Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Although lawsonite-bearing rocks are rare in exhumed high-pressure (HP) terranes, they are considered to exert a primary role in subduction dynamics. Recent observations in natural settings have shown that fluid–rock interaction at HP conditions, including metasomatism, may lead to unusually high lawsonite amounts even in rocks that originally contained little or no lawsonite. This process may therefore bear important implications for element recycling in subduction zones. A detailed characterization of the geochemical fingerprints associated with lawsonite metasomatism is presented in this contribution. The studied rocks belong to the HP terranes of Alpine Corsica (France), which is the largest documented exposure for lawsonite metasomatism. Metasomatic lawsonite displays complex compositional zoning, including high trace element, Cr and Ti content. The trace element content is much higher compared with the average of non-metasomatic lawsonite, and is in line with the re-incorporation of large amounts of trace elements (e.g. REE, Sr, Pb, Th) in the rock during metasomatism, as shown by mass transfer calculations. Our data suggest that serpentinites represented the main fluid source for the metasomatism, with concurrent contribution of other, possibly Ca-rich lithologies, such as mafic or meta-sedimentary rocks. We propose that the breakdown of metasomatic lawsonite may contribute to the genesis of magmas and their characteristic geochemical signatures.
ISSN: 0263-4929

hal-01107395
https://hal.archives-ouvertes.fr/hal-01107395
DOI : 10.1111/jmg.12074

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : In this study, we investigate the Lesser Antilles forearc basin, focusing on the late Pliocene to Pleistocene sedimentary archives in order to track the occurrence of extreme events triggered by enhanced subduction-related tectono-volcanic activity. We identify late Piacenzian deposits covering a major regional erosional surface, displaying sedimentary dykes and large marine boulders embedded in a mixed continental–marine matrix, characteristic of tsunamites. We interpret this episode of platform emersion and the successive cataclysmic deposits as resulting from enhanced tectonic activity at the interface of the subduction zone, synchronous with the initiation of the Lesser Antilles volcanic arc. We then discuss the implications in terms of the mechanical behaviour of the Lesser Antilles subduction zone.
ISSN: 0954-4879

hal-01571956
https://hal.archives-ouvertes.fr/hal-01571956
DOI : 10.1111/ter.12271

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
ISSN: 1755-098X

hal-01094222
https://hal-agroparistech.archives-ouvertes.fr/hal-01094222
DOI : 10.1111/j.1755-0998.2010.02916.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
This study examines the response of the Central Patagonian Cordillera to the subduction of the active South Chile Ridge and the development of the asthenospheric slab window beneath Patagonia since the Pliocene. We investigated the eastern part of the Cordillera where the glacio-volcanic piedmont is topographically inverted. Glacial morphology and associated deposits capping the top of these piedmonts reveal that during the Pliocene (after 3 Ma), glaciers were flowing to the east over a regional surface connecting the western Cordillera and the palaeo-piedmont. N160-trending normal faulting along the western edge of the inverted plateau disrupted the geomorphic surface after 3 Ma. At a regional scale, extensional tectonics is responsible for a relief inversion with a minimum value of 800 m. The timing of extensional tectonics is contemporaneous with the subduction of the spreading axis and the development of the slab window beneath Central Patagonia.
ISSN: 0954-4879

hal-00595547
https://hal.archives-ouvertes.fr/hal-00595547
DOI : 10.1111/j.1365-3121.2010.00981.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Heterocyclic aromatic amines (HAA) are formed in cooked meat, poultry and fish but also arise in tobacco smoke and exhaust gases. HAA are potential human carcinogens, which require metabolic activation to exert their genotoxicity. Human tissues can bioactivate HAA to produce reactive intermediates that bind to DNA. HAA DNA adduct formation occurs in human hepatocytes; however, the potential of HAA to form DNA adducts has not been investigated in human T lymphocytes. In this study, we investigated the ability of human T lymphocytes activated with PMA/Ionomycin or CD3/CD28 to express functional CYP1 activity and bioactivate three major HAA: 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), and 2-amino-9H-pyrido[2,3-b]indole (AαC) to form DNA adducts. Adducts were measured by ultraperformance liquid chromatography-electrospray ionization/multistage scan mass spectrometry. The highest level of DNA adducts occurred for AαC (16 adducts per 109 nucleotides), followed by PhIP (9 adducts per 109 nucleotides). In contrast, DNA adducts formed from MeIQx and the structurally related aromatic amine 4-aminobiphenyl, a known human carcinogen, were below the limit of detection (< 3 adducts per 109 nucleotides). Moreover, we demonstrate that AαC is a potent inducer of CYP1A1 and CYP1B1 activity through a transcriptional mechanism involving the AhR pathway. Overall, our results highlight the capacity of activated human T lymphocytes to more efficiently bioactivate AαC to form DNA adducts than other prominent HAA or 4-ABP. Environ. Mol. Mutagen. 57:656-667, 2016.
ISSN: 0893-6692

hal-01400486
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01400486
DOI : 10.1002/em.22059
PUBMED : 27801952

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : 1. This study focuses on the importance in hyperdiverse regions, such as the Amazonian forest, of accelerating and optimising the census of invertebrate communities.2. We carried out low-intensity sampling of tropical moth (Lepidoptera) assemblages in disturbed forest fragments in Brazil.3. We combined DNA barcoding and taxonomists' expertise to produce fast and accurate surveys of local diversity, including the recognition and census of undescribed and endemic species.4. Integrating expert knowledge of species distributions, we show that despite limited sampling effort, our approach revealed an unexpectedly high number of new and endemic species in severely threatened tropical forest fragments.5. These results highlight the risk of silent centinelan extinctions and emphasise the urgent need for accelerated invertebrate surveys in high-endemism and human-impacted tropical forests.
EISSN: 1752-458X

hal-01602363
https://hal.archives-ouvertes.fr/hal-01602363
DOI : 10.1111/icad.12187
PRODINRA : 389851

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé :  
Cross-species analyses of plant functional traits have shed light on factors contributing to differences in performance and distribution, but to date most studies have focused on either leaves or stems. We extend these tissue-specific analyses of functional strategy towards a whole-plant approach by integrating data on functional traits for 13 448 leaves and wood tissues from 4672 trees representing 668 species of Neotropical trees. Strong correlations amongst traits previously defined as the leaf economics spectrum reflect a tradeoff between investments in productive leaves with rapid turnover vs. costly physical leaf structure with a long revenue stream. A second axis of variation, the 'stem economics spectrum', defines a similar tradeoff at the stem level: dense wood vs. high wood water content and thick bark. Most importantly, these two axes are orthogonal, suggesting that tradeoffs operate independently at the leaf and at the stem levels. By simplifying the multivariate ecological strategies of tropical trees into positions along these two spectra, our results provide a basis to improve global vegetation models predicting responses of tropical forests to global change.
Ecology Letters

hal-01032142
https://hal.archives-ouvertes.fr/hal-01032142
DOI : 10.1111/j.1461-0248.2010.01517.x

Éditeur(s) : Wiley-blackwell Publishing, Inc
Résumé : Oceanic larvae of the European (Anguilla anguilla) and American (A. rostrata) eels have to cross the Atlantic Ocean from the Sargasso Sea to European or North American coasts before entering continental habitats. In some European rivers, eel recruitment is now < 1% of levels in the 1980s. A better understanding of the effects of anthropogenic pressures and environmental fluctuations on eel larvae and subsequent recruitment is a prerequisite to build efficient management plans. The present paper provides insight into the critical oceanic phase of the eel life cycle with a focus on the duration of the larval migration whose estimates varies between 7 months and more than 2 years in both species. Does this range correspond to a natural variability in larval duration or does it stem from methodological artefacts? We first review the different methods used to estimate the duration of larval migration and critically describe their possible sources of misinterpretation. We then evaluate the consistency of these methods with the current knowledge about the ecology and physiology of eel larvae and the physical oceanography. While a moderate discrepancy in migration duration was found between methods for the American eel, the discrepancy was large in the European eel. In this species, otolith microstructure studies indicated migration durations between 7 and 9 months, while other methods pointed to durations of about 2 years. We show that estimates in favour of a long migration duration seem more robust to methodological caveats than methods estimating short durations of migration.
Fish And Fisheries (1467-2960) (Wiley-blackwell Publishing, Inc), 2010-09 , Vol. 11 , N. 3 , P. 289-306

Droits : 2010 Blackwell Publishing Ltd.
http://archimer.ifremer.fr/doc/00011/12208/9033.pdf
DOI:10.1111/j.1467-2979.2010.00362.x
http://archimer.ifremer.fr/doc/00011/12208/

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Serpentinization of the oceanic lithosphere contributes significantly to the geochemical cycle from spreading ridges to subduction zones. In situ trace element analysis of oceanic serpentinites from the Mid-Atlantic Ridge and the Greater Antilles (Cuba, Dominican Republic) shows that all serpentine minerals are enriched in fluid-mobile elements (FME: As, Sb, B, Li, Cs, Pb, U, Ba, Sr). We observe no loss of these elements from abyssal to subduction environments during prograde metamorphism. Moreover, the transition from lizardite/chrysotile to antigorite during subduction is marked by a strong over-enrichment in As and Sb in antigorite, indicating late contamination by a sedimentary source. This suggests that a second stage of serpentinization occurs in the earlier stages of subduction, when newly formed or reactivated normal faults ease fluid penetration, and/or in the subduction channel. Our study shows that, from spreading ridges to forearc environments, serpentines act as sponges for FME. We posit that, until ultimate antigorite breakdown, serpentinites efficiently transport significant amounts of FME down to great depths in the mantle.
ISSN: 0954-4879

insu-00603792
https://hal-insu.archives-ouvertes.fr/insu-00603792
DOI : 10.1111/j.1365-3121.2011.00995.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
The shallow-water bivalve Codakia orbiculata which harbors gill-endosymbiotic sulfur-oxidizing g-proteobacteria can lose and acquire its endosymbionts throughout its life. Longterm starvation and recolonization experiments led to changes in the organization of cells in the lateral zone of gill filaments. This plasticity is linked to the presence or absence of gill-endosymbionts. Herein, we propose that this reorganization can be explained by three hypotheses: (a) a variation in the number of bacteriocytes and granule cells due to proliferation or apoptosis processes, (b) a variation of the volume of these two cell types without modification in the number, and (c) a combination of both number and cell volume variation. To test these hypotheses, we analyzed cell reorganization in terms of proliferation and apoptosis in adults submitted to starvation and returned to the field using catalyzed reporter deposition fluorescence in situ hybridization, immunohistochemistry, and structural analyses. We observed that cell and tissue reorganization in gills filaments is due to a variation in cell relative abundance that maybe associated with a variation in cell apparent volume and depends on the environment. In fact, bacteriocytes mostly multiply in freshly collected and newly recolonized individuals, and excess bacteriocytes are eliminated in later recolonization stages. We highlight that host tissue regeneration in gill filaments of this symbiotic bivalve can occur by both replication of existing cells and division of undifferentiated cells localized in tissular bridges, which might be a tissue-specific multipotent stem cell zone.
Microscopy Research and Technique

hal-00743036
https://hal-uag.archives-ouvertes.fr/hal-00743036

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : We use InSAR to measure deformation and kinematics of the Mw = 4.9 Borujerd (2005/05/03) and Mw = 6.1 Chalan-Chulan (2006/03/31) earthquakes that occurred in the Zagros fold-and-thrust belt. The focal mechanism of the 2006 event is consistent with right lateral strike-slip motion and the event ruptured the Dorud-Borujerd segment of the Main Recent Fault. An Envisat interferogram spanning the 2006 event shows peak ground deformation of 9 cm in the satellite line-of-sight along a 10 km long fault portion. The interferogram spanning the 2005 earthquake is rather related to atmospheric artefact than to ground deformation. Dislocation models of the 2006 Chalan-Chulan event indicate dextral slip amounting to a maximum of 90 cm at a depth of 4 km. The predicted vertical displacements are in good agreement with differential levelling data. The 2006 event filled only a small part of the seismic gap located between large M = 7 events that occurred in 1909 and 1957.
ISSN: 0954-4879

hal-00411313
https://hal.archives-ouvertes.fr/hal-00411313
DOI : 10.1111/j.1365-3121.2008.00797.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Physical modeling of oblique subduction is performed to study the mechanism of strain partitioning. The model is two-layer and includes the elasto-plastic lithosphere (the overriding and subducting plates) and the low-viscosity liquid asthenosphere. The subduction is driven by a push force from a piston and a pull force when the density contrast Ap between the subducting plate and the asthenosphere is positive. We vary both Ap and the interplate friction (frictional stresses). Slip partitioning is obtained only in the models with high interplate friction and only when the overriding plate contains a weak zone. This zone in the models corresponds either to locally thinned litho-sphere or to cut (fault). The horizontal, trench-normal component of the interplate friction force [Ffh[ can be comparable with the absolute value of the horizontal component of the nonhydrostatic interplate pressure force [Fph [ in the subduction zone. Ffh is always negative (compression), while Fph can be either negative (compressional subduction regime) or positive (extensional regime). High friction, which promotes partitioning, can completely cancel the extensional (suction) force Fph. Back arc tension and strike-slip faulting appear thus as conflicting processes, although they can coexist in the same subduction zone, depending on the relative values of relevant forces. It appears that high friction can exist only in compressional subduction zones where partitioning should develop more easily. This conclusion is supported by the comparison of two oblique subduction zones, having similar geometry: the compressional southern Kurile zone (strong partitioning) and extensional southern Ryukyu zone (no lithospheric-scale partitioning). Other factors controlling the strain partitioning are the length of the oblique subductlon zone, the boundary conditions at the transverse limits of the forearc sliver, and of course, the obliquity of subduction.
ISSN: 2169-9275

hal-01261396
https://hal.archives-ouvertes.fr/hal-01261396
https://hal.archives-ouvertes.fr/hal-01261396/document
https://hal.archives-ouvertes.fr/hal-01261396/file/chemendaJGR2000.pdf
DOI : 10.1029/1999JB900332

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
U-Pb zircon and Ar-Ar amphibole and biotite ages from rocks of the West Congo Belt of Angola indicate that this area underwent two main deformation events of amphibolite facies grade at c. 540 and 490 Ma, which were followed by tectonically assisted exhumation during eastward thrusting of the hinterland domain onto the foreland domain. High-grade conditions in the West Congo Belt are 20-40 Ma younger than in the Ribeira-Araçuai Belt of Brazil, its South American counterpart, or than in the westernmost Kaoko Belt of Namibia, its African correlative. In the present state of knowledge, a more appropriate counterpart to the southern part of the West Congo Belt may be restricted to the Cabo Frio Terrane in the eastern Ribeira Belt, which yields a broadly similar evolution.
ISSN: 0954-4879

hal-00716463
https://hal.archives-ouvertes.fr/hal-00716463
DOI : 10.1111/j.1365-3121.2012.01060.x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
American Journal of Hematology

hal-01113050
https://hal.archives-ouvertes.fr/hal-01113050
DOI : 10.1002/ajh.23941

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.
ISSN: 1755-098X

hal-01342973
https://hal-univ-perp.archives-ouvertes.fr/hal-01342973
DOI : 10.1111/1755-0998.12293

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Dating the timing of motion on crustal shear zones is of tremendous importance for understanding the assembly of orogenic terranes. This objective is achieved in this paper by combining petrological and structural observations with novel developments in in situ U-Th-Pb geochronology of allanite. A greenschist facies shear zone within the Mont Blanc Massif is documented. Allanite is synkinematic and belongs to the mylonitic assemblage. LA-ICP-MS U-Th-Pb isotope analyses of allanite reveal high contents and highly radiogenic isotopic compositions of the common-Pb component. The use of measured Pb-isotope compositions of associated minerals (feldspars and chlorite) is critical for accurate common-Pb correction, and provides a powerful mechanism for linking allanite growth to the metamorphic assemblage. A mean 208Pb/232Th age of 29.44 ± 0.95 Ma is accordingly taken for synkinematic allanite crystallisation under greenschist facies conditions. This age reflects the timing of the Mont Blanc underthrusting below the Penninic Front and highlights the potential of directly dating deformation with allanite.
ISSN: 0954-4879

hal-00963545
https://hal.archives-ouvertes.fr/hal-00963545
DOI : 10.1111/ter.12066

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Despite convergent margins being unstable systems, most reports of huge submarine slope failure have come from oceanic volcanoes and passive margins. Swath bathymetry and seismic profiles of the northern Hikurangi subduction system, New Zealand, show a tapering 65-30 km wide by 65 km deep margin indentation, with a giant, 3150+_630 km 3, blocky, debris avalanche deposit projecting 40 km out across horizontal trench fill, and a debris flow deposit projecting over 100 km. Slide blocks are well-bedded, up to 18 km across and 1.2 km high, the largest being at the avalanche deposit's leading edge. Samples dredged from them are mainly Miocene shelf calc-mudstones similar to those outcropping around the indentation. Cores from cover beds suggest that failure occurred-170 +_40 ka, possibly synchronously with a major extension collapse in the upper indentation. However, the northern part of the indentation is much older. The steep, straight northern wall is close to the direction of plate convergence and probably formed around 2.0-0.16 Ma as a large seamount subducted, leaving in its wake a deep groove obliquely across the margin and an unstable triangle of fractured rock in the 60 ø angle between groove and oversteepened margin front. The triangle collapsed as a blocky avalanche, leaving a scalloped southern wall and probably causing a large tsunami. Tentative calculations of compacted volumes suggest that the indentation is over 600 km 3 larger than the avalanche, supporting a two-stage origin that includes subduction erosion. Since failure, convergence has carried the deposits-9 km back toward the margin, causing internal compression. The eventual subduction/accretion of the Ruatoria avalanche explains the scarcity of such features on active margins and perhaps the nature of olistostromes in fold belts.
ISSN: 2169-9275

hal-01261406
https://hal.archives-ouvertes.fr/hal-01261406
https://hal.archives-ouvertes.fr/hal-01261406/document
https://hal.archives-ouvertes.fr/hal-01261406/file/CollotJGR2001.pdf
DOI : 10.1029/2001JB900004

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : The Oman-Emirates is the largest and best-exposed ophiolite; consequently, it has attracted significant interest among scientists, together with serious conflicts. Most geologists regard this ophiolite as having formed in an intra-oceanic subduction zone before being accreted to the Arabian continent. Here, we propose an alternative scenario, supported by detailed field observations and integrated geophysics. The smaller Emirates part of the ophiolite was forced into a nearby continent, in the pre-collision stage of Tethyan closure. The contraction led to the exhumation of the mantle floor of segmented basins accreted in a rifted system similar to the present-day Gulf of California. The implied high temperature–high pressure metamorphism and the range of geochemical signatures were introduced during the process of rifting, whereas the larger Oman ophiolite was emplaced by obduction onto and along the subducting continental shore. This Ridge–Trench–Transform system might call for a new process to obduct over continents in particular Tethyan ophiolites.
ISSN: 0954-4879

hal-01526919
https://hal.archives-ouvertes.fr/hal-01526919
DOI : 10.1111/ter.12256

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
We mainly study a system of two coupled nonlinear Schrödinger equations where one equation includes gain and the other one includes losses. This model constitutes a generalization of the model of pulse propagation in bire-fringent optical fibers. We answered partially to a question of some authors in [8], that in the Manakov case, the solution stays in L 2 (0, T ; H 1), that means that the solution can not blow up in finite time. More precisely, the bound that is provided in this paper does not seem to be optimal but different than those that has been given from a previous study [8]. Thanks to the way we treat the a priori estimate, we obtain a sharp bound in L 2 (0, T ; H 1), which would be difficult to reach from the study of other authors [8]. The result is illustrated by numerical results which have been obtained with a finite element solver well adapted for that purpose.
ISSN: 0022-2526

Droits : http://creativecommons.org/licenses/by/
hal-01270459
https://hal.archives-ouvertes.fr/hal-01270459
https://hal.archives-ouvertes.fr/hal-01270459/document
https://hal.archives-ouvertes.fr/hal-01270459/file/paperver2.pdf

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