mesic and monsoon tropical lineages are older than the onset of aridification, with mesic distribution appearing as ancestral on phylogenies. After the onset of aridification, lineages persisted and diversified in mesic, tropical and/or rocky refugia. Arid lineages diversified more recently (< 5 Ma). Main conclusions: Australian blindsnakes join several other Australian squamate lineages with tropical-mesic origins that successfully adapted to the expansion of aridity since the mid-Miocene (c. 17 Ma) and now show evidence of multiple relatively recent evolutionary radiations across Australia. We further demonstrate that localized refugia permitted persistence and diversification of mesic taxa, with arid lineages diversifying much later (< 5 Ma) when the arid zone was well established. © 2012 Blackwell Publishing Ltd.

Koffi K.G.,Roosevelt University | Hardy O.J.,Roosevelt University | Doumenge C.,CIRAD - Agricultural Research for Development | Cruaud C.,Genoscope Center National Of Sequencage | Heuertz M.,Roosevelt University
American Journal of Botany | Year: 2011

Premise of the study: New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests. Methods: We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbcL, and rpl36-infA-rps8) in 377 individuals from 42 populations. Results: Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of S ã o Tom é, did not share any haplotype, indicating allopatric divergence. In Lower Guinea, Gabonese forests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogoou é River, suggesting refuges on both sides of the river bed. Conclusions: The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity. © 2011 Botanical Society of America.

Chan C.-M.,University of Hong Kong | Danchin A.,AMAbiotics SAS | Marliere P.,Genoscope Center National Of Sequencage | Sekowska A.,AMAbiotics SAS
Environmental Microbiology | Year: 2014

Metabolism is prone to produce analogs of essential building blocks in the cell (here named paralogous metabolism). The variants result from lack of absolute accuracy in enzyme-templated reactions as well as from molecular aging. If variants were left to accumulate, the earth would be covered by chemical waste. The way bacteria cope with this situation is essentially unexplored. To gain a comprehensive understanding of Bacillus subtilis sulphur paralogous metabolism, we used expression profiling with DNA arrays to investigate the changes in gene expression in the presence of S-methyl-cysteine (SMeC) and its close analog, methionine, as sole sulphur source. Altogether, more than 200 genes whose relative strength of induction was significantly different depending on the sulphur source used were identified. This allowed us to pinpoint operon ytmItcyJKLMNytmO_ytnIJ_rbfK_ytnLM as controlling the pathway cycling SMeC directly to cysteine, without requiring sulphur oxygenation. Combining genetic and physiological experiments, we deciphered the corresponding pathway that begins with protection of the metabolite by acetylation. Oxygenation of the methyl group then follows, and after deprotection (deacetylation), N-formyl cysteine is produced. This molecule is deformylated by the second deformylase present in B.subtilisDefB, yielding cysteine. This pathway appears to be present in plant-associated microbes. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Heilig R.,Genoscope Center National Of Sequencage
Seminars in Thrombosis and Hemostasis | Year: 2011

Glanzmann thrombasthenia (GT) is the most widely studied inherited disorder of platelets; it is caused by the absence of platelet aggregation due to quantitative and/or qualitative deficiencies of the IIb3 integrin coded by the ITGA2B and ITGB3 genes located at 17q2123. Although platelet count and platelet volume (and morphology) are normal in classic GT, some reports have inferred a role for IIb3 in megakaryocytopoiesis and some novel but rare point mutations in either of the ITGA2B and ITGB3 genes have been associated with an altered platelet production and selective deficiencies in platelet function. This was brought to light by the discovery of mutations at Arg995 in IIb and Asp723 in 3 that lead to platelet anisotropy (increased size variation) and thrombocytopenia. Significantly, Arg995 and Asp723 form a salt linkage binding the cytoplasmic tails of IIb3 together keeping the integrin in a bent resting state. Mutations weakening this link (if not abolishing it) increase the activation state of IIb3 and interfere with megakaryocytopoiesis. Other mutations affecting platelet production involve extracellular but membrane proximal domains of 3. Our purpose is to review the mutations in the ITGA2B and ITGB3 genes that lead to anisotropy and to discuss mechanisms by which this can be brought about. Copyright © 2011 by Thieme Medical Publishers, Inc.

Davis E.E.,Duke University | Zhang Q.,University of Pennsylvania | Liu Q.,University of Pennsylvania | Diplas B.H.,Duke University | And 46 more authors.
Nature Genetics | Year: 2011

Ciliary dysfunction leads to a broad range of overlapping phenotypes, collectively termed ciliopathies. This grouping is underscored by genetic overlap, where causal genes can also contribute modifier alleles to clinically distinct disorders. Here we show that mutations in TTC21B, which encodes the retrograde intraflagellar transport protein IFT139, cause both isolated nephronophthisis and syndromic Jeune asphyxiating thoracic dystrophy. Moreover, although resequencing of TTC21B in a large, clinically diverse ciliopathy cohort and matched controls showed a similar frequency of rare changes, in vivo and in vitro evaluations showed a significant enrichment of pathogenic alleles in cases (P < 0.003), suggesting that TTC21B contributes pathogenic alleles to ∼5% of ciliopathy cases. Our data illustrate how genetic lesions can be both causally associated with diverse ciliopathies and interact in trans with other disease-causing genes and highlight how saturated resequencing followed by functional analysis of all variants informs the genetic architecture of inherited disorders. © 2011 Nature America, Inc. All rights reserved.

Gangloff B.,CNRS Chizé Center for Biological Studies | Zino F.,Freiras Associacao Para A Conservacao e Proteccao da Natureza | Shirihai H.,c o Ausserdorfstrasse 6 | Gonzalez-Solis J.,University of Barcelona | And 3 more authors.
Molecular Ecology | Year: 2013

Macaronesia (north-east Atlantic archipelagos) has been host to complex patterns of colonization and differentiation in many groups of organisms including seabirds such as gadfly petrels (genus Pterodroma). Considering the subspecies of widely distributed soft-plumaged petrel for many years, the taxonomic status of the three gadfly petrel taxa breeding in Macaronesia is not yet settled, some authors advocating the presence of three, two or one species. These birds have already been the subject of genetic studies with only one mtDNA gene and relatively modest sample sizes. In this study, using a total of five genes (two mitochondrial genes and three nuclear introns), we investigated the population and phylogeographical histories of petrel populations breeding on Madeira and Cape Verde archipelagos. Despite confirming complete lineage sorting with mtDNA, analyses with nucDNA failed to reveal any population structuring and Isolation with Migration analysis revealed the absence of gene flow during the differentiation process of these populations. It appears that the three populations diverged in the late Pleistocene in the last 150 000 years, that is 10 times more recently than previous estimates based solely on one mtDNA gene. Finally, our results suggest that the Madeira petrel population is ancestral rather than that from Cape Verde. This study strongly advocates the use of nuclear loci in addition to mtDNA in demographical and phylogeographical history studies. © 2012 Blackwell Publishing Ltd.

Gangloff B.,CNRS Chizé Center for Biological Studies | Shirihai H.,c o Ausserdorfstrasse 6 | Watling D.,NatureFiji MareqetiViti | Cruaud C.,Genoscope Center National Of Sequencage | And 4 more authors.
Conservation Genetics | Year: 2012

Pseudobulweria is one of the least known and most endangered of all seabird genera. It comprises six taxa, of which two are extinct, three are critically endangered and one is near threatened. Phylogenetic relationships between these taxa and position of the genus in the Order Procellariiformes have never been studied, and the taxonomic status of several taxa remains unsettled. Conservation management of Pseudobulweria taxa will be enhanced if these uncertainties are resolved. We used a multilocus gene tree approach with two mitochondrial DNA markers (cytochrome oxidase subunit 1 and cytochrome b gene) and one nuclear intron (β Fibrinogen intron 7) to investigate phylogenetic relationships within the genus using sequences from all taxa. We combined gene trees to estimate a phylogeny of the genus using a multispecies coalescent methodology. We confirmed the link between Pseudobulweria and a clade comprising Puffinus and Bulweria genera. The Fiji petrel's status, as belonging to the genus, is confirmed, as is the specific status of newly rediscovered Beck's petrel. Maintenance of the two sub-species of Tahiti petrel as currently described is not supported. Discovering the breeding grounds of all taxa is the key for their conservation, which is vital to both the marine and fragile insular tropical ecosystems where Pseudobulweria are apical predators. © 2011 Springer Science+Business Media B.V.

Silberfeld T.,University Pierre and Marie Curie | Leigh J.W.,University Paris Diderot | Verbruggen H.,Ghent University | Cruaud C.,Genoscope Center National Of Sequencage | And 2 more authors.
Molecular Phylogenetics and Evolution | Year: 2010

The most conspicuous feature in previous phaeophycean phylogenies is a large polytomy known as the brown algal crown radiation (BACR). The BACR encompasses 10 out of the 17 currently recognized brown algal orders. A recent study has been able to resolve a few nodes of the BACR, suggesting that it may be a soft polytomy caused by a lack of signal in molecular markers. The present work aims to refine relationships within the BACR and investigate the nature and timeframe of the diversification in question using a dual approach. A multi-marker phylogeny of the brown algae was built from 10 mitochondrial, plastid and nuclear loci (>10,000 nt) of 72 phaeophycean taxa, resulting in trees with well-resolved inter-ordinal relationships within the BACR. Using Bayesian relaxed molecular clock analysis, it is shown that the BACR is likely to represent a gradual diversification spanning most of the Lower Cretaceous rather than a sudden radiation. Non-molecular characters classically used in ordinal delimitation were mapped on the molecular topology to study their evolutionary history. © 2010 Elsevier Inc. All rights reserved.

Guillaume Koffi K.,Roosevelt University | Heuertz M.,Roosevelt University | Heuertz M.,Japan Forestry and Forest Products Research Institute | Doumenge C.,CIRAD - Agricultural Research for Development | And 3 more authors.
Plant Ecology and Evolution | Year: 2010

Background and aims - Species delimitation remains a difficult task in many groups of organisms. Even widespread and conspicuous tropical trees make no exception. Santiria trimera, an African rainforest tree, displays substantial morphological variability. While classical analysis of historical herbarium samples lead to the recognition of a single species, two morphotypes of S. trimera are regularly collected in Gabon and Equatorial Guinea, sometimes in sympatry: one form with stilt roots (SR) and another form without stilt roots (NSR). Methods - To assess whether these forms constitute distinct taxa and to understand evolutionary processes within African Santiria, we combined a morphological and a spatial analysis of both sympatric morphotypes in northern Gabon with a phylogenetic analysis of samples from West and Central Africa, including the island of São Tomé. Key results - In Gabon, morphological traits, chloroplast DNA (cpDNA) and nuclear DNA (nuDNA) sequences congruently lead to the recognition of two well differentiated and reproductively isolated taxa corresponding to SR and NSR morphotypes. However, rare cases of the SR morphotype bearing DNA sequences typical of NSR individuals suggest that hybridization might sometimes occur. No evidence for habitat specialization of the two taxa was found. DNA sequences from São Tomé formed monophyletic clades at both marker types and the nuDNA gene tree suggests that the São Tomé population probably originated from Central Africa and subsequently underwent allopatric differentiation from continental populations. Conclusion - In Central Africa, S. trimera is composed of at least two distinct sympatric species following the Biological Species Concept and calls for further morphological and phenological studies and experimental crosses between them to specify their taxonomic status. Our results also show that classical taxonomic species delimitation may not always be congruent with the Biological Species Concept, calling for more population-based in situ morphological and molecular genetic analyses. © 2010 National Botanic Garden of Belgium and Royal Botanical Society of Belgium.

PubMed | Okinawa Institute of Science and Technology, Leibniz Institute of Marine Science, Genoscope Center National Of Sequencage, Institute of Clinical Molecular Biology and 3 more.
Type: | Journal: eLife | Year: 2015

Bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (SOX) bacteria that provide them with nutrition. We sequenced the SOX symbiont genomes from two Bathymodiolus species. Comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. Many of the genes specific to the symbionts were homologs of virulence genes. We discovered an abundant and diverse array of genes similar to insecticidal toxins of nematode and aphid symbionts, and toxins of pathogens such as Yersinia and Vibrio. Transcriptomics and proteomics revealed that the SOX symbionts express the toxin-related genes (TRGs) in their hosts. We hypothesize that the symbionts use these TRGs in beneficial interactions with their host, including protection against parasites. This would explain why a mutualistic symbiont would contain such a remarkable arsenal of TRGs.

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