Center National Of Sequencage

Évry, France

Center National Of Sequencage

Évry, France
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Hassanin A.,CNRS Systematics, Biodiversity and Evolution Institute | An J.,CNRS Systematics, Biodiversity and Evolution Institute | Ropiquet A.,Stellenbosch University | Nguyen T.T.,CNRS Systematics, Biodiversity and Evolution Institute | Couloux A.,Center National Of Sequencage
Molecular Phylogenetics and Evolution | Year: 2013

Mitochondrial sequences are widely used for species identification and for studying phylogenetic relationships among closely related species or populations of the same species. However, many studies of mammals have shown that the maternal history of the mitochondrial genome can be discordant with the true evolutionary history of the taxa. In such cases, the analyses of multiple nuclear genes can be more powerful for deciphering interspecific relationships. Here, we designed primers for amplifying 13 new exon-primed intron-crossing (EPIC) autosomal loci for studying shallow phylogeny and taxonomy of Laurasiatherian mammals. Three criteria were used for the selection of the markers: gene orthology, a PCR product length between 600 and 1200 nucleotides, and different chromosomal locations in the bovine genome. Positive PCRs were obtained from different species representing the orders Carnivora, Cetartiodactyla, Chiroptera, Perissodactyla and Pholidota. The newly developed markers were analyzed in a phylogenetic study of the tribe Bovini (the group containing domestic and wild cattle, bison, yak, African buffalo, Asian buffalo, and saola) based on 17 taxa and 18 nuclear genes, representing a total alignment of 13,095 nucleotides. The phylogenetic results were compared to those obtained from analyses of the complete mitochondrial genome and Y chromosomal genes. Our analyses support a basal divergence of the saola (Pseudoryx) and a sister-group relationship between yak and bison. These results contrast with recent molecular studies but are in better agreement with morphology. The comparison of pairwise nucleotide distances shows that our nuDNA dataset provides a good signal for identifying taxonomic levels, such as species, genera, subtribes, tribes and subfamilies, whereas the mtDNA genome fails because of mtDNA introgression and higher levels of homoplasy. Accordingly, we conclude that the genus Bison should be regarded as a synonym of Bos, with the European bison relegated to a subspecies rank within Bos bison. We compared our molecular dating estimates to the fossil record in order to propose a biogeographic scenario for the evolution of Bovini during the Neogene. © 2012 Elsevier Inc.

Buyck B.,French Natural History Museum | Kauff F.,University of Kaiserslautern | Cruaud C.,Center National Of Sequencage | Hofstetter V.,Agroscope Changins Wadenswil Research Station ACW
Fungal Diversity | Year: 2013

The authors present a combined morphological and molecular approach of the genus Cantharellus in Africa. Morphological descriptions and detailed illustrations are provided for five new species from the Zambezian savannah woodlands in tropical Africa: C. afrocibarius, C. gracilis, C. humidicolus, C. miomboensis and C. tanzanicus. A maximum likelihood analysis of tef-1 sequences obtained for 83 collections of Cantharellus that are representative of all major groups in world wide Cantharellus, places a total of 13 African chanterelles, including the five newly described taxa. The recognition of a separate genus Afrocantharellus is rejected. An identification key based on the re-examination of all existing type material is provided for all presently known African Cantharellus. © 2012 Mushroom Research Foundation.

Buyck B.,CNRS Systematics, Biodiversity and Evolution Institute | Kauff F.,University of Kaiserslautern | Eyssartier G.,boulevard Stalingrad | Couloux A.,Center National Of Sequencage | Hofstetter V.,Agroscope Changins Wadenswil Research Station ACW
Fungal Diversity | Year: 2014

After a short historical overview of past systematic studies on Cantharellus, discussing delimitation and species diversity of the genus as well as previous, morphology-based, infrageneric classifications, this paper presents the first molecularly-based infrageneric classification of this genus using a multigene phylogenetic approach (nucLSU, mitSSU, RPB2 and tef-1) on a dataset that covers approximately halve of the described chanterelles worldwide, including many type specimens. Six subgenera are recognized and the recognition of subgenus Afrocantharellus as a separate genus is not accepted. The taxonomic value of individual morphological features is discussed as challenged by this new multigene phylogeny which comprises five new sections, one new subgenus and many emendations for previously recognized infrageneric groups. The paper discusses the observed discrepancy in biodiversity of Cantharellus when comparing between studies that focus either on below- or above-ground presence. A preliminary biogeographic hypothesis suggests an 'out of Africa' Gondwanan origin as a result of vicariance and subsequent migrations. © 2013 Mushroom Research Foundation.

Puillandre N.,French Natural History Museum | Modica M.V.,University of Rome La Sapienza | Zhang Y.,Mount Sinai School of Medicine | Sirovich L.,Mount Sinai School of Medicine | And 5 more authors.
Molecular Ecology | Year: 2012

Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell-based PSHs can be arduous. A four-pronged approach was employed to generate robust species hypotheses of a 1000 specimen South-West Pacific Turridae data set in which: (i) analysis of COI DNA Barcode gene is coupled with (ii) species delimitation tools GMYC (General Mixed Yule Coalescence Method) and ABGD (Automatic Barcode Gap Discovery) to propose PSHs that are then (iii) visualized using Klee diagrams and (iv) evaluated with additional evidence, such as nuclear gene rRNA 28S, morphological characters, geographical and bathymetrical distribution to determine conclusive secondary species hypotheses (SSHs). The integrative taxonomy approach applied identified 87 Turridae species, more than doubling the amount previously known in the Gemmula genus. In contrast to a predominantly shell-based morphological approach, which over the last 30 years proposed only 13 new species names for the Turridae genus Gemmula, the integrative approach described here identified 27 novel species hypotheses not linked to available species names in the literature. The formalized strategy applied here outlines an effective and reproducible protocol for large-scale species delimitation of hyperdiverse groups. © 2012 Blackwell Publishing Ltd.

Hofstetter V.,Agroscope Changins Wadenswil ACW | Buyck B.,CNRS Systematics, Biodiversity and Evolution Institute | Croll D.,ETH Zurich | Viret O.,Agroscope Changins Wadenswil ACW | And 2 more authors.
Fungal Diversity | Year: 2012

Esca disease, which attacks the wood of grapevine, has become increasingly devastating during the past three decades and represents today a major concern in all wine-producing countries. This disease is attributed to a group of systematically diverse fungi that are considered to be latent pathogens, however, this has not been conclusively established. This study presents the first in-depth comparison between the mycota of healthy and diseased plants taken from the same vineyard to determine which fungi become invasive when foliar symptoms of esca appear. An unprecedented high fungal diversity, 158 species, is here reported exclusively from grapevine wood in a single Swiss vineyard plot. An identical mycota inhabits wood of healthy and diseased adult plants and presumed esca pathogens were widespread and occurred in similar frequencies in both plant types. Pioneer esca-associated fungi are not transmitted from adult to nursery plants through the grafting process. Consequently the presumed esca-associated fungal pathogens are most likely saprobes decaying already senescent or dead wood resulting from intensive pruning, frost or other mecanical injuries as grafting. The cause of esca disease therefore remains elusive and requires well executive scientific study. These results question the assumed pathogenicity of fungi in other diseases of plants or animals where identical mycota are retrieved from both diseased and healthy individuals. © 2012 The Author(s).

Aubriot X.,CNRS Systematics, Biodiversity and Evolution Institute | Lowry P.P.,CNRS Systematics, Biodiversity and Evolution Institute | Lowry P.P.,Missouri Botanical Garden | Cruaud C.,Center National Of Sequencage | And 2 more authors.
Molecular Ecology Resources | Year: 2013

The island of Madagascar is a key hot spot for the genus Euphorbia, with at least 170 native species, almost all endemic. Threatened by habitat loss and illegal collection of wild plants, nearly all Malagasy Euphorbia are listed in CITES Appendices I and II. The absence of a reliable taxonomic revision makes it particularly difficult to identify these plants, even when fertile, and thereby compromises the application of CITES regulations. DNA barcoding, which can facilitate species-level identification irrespective of developmental stage and the presence of flowers or fruits, may be a promising tool for monitoring and controlling trade involving threatened species. In this study, we test the potential value of barcoding on 41 Euphorbia species representative of the genus in Madagascar, using the two widely adopted core barcode markers (matK and rbcL), along with two additional DNA regions, nuclear internal transcribed spacer (ITS) and the chloroplastic intergenic spacer psbA-trnH. For each marker and for selected marker combinations, inter- and intraspecific distance estimates and species discrimination rates are calculated. Results using just the 'official' barcoding markers yield overlapping inter- and intraspecific ranges and species discrimination rates below 60%. When ITS is used, whether alone or in combination with the core markers, species discrimination increases to nearly 100%, whereas the addition of psbA-trnH produces less satisfactory results. This study, the first ever to test barcoding on the large, commercially important genus Euphorbia shows that this method could be developed into a powerful identification tool and thereby contribute to more effective application of CITES regulations. © 2012 Blackwell Publishing Ltd.

Nattier R.,CNRS Systematics, Biodiversity and Evolution Institute | Robillard T.,CNRS Systematics, Biodiversity and Evolution Institute | Desutter-Grandcolas L.,CNRS Systematics, Biodiversity and Evolution Institute | Couloux A.,Center National Of Sequencage | Grandcolas P.,CNRS Systematics, Biodiversity and Evolution Institute
Journal of Biogeography | Year: 2011

Aim A New Caledonian insect group was studied in a world-wide phylogenetic context to test: (1) whether local or regional island clades are older than 37Ma, the postulated re-emergence time of New Caledonia; (2) whether these clades show evidence for local radiations or multiple colonizations; and (3) whether there is evidence for relict taxa with long branches in phylogenetic trees that relate New Caledonian species to geographically distant taxa. Location New Caledonia, south-west Pacific. Methods We sampled 43 cricket species representing all tribes of the subfamily Eneopterinae and 15 of the 17 described genera, focusing on taxa distributed in the South Pacific and around New Caledonia. One nuclear and three mitochondrial genes were analysed using Bayesian and parsimony methods. Phylogenetic divergence times were estimated using a relaxed clock method and several calibration criteria. Results The analyses indicate that, under the most conservative dating scenario, New Caledonian eneopterines are 5-16 million years old. The largest group in the Pacific region dates to 18-29Ma. New Caledonia has been colonized in two phases: the first around 10.6Ma, with the subsequent diversification of the endemic genus Agnotecous, and the second with more recent events around 1-4Ma. The distribution of the sister group of Agnotecous and the lack of phylogenetic long branches in the genus refute an assumption of major extinction events in this clade and the hypothesis of local relicts. Main conclusions Our phylogenetic studies invalidate a simple scenario of local persistence of this group in New Caledonia since 80Ma, either by survival on the New Caledonian island since its rift from Australia, or, if one accepts the submergence of New Caledonia, by local island-hopping among other subaerial islands, now drowned, in the region during periods of New Caledonian submergence. © 2011 Blackwell Publishing Ltd.

Ropars J.,CNRS Systematics, Biodiversity and Evolution Institute | Cruaud C.,Center National Of Sequencage | Lacoste S.,CNRS Systematics, Biodiversity and Evolution Institute | Dupont J.,CNRS Systematics, Biodiversity and Evolution Institute
International Journal of Food Microbiology | Year: 2012

Cheese is made from milk by a succession of microbes (bacteria, yeasts and fungi) that determine the consistency and flavor of the cheese. Apart from the emblematic species, Penicillium camemberti and Penicillium roqueforti, cheese fungi are not well known. Here we present a taxonomic and phylogenetic overview of the most important filamentous cheese Ascomycota based on 133 isolates provided by the producers of cheese and cheese starter cultures and 97 isolates from culture collections. We checked the congruence of different gene genealogies to circumscribe cheese species and our results allow us to propose molecular targets for their identification. To study their phylogenetic affiliation, we used LSU rDNA and showed that cheese fungi are found in two classes, the Eurotiomycetes with Penicillium species (Eurotiales) and Sporendonema casei/. Sphaerosporium equinum (Onygenales), and the Sordariomycetes with Scopulariopsis species (Microascales) and Fusarium domesticum (Hypocreales). Some of these fungi, such as, P. camemberti, F. domesticum, Scopulariopsis flava and S. casei, are only known from cheeses and are probably adapted to this particular habitat, which is extremely rich in protein and fat. Other cheese fungi are ubiquitous, such as, P. roqueforti, Scopulariopsis candida and Scopulariopsis fusca. © 2012 Elsevier B.V.

Bechah Y.,Institut Universitaire de France | El Karkouri K.,Institut Universitaire de France | Mediannikov O.,Institut Universitaire de France | Leroy Q.,Institut Universitaire de France | And 5 more authors.
Genome Research | Year: 2010

Rickettsia prowazekii, the agent of epidemic typhus, is an obligate intracellular bacterium that is transmitted to human beings by the body louse. Several strains that differ considerably in virulence are recognized, but the genetic basis for these variations has remained unknown since the initial description of the avirulent vaccine strain nearly 70 yr ago. We use a recently developed murine model of epidemic typhus and transcriptomic, proteomic, and genetic techniques to identify the factors associated with virulence. We identified four phenotypes of R. prowazekii that differed in virulence, associated with the up-regulation of antiapoptotic genes or the interferon I pathway in the host cells. Transcriptional and proteomic analyses of R. prowazekii surface protein expression and protein methylation varied with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) in eight genes in an avirulent strain that split and inactivated these genes. These included recO, putative methyltransferase, and exported protein. Passage of the avirulent Madrid E strain in cells or in experimental animals was associated with a cascade of gene reactivations, beginning with recO, that restored the virulent phenotype. An area of genomic plasticity appears to determine virulence in R. prowazekii and represents an example of adaptive mutation for this pathogen. © 2010 by Cold Spring Harbor Laboratory Press.

Schoelinck C.,French Natural History Museum | Cruaud C.,Center National Of Sequencage | Justine J.-L.,French Natural History Museum
Parasitology International | Year: 2012

Species of the diplectanid monogenean genus Pseudorhabdosynochus are strictly host-specific (specialist), with the exception of P. cyanopodus, which was reported in New Caledonia, South Pacific, from two host species, Epinephelus cyanopodus and E. chlorostigma. We sequenced the COI gene of both host fish species and of their monogeneans. Morphological identification and pairwise distances showed that the two fish species were distinct (difference 6.1-6.6%), but that their monogeneans were not (difference 0-1.5%). A morphological study of sclerotised parts showed that specimens of P. cyanopodus are similar in both fish. Most species of groupers and their associated Pseudorhabdosynochus species are from warm surface waters, but the two groupers E. cyanopodus and E. chlorostigma are usually caught in deep-sea on the outer slope of the coral reef. This suggests that acquisition of a less strict host specificity is an adaptation of P. cyanopodus to deep-sea hosts. © 2012 Elsevier Ireland Ltd.

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