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10 Pág. Centro de Biotecnología y Genómica de Plantas (CBGP), The poverty of disease resistance gene reservoirs limits the breeding of crops for durable resistance against evolutionary dynamic pathogens. Zymoseptoria tritici which causes Septoria tritici blotch (STB), represents one of the most genetically diverse and devastating wheat pathogens worldwide. No fully virulent Z. tritici isolates against synthetic wheats carrying the major resistant gene Stb16q have been identified. Here, we use comparative genomics, mutagenesis and complementation to identify Stb16q, which confers broad-spectrum resistance against Z. tritici. The Stb16q gene encodes a plasma membrane cysteine-rich receptor-like kinase that was recently introduced into cultivated wheat and which considerably slows penetration and intercellular growth of the pathogen., Our works was supported by the “Fond de Soutien à l’Obtention Vegetale” (FSOV), the French National Institute for Agricultural Research (INRA), and the ETH Zurich Career Seed Grant (SEED-58 16-1). We thank Sreedhar Kilaru and Gero Steinberg for providing the strain 3D7 expressing eGFP. Confocal laser scanning microscopy experiments were performed in the Scientific Center for Optical and Electron Microscopy (ScopeM), ETH Zurich and at the SPIBOC imaging facility of the Institut Sophia Agrobiotech. B.F. was supported by INRA and the French Government (National Research Agency, ANR) through the ‘Investments for the Future’ LabEx SIGNALIFE: program reference #ANR-11-LABX-0028-01.

Individuals' distribution across habitats may depend on their personality. Human activities and infrastructures are critical elements of the landscape that may impact the habitat selection process. However, depending on their personality, individuals may respond differently to these unnatural elements. In the present study, we first investigated whether some human infrastructures (buildings, roads and paths) shaped Montagu's harrier nest spatial distribution in the landscape according to female personality (boldness). Second, we tested if the reproductive success of females depended on their boldness and nest location regarding infrastructures. Using a long-term (19 years) dataset, we calculated, for each infrastructure type, the distance from each nest to the nearest infrastructure and the infrastructure density around the nest. We tested the effects of female boldness (bold vs. shy) and its interaction with egg-laying date on these six metrics. Nest location in the landscape depended on female personality and on some human infrastructures: the building density was smaller around nests from shy females than from bold ones. Nest distribution related to other infrastructure metrics did not depend on female boldness. The pattern related to building density is consistent with some habitat choice hypotheses, which are discussed. Path density around nests negatively affected reproductive success regardless of female boldness, and late breeders nested further away from paths than early breeders. Human activities on paths (more common later in the season) could lead to disturbance and a decrease in parental care, reducing reproductive success. Increasing human presence in farmlands implies a need to better understand its impact on population composition, in terms of personality. Our results suggest that individual behavioural differences should be taken into account in studies assessing the effects of human disturbance on animal populations, to propose more appropriate conservation measures., This work was supported by La Rochelle Université, the Centre National de la Recherche Scientifique and the Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement. We thank Catherine Menard (Direction régionale de l'Environnement, de l'Aménagement et du Logement de Nouvelle Aquitaine) and Fondation LISEA for partial funding and administrative support.

In tissue engineering, biological, physical, and chemical inputs have to be combined to properly mimic cellular environments and successfully build artificial tissues which can be designed to fulfill different biomedical needs such as the shortage of organ donors or the development of in vitro disease models for drug testing. Inclusion body-like protein nanoparticles (pNPs) can simultaneously provide such physical and biochemical stimuli to cells when attached to surfaces. However, this attachment has only been made by physisorption. To provide a stable anchoring, a covalent binding of lactic acid bacteria (LAB) produced pNPs, which lack the innate pyrogenic impurities of Gram-negative bacteria like Escherichia coli, is presented. The reported micropatterns feature a robust nanoscale topography with an unprecedented mechanical stability. In addition, they are denser and more capable of influencing cell morphology and orientation. The increased stability and the absence of pyrogenic impurities represent a step forward towards the translation of this material to a clinical setting., The authors are grateful for the financial support received from MOTHER (MAT2016-80826-R) granted by the DGI (Spain), GenCat (SGR-918 and SGR-229) financed by DGR (Catalunya), the Spanish Ministry of Economy and Competitiveness (MINECO) through the “Severo Ochoa” Programme for Centres of Excellence in R&D (SEV-2015-0496), the COST Action CA15126 Between Atom and Cell, Fundació La Marató de TV3 (Nr. 201812), the European Social Fund, and EU to J. V., A. V., and I. R. (H2020-INFRAIA-2014-2015; NFFA-654360). J. G. is also grateful to MINECO for a “Ramón y Cajal” fellowship as well as to the Max Planck Society through the Max Planck Partner Group “Dynamic Biomimetics for Cancer Immunotherapy” in collaboration with the Max Planck Institute for Medical Research (Heidelberg, Germany). This study has been also supported by the Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), an initiative funded by the VI National R&D&I Plan, Iniciativa Ingenio 2010, Consolider Program, CIBER Actions and financed by the Instituto de Salud Carlos III with assistance from the European Regional Development Fund. The authors also acknowledge Micalis Institute, INRA, France that kindly provided us the strain clpP− htrA−-NZ9000 (patent Nr. EP1141337B1/US6994997B1). M. M. M. and O. C. G. received a PhD fellowship from MECD (FPU) and E. G. F. a post-doctoral fellowship from INIA (DOC-INIA, MINECO). A. V. received an ICREA ACADEMIA Award. This work has been developed under the biochemistry and biomedicine program of Universitat Autònoma de Barcelona (UAB). The characterization of the pNPs has been performed by the ICTS “NANBIOSIS”, more specifically by the Biomaterial Processing and Nanostructuring Unit (U6), Unit of the CIBER in Bioengineering, Biomaterials & Nanomedicine (CIBER-BBN) located at the Institute of Materials Science of Barcelona (ICMAB-CSIC).

Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there are a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid Acyrthosiphon pisum are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation., R.F. was funded by a Juan de la Cierva-Incorporacion Fellowship (Government of Spain, IJCI-2015-26627) and a Marie Skłodowska-Curie Fellowship (747607). T.G. acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and grants “Centro de Excelencia Severo Ochoa 2013– 2017” SEV-2012-0208, and BFU2015-67107 cofunded by European Regional Development Fund (ERDF); from the CERCA Programme/Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and grant from the European Union’s Horizon 2020 research and innovation program under the grant agreement ERC-2016-724173 and the Marie Sklodowska-Curie (Grant Agreement No. H2020-MSCA-ITN-2014-642095). D.T. was funded by “Severo Ochoa visiting scientific program” for a 6 months stay at the Center for Genomic Regulation—Barcelona—to start the project, supported as well by INRA SPE. Dr Roderic Guigo (CRG, Barcelona) is warmly acknowledged for his welcome in his lab. Dr Akiko Sugio, Dr Julie Jaquiery, Dr Ga€el Le Trionnaire, and Dr Jean-Christophe Simon (INRAE, UMR 1349 Igepp, Rennes, France) are acknowledged for access to unpublished data of RNA-Seq. Daktulosphaira vitifoliae data were provided by the Phylloxera Genome Project (https://bipaa. genouest.org/is/aphidbase/): funding for D. vitifoliae clone Pcf genomic sequencing was provided by INRA (AIP Bioresources) and BGI Biotech in the frame of i5k initiative. Parts of the transcriptomic resources were obtained within the 1KITE projects (Bernhard Misof, Bonn, Germany). The Acyrthosiphon pisum phylome can be accessed at PhylomeDB 4.0 under phylome number 441. RNA-Seq data are accessible at NCBI, see supplementary table S2, Supplementary Material online.

Lactic acid bacteria (LAB) encompasses industrially relevant bacteria involved in food fermentations as well as health-promoting members of our autochthonous microbiota. In the last years, we have witnessed major progresses in the knowledge of the biology of their cell wall, the outermost macrostructure of a Gram-positive cell, which is crucial for survival. Sophisticated biochemical analyses combined with mutation strategies have been applied to unravel biosynthetic routes that sustain the inter- and intra-species cell wall diversity within LAB. Interplay with global cell metabolism has been deciphered that improved our fundamental understanding of the plasticity of the cell wall during growth. The cell wall is also decisive for the antimicrobial activity of many bacteriocins, for bacteriophage infection and for the interactions with the external environment. Therefore, genetic circuits involved in monitoring cell wall damage have been described in LAB, together with a plethora of defence mechanisms that help them to cope with external threats and adapt to harsh conditions. Since the cell wall plays a pivotal role in several technological and health-promoting traits of LAB, we anticipate that this knowledge will pave the way for the future development and extended applications of LAB., The work of BM and AR was supported by Spanish State Research Agency and European Regional Development Funds [BIO2017–88147-R] and Asturias Innovation 2018–2020, Principado de Asturias, Spain, and European Regional Development Funds [IDI/2018/000119]. The work of MPCC and SK was supported by INRA, Region Ile de France and French National ´ Research Agency (ANR-11-BSV8–004-01 and ANR-18-CE5–01-02).

International audience; Analysis of yeasts isolated from various biotopes in French Guiana led to the identification of two strains isolated from flowers and designated CLIB 1634(T) and CLIB 1707(T). Comparison of the D1/D2 domain of the large subunit (LSU D1/D2) rRNA gene sequences of CLIB 1634(T) and CLIB 1707(T) to those in the GenBank database revealed that these strains belong to the Starmerella Glade. Strain CLIB 1634(T) was shown to diverge from the closely related Starmerella apicola type strain CBS 2868 T with a sequence divergence of 1.34 and 1.30 %, in the LSU D1/D2 rRNA gene and internal transcribed spacer (ITS) sequences respectively. Strain CLIB 1634(T) and Candida apicola CBS 2868(T) diverged by 3.81 and 14.96 % at the level of the protein-coding gene partial sequences EF-1 alpha and RPB2, respectively. CLIB 1707(T) was found to have sequence divergence of 3.88 and 9.16 % in the LSU D1/D2 rRNA gene and ITS, respectively, from that of the most closely related species Starmerella ratchasimensis type strain CBS 10611(T). The species Starmerella reginensis f.a., sp. nov. and Starmerella kourouensis f.a., sp. nov. are proposed to accommodate strains CLIB 1634(T) (=CBS 15247(T)) and CLIB 1707(T) (=CBS 15257(T)), respectively.

The wheat dwarf disease is among the most damaging diseases in cereals. Its aetiological agent is theWheat dwarf virus(WDV), which is exclusively transmitted from plant to plant by leafhoppers from the genusPsammotettix(Hemiptera, Cicadellidae). The parameters linked to the WDV/Psammotettixpathosystem are still poorly understood. We studiedPsammotettixindividuals collected in wheat and barley fields in France and, as a comparison, from grassland at agroecological interface in West Slovenia. Species identity of males and females has been determined using multiple criteria. In the first step, the characterization of the collected individuals included recordings of vibrational signals used in mating behaviour and morphometric analyses. In addition, a 442 nt sequence of the mitochondrial cytochrome oxydase I (COI) gene was obtained for some individuals and compared to COI sequences of thePsammotettixleafhoppers available in public databases. In the cereal fields in France,Psammotettix alienuswas the most numerous species; however, it sometimes occurred together withPsammotettix confinis, while in the grasslands in Slovenia, the third syntopic species inPsammotettixcommunity wasPsammotettix helvolus. The temporal parameters of theP. alienusmale calling song that were measured in this study were very similar to those measured in a previous study. The local biotic and/or abiotic parameters most likely influence the life history ofPsammotettixleafhoppers, and the proportion of viruliferous individuals collected in cereal fields was 14.9%, while leafhoppers collected in Slovenia were virus-free. Taken together, results show that more detailed information on population structure ofPsammotettixleafhoppers is crucial for providing an insight into the epidemiology of wheat dwarf disease.

International audience; The extent of the diversity of yeasts in tropical rain forest and different environments from French Guiana was investigated. A total of 365 samples were collected from various substrates, such as plants, fruits and insects, at 13 locations, yielding 276 pure yeast isolates. Sequence analysis of the D1/D2 domains of the large subunit rRNA gene indicated that 210 isolates out of 276 belonged to 82 described species (67 Saccharomycotina, 14 Basidiomycota and 1 Pezizomycotina). In addition to these, a total of 54 Saccharomycotina isolates could not be assigned to a known species. These belonged to 14 genera and should be studied further from a taxonomic point of view. In addition, among the 43 Basidiomycotina isolates found, 12 could not be assigned to a known species. This report shows an unexpected biodiversity and indicates that oversea territories, such as French Guiana, constitute a largely unexplored reservoir for yeast diversity. Two Saccharomycotina strains, CLIB 1706 and CLIB 1725, isolated from an insect and from a fern respectively, were characterized further and were shown to belong to the Suhomyces Glade on the basis of the rDNA sequence comparison. CLIB 1706(T) rDNA sequences showed nine substitutions and three indels out of 556 bp (D1/D2 domains) and 32 substitutions and 12 indels out of 380 bp [internal transcribed spacer (ITS)] with that of the most closely related species Suhomyces guaymorum CBS 9823(T). CLIB 1725(T) rDNA sequences presented 18 substitutions and one indel out of 549 bp (D1/D2 domains) and 48 substitutions and 11 indels out of 398 bp (ITS) with that of its closest relative Suhomyces vadensis CBS 9454(T). Two novel species of the genus Suhomyces were described to accommodate these two strains: Suhomyces coccinellae f.a. sp. nov. (CLIB 1706(T) =CBS 14298(T)) and Suhomyces faveliae f.a. sp. nov. (CLIB 1725(T) =CBS 14299(T)).

Temporal aroma compound release during eating is a function of the physicochemical properties of the food matrix, aroma compounds, and oral physiology of individuals. However, the influence of each parameter on the release of each aroma component should be clarified. Two flavored lipoprotein matrices varying in composition were chewed in a chewing simulator that reproduced most of the physiological functions of the mouth. Aroma compound releases (butanoic acid, 2-heptanone, ethyl butyrate, 3-octanone, and 2-nonanone) were followed in real time by direct connection of the device to APCI-MS (atmospheric pressure chemical ionization mass spectrometry). Each oral parameter was controlled and decoupled using the in vitro device. The food matrix composition had only a low impact on aroma compound release, but the controlled oral parameters had significantly different influences on the release of aroma compounds according to their physicochemical characteristics. The release of certain compounds seemed more sensitive to bite force, while others seemed more sensitive to the shearing angle. The salivary flow rate primarily influenced the more hydrophobic compounds. Significant interactions were also observed between shear angle, salivary flow rate, and lipoprotein matrix composition, mainly for the release of the more hydrophobic volatile compounds; this needs further investigations to be clarified., This research was funded by INRA (Internal); the Conseil Régional de Bourgogne (France) and European Regional Development Fund (ERDF) funded the equipment used in this project (development of chewing simulator, mass spectrometer), We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI)

Sunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant that causes major yield losses to sunflower crops in the Old World. Efforts to understand how this parasitic weed recognizes and interacts with sunflowers are important for developing long-term genetic resistance strategies. However, such studies are hampered by the lack of genetic tools for O. cumana. The objectives of this research were to construct a genetic linkage map of this species using SSR and SNP markers, and mapping the Pg locus that is involved in plant pigmentation. The genetic map was developed from the progenies of a cross between the O. cumana inbred lines EK-12 and EK-A1, which originated from populations belonging to two distant and geographically separated gene pools identified in Spain. The inbred lines also differed in plant pigmentation, with EK-A1 lacking anthocyanin pigmentation (pgpg genotype). A genetic map comprising 26 SSR and 701 SNP markers was constructed, which displayed 19 linkage groups (LGs), corresponding to the 19 chromosome pairs of O. cumana. The total length of the map was 1795.7 cM, with an average distance between two adjacent positions of 2.5 cM and a maximum map distance of 41.9 cM. The Pg locus mapped to LG19 between the SNP markers OS02468 and OS01653 at 7.5 and 3.4 cM, respectively. This study constitutes the first linkage map and trait mapping study in Orobanche spp., laying a key foundation for further genome characterization and providing a basis for mapping additional traits such as those having a key role in parasitism., This study has been partially funded by the research project AGL2017-87693-R of the Spanish Ministry of Economy and Innovation (cofunded with EU FEDER Funds), Biogemma and INRA (Institut National de la Recherche Agronomique, Paris, France).

The gut microbiota has been evolving with its host along the time creating a symbiotic relationship. In this study, we assess the role of the host genome in the modulation of the microbiota composition in pigs. Gut microbiota compositions were estimated through sequencing the V3-V4 region of the 16S rRNA gene from rectal contents of 285 pigs. A total of 1,261 operational taxonomic units were obtained and grouped in 18 phyla and 101 genera. Firmicutes (45.36%) and Bacteroidetes (37.47%) were the two major phyla obtained, whereas at genus level Prevotella (7.03%) and Treponema (6.29%) were the most abundant. Pigs were also genotyped with a high-throughput method for 45,508 single nucleotide polymorphisms that covered the entire pig genome. Subsequently, genome-wide association studies were made among the genotypes of these pigs and their gut microbiota composition. A total of 52 single-nucleotide polymorphisms distributed in 17 regions along the pig genome were associated with the relative abundance of six genera; Akkermansia, CF231, Phascolarctobacterium, Prevotella, SMB53, and Streptococcus. Our results suggest 39 candidate genes that may be modulating the microbiota composition and manifest the association between host genome and gut microbiota in pigs., This work was funded by the Fondo Europeo de Desarrollo Regional (FEDER) and the Spanish Ministerio de Economía y Competitividad (MINECO AGL2014-56369-C2 and AGL2017-82641-R). D. Crespo-Piazuelo was funded by a “Formació i Contractació de Personal Investigador Novell” (FI-DGR) Ph.D grant from the Generalitat de Catalunya (ECO/1788/2014) and by the PiGutNet COST Action (www.pigutnet.eu) for a Short Term Scientific Mission at the GABI laboratory (INRA, France) under the supervision of J. Estellé. Contract of L. Migura-Garcia was supported by INIA and the European Social Fund. L. Criado-Mesas was funded with a FPI grant from the AGL2014-56369-C2 project. M. Revilla was also funded by a FI-DGR (ECO/1639/2013). M. Ballester was financially supported by a “Ramón y Cajal” contract (RYC-2013-12573) from the Spanish Ministry of Economy and Competitiveness. We acknowledge the support of the Spanish Ministry of Economy and Competitiveness for the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics and the CERCA Programme/Generalitat de Catalunya.

[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCA [ADD1_IRSTEA]Systèmes aquatiques soumis à des pressions multiples; International audience; To improve the assessment of aquatic organism responses to environmental stressors, there is an interest in studying epigenetic marks in addition to other validated biomarkers. Indeed, the epigenetic marks may be influenced by the surrounding environment. Non-model invertebrates such as gammarids are sentinel organisms representative of the diversity of natural stream communities. Despite their ecologically relevance, the epigenetic responses have been to date poorly documented in these species. The present study explores the measurement of the global cytosine methylation level in the genome of the freshwater crustacean Gammarus fossarum. In a first step, natural variability of global cytosine methylation level (basal level) was assessed by studying the effect of sex, age and sampling site of organisms. Results showed a significant effect of age and sampling site. In a second step, effects of water temperature and food starvation were studied. For both factors, a hypermethylation was observed after 1 month of exposure. In a third step, gammarids were exposed to a range of environmentally relevant cadmium concentrations (0.05-5 µg/L) in order to assess the effect of a chemical stress. Whatever the cadmium concentration used, a significant hypomethylation was observed after 14 days followed by a trend for hypermethylation after 1 month of exposure. These results are the first ones dealing with the 5Cmethylation status in gammarids. The results constitute potential markers of environmental stresses in relevant sentinel species widely used in ecotoxicological studies.

Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that infects sunflower roots, causing yield losses. Here, by using a map-based cloning strategy, we identified HaOr7—a gene that confers resistance to O. cumana race F—which was found to encode a leucine-rich repeat receptor-like kinase. The complete HAOR7 protein is present in resistant lines of sunflower and prevents O. cumana from connecting to the vascular system of sunflower roots, whereas susceptible lines encode a truncated protein that lacks transmembrane and kinase domains., This work was supported by INRA, Syngenta seeds and the French Laboratory of Excellence project TULIP (ANR-10-LABX-41; ANR-11-IDEX-0002-02).

International audience; Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA1, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA1 in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA1 . dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA1 . Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.

International audience; Six yeast strains representing two novel Wickerhamiella species were isolated from plants and insects collected in Costa Rica, Brazil, and French Guiana. They belong to a subclade containing Wickerhamiella domercqiae and Wickerhamiella bombiphila, and differ by approximately 12 % in the D1 /D2 sequences of the large subunit rRNA gene from these species. The intergenic spacer (ITS) regions of the two novel species differ by around 19 and 27%, respectively, from those of W. domercqiae. The novel species exhibit 5 % divergence in the D1 /D2 sequences among them (around 4 % in the ITS). The names Wickerhamiella dianesei f.a., sp. nov. and Wickerhamiella kurtzmanii f.a., sp. nov. are proposed to accommodate these species, for which a sexual cycle has not been observed. Wickerhamiella dianesei was isolated from the stingless bee, Trigona fulviventris, collected in an Asteraceae flower in Costa Rica, and from leaves of Sabicea brasiliensis (Rubiaceae) and a flower of Byrsonima crassifolia (Malpighiaceae) in Brazil. Wickerhamiellsa kurtzmanii was isolated from a flower of Ipomoea batatoides (Convolvulaceae) in Costa Rica, the surface of a fruit of B. crassifolia in Brazil, and flowers in French Guiana. The type strains are Wickerhamiella dianesei UWOPS 00-107.1(T) (=CBS 14185=NRRL Y-63789; Mycobank number MB 827008) and Wickerhamiella kurtzmanii UWOPS 00-192.1(T) (=CBS 15383=NRRL Y-63979; MB 827011).

Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago. Its complete DNA sequence was reported in 1997. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family., Research in our teams was funded by the CNRS, INRA, MINECO grant BFU2015-67065-P (to S.A.), ANR grants 09-BLAN-0149-0 (to P.T.), ANR-12-Blanc-BSV3-0021 (to P.T. and R.C.L.), ANR-15-CE11-0 010-01 (to P.T. and R.C.L.), and an “Equipe de la Fondation Médicale (FRM)” grant (to P.T.).

14 páginas, 6 tablas., A direct comparison of cow and goat performance and milk fatty acid (FA) responses to diets known to induce milk fat depression in the bovine has suggested interspecies differences in rumen and mammary lipid metabolism. Thus, this study was conducted to infer some potential mechanisms responsible for the differences in mammary lipogenesis due to diet and ruminant species. To meet this objective, 12 cows and 15 goats were fed a basal diet (control), a similar diet supplemented with 2.2% fish oil (FO), or a diet containing 5.3% sunflower oil and additional starch (+38%; SOS) according to a 3 × 3 Latin square design with 26-d experimental periods. Milk yield, milk composition, FA profile, and FA secretion were measured. On the last day of each period, the mRNA abundance of 19 key genes in mammary metabolism or the enzyme activity or both were measured in mammary tissue sampled by biopsy or at slaughter or both. The results show significant differences in the response of cows and goats to the dietary treatments. In cows, milk fat content and yield were lowered by FO and SOS (−31%), whereas only FO decreased milk fat content in goats (−21%) compared with the control. In cows and to a lesser extent in goats, FO and SOS decreased the secretion of C16 FA output (mmol/kg of BW). However, SOS increased the secretion of >C16 FA in goats. These changes in milk fat content and FA secretion were not associated with modifications in mammary expression or the activity of 19 proteins involved in the major lipogenic pathways. This absence of variation may be attributable to posttranscriptional regulation for these genes or related to the time of sampling of the mammary tissue relative to the previous meal and milking. Otherwise, the abundances of 15 mRNA among the 19 encoding for genes involved in lipid metabolism in the mammary gland were different among species, with 9 more abundant in cows (FASN, FADS1, SCD1, GPD1, LALBA, SREBF1, LXRA, PPARA, and PPARG1) and 6 more abundant in goats (G6PD, GPAM, SCD5, XDH, CSN2, and SP1). Similarly, a significant effect of the species was observed in the 4 enzyme activities measured; glycerol-3-phosphate dehydrogenase and malic enzyme were higher in cows, and FA synthase and glucose-6-phosphate dehydrogenase activities were higher in goats. In conclusion, the differences between cow and goat performance and milk FA responses to the FO and SOS treatments were not related to changes in the measured mammary lipogenic gene expression. Furthermore, the data provide evidence that the major mammary lipogenic pathways differ between the caprine and the bovine, whose biological significance remains to be unraveled., This study is dedicated to Kevin Shingfield, who passed away during the redaction of the paper. Kevin collaborated for a while with our team and added much to our work. Pablo G. Toral was granted a postdoctoral fellowship from the Fundación Alfonso Martín Escudero (Madrid, Spain). The authors gratefully acknowledge Jacques Rouel for assistance during the animal feeding experiment and with statistics; the staff of Unité Expérimentale des Ruminants de Theix [L’Institut National de la Recherche Agronomique INRA, SaintGenes-Champanelle, France] for the diligent care of the experimental animals; Philippe Gaydier, Simon Collange, Julien Mongiat, Dominique Roux, and Denys Durand for the collection of the mammary biopsies; and Sébastien Bes, Cyril Labonne, and Yannick Faulconnier from UMR 1213 Herbivores (INRA, Theix, France) for assistance in sampling collection and laboratory analysis. The advice of Christine Leroux (UMR 1213 Herbivores, INRA, Theix, France) during this work is acknowledged and appreciated.

The FLESHLESS BERRY (Flb) somatic variant identified in the grapevine cultivar Ugni Blanc develops grape berries without flesh, suggesting a role for the altered gene in differentiation of flesh cells. Here we describe identification of the molecular defect responsible for this phenotype. Using a combination of genetic and transcriptomic approaches, we detected the insertion of a miniature inverted-repeat transposable element in the promoter region of the PISTILLATA-like (VvPI) gene, the grapevine homologue of Arabidopsis PISTILLATA. The transposon insertion causes specific ectopic expression of the corresponding VvPI allele during early fruit development, causing expression of genes specific for petal and stamen development within the fruit. A causal relationship between the insertion and the phenotype was demonstrated by phenotypic and molecular analyses of somatic revertants showing that ectopic expression and mutant phenotype were always linked to the presence of the transposon insertion. The various phenotypic effects of the flb mutation on ovary morphology, fruit set and fruit development, depending on the cell lineage affected, are presented for each phenotype, offering new insights into floral and fleshly fruit development. The results highlight the importance of VvPI repression after fertilization to achieve normal fleshy fruit development, and the complex genetic, genomic and cellular interactions required for the flower to fruit transition in grapevine. © 2012 The Authors., This project was funded by the Grape and Wine Research and Development Corporation, Commonwealth Scientific and Industrial Research Organisation - Plant Industry Department, the Institut National de la Recherche Agronomique Research Division for Plant Breeding and Genetics, and the Spanish Ministerio de Ciencia e Innovacion (projects BIO2008-03892 and BIO2011-26229).

Crop attack by parasitic weeds such as Striga and Orobanche occurs through developmental processes triggered by host chemodetection. Seeds of those weed species remain dormant in the soil until germination is triggered by host root exudates. The development of haustorium, a parasitic plant organ that invades the host to withdraw its nutrients, is also initiated in Orobanchaceae by host molecular cues. The induction of haustorium development by exogenous signals has previously been reported for Striga but not for Orobanche species. In this work, we demonstrate that sphaeropsidone and epi-sphaeropsidone, two phytotoxic cyclohexene oxides isolated from the fungus Diplodia cupressi, a causal agent of cypress canker, induce haustorium development in radicles of the parasitic weeds Striga hermonthica, Orobanche crenata, and Orobanche cumana. This is the first report of chemical stimulation of haustorium development in radicles of Orobanche in the absence of host. In addition, SAR studies were carried out by testing the haustorium-inducing activity of the natural cyclohexene oxides, seven already known and four new hemisynthetic derivatives, in O. cumana, O. crenata, and S. hermonthica, to find a molecular specificity model required for haustorium induction. The results suggested that the haustorium-inducing activity is due to the possibility to convert the natural sphaeropsidone and natural and hemisynthetic derivatives in the corresponding 3-methoxyquinone and that the stereochemistry at C-5 also seems to affect this activity., The work was carried out in the frames of COST Action FA1206 Strigolactones: biological roles and applications. M. Fernández-Aparicio was supported by the European Union, Marie-Curie FP7 COFUND People Programme, through the award of an AgreenSkills fellowship (under grant agreement no. PCOFUND-GA-2010-267196) with additional support from INRA Division “Santé des Plantes et Environment, appel à projets scientifiques 2015 - Catégorie Biocontrôle”.

Many aquatic ecosystems are experiencing a decline in their oxygen (O2) content and this is predicted to continue. Implications of this change on several properties of bacterioplankton (heterotrophic prokaryotes) remain however are poorly known. In this study, oxic samples (~170 µM O2?=?controls) from an oligohaline region of the Scheldt Estuary were purged with N2 to yield low-O2 samples (~69 µM O2?=?treatments); all were amended with 13C-glucose and incubated in dark to examine carbon incorporation and cell size of heterotrophic prokaryotes, and relationships between organic matter (OM) degradation and phosphate (P) availability in waters following O2 loss. Stable isotope (13C) probing of phospholipid fatty acids (PLFA) and flow cytometry were used. In samples that have experienced O2 loss, PLFA biomass became higher, prokaryotic cells had significantly larger size and higher nucleic acid content, but P concentrations was lower, compared to controls. P concentration and OM degradation were positively related in controls, but uncoupled in low-O2 samples. Moreover, the dominant PLFA 16:1?7c (likely mainly from Gram-negative bacteria) and the nucleic acid content of heterotrophic prokaryotic cells in low-O2 samples explained (62–72 %) differences between controls and low-O2 samples in P amounts. Shortly after incubations began, low-O2 samples had consistently lower bacterial PLFA 13C-enrichments, suggesting involvement of facultatively anaerobic metabolism in carbon incorporation, and supporting the view that this metabolic pathway is widespread among pelagic bacteria in coastal nutrient-rich ecosystems. Estimates based on 13C-enrichment of PLFAs indicated that grazing by protozoa on some bacteria was stronger in low-O2 samples than in controls, suggesting that the grazing pressure on some heterotrophic prokaryotes may increase at the onset of O2 deficiency in nutrient-rich aquatic systems. These findings also suggest that physiological responses of heterotrophic prokaryotes to O2 loss in such ecosystems include increases in cell activity, high carbon incorporation, and possibly phosphorus retention by cells that may contribute to reduce phosphate availability in waters.

We present the first dated higher-level phylogenetic and biogeographic analysis of the butterfly family Riodinidae. This family is distributed worldwide, but more than 90% of the c. 1500 species are found in the Neotropics, while the c. 120 Old World species are concentrated in the Southeast Asian tropics, with minor Afrotropical and Australasian tropical radiations, and few temperate species. Morphologically based higher classification is partly unresolved, with genera incompletely assigned to tribes. Using 3666 bp from one mitochondrial and four nuclear markers for each of 23 outgroups and 178 riodinid taxa representing all subfamilies, tribes and subtribes, and 98 out of 145 described genera of riodinids, we estimate that Riodinidae split from Lycaenidae about 96 Mya in the mid-Cretaceous and started to diversify about 81 Mya. The Riodinidae are monophyletic and originated in the Neotropics, most likely in lowland proto-Amazonia. Neither the subfamily Euselasiinae nor the Nemeobiinae are monophyletic as currently constituted. The enigmatic, monotypic Neotropical genera Styx and Corrachia (most recently treated in Euselasiinae: Corrachiini) are highly supported as derived taxa in the Old World Nemeobiinae, with dispersal most likely occurring across the Beringia land bridge during the Oligocene. Styx and Corrachia, together with all other nemeobiines, are the only exclusively Primulaceae-feeding riodinids. The steadily increasing proliferation of the Neotropical Riodininae subfamily contrasts with the decrease in diversification in the Old World, and may provide insights into factors influencing the diversification rate of this relatively ancient clade of Neotropical insects., The study was funded by grant #204308 from the Research Council of Norway to M.E., and grants from the Baker Foundation, the Putnam Expeditionary Fund of the Museum of Comparative Zoology, and NSFDEB-0447242 to N.E.P. D.C.L. was funded by INRA and by ERC EMARES #250325 during writing. L.-W.W. and Y-F.H. were funded by NSC97-2621-B-003-003-MY3 and COA101-CF-02.1-C12.

Levels of exposure to pesticides in rice fields can be significant depending on the environmental policies practiced. The aim of European Union integrated management policy is to reduce pesticide use and impact on environment. Rice fields provide an alternative breeding habitat for many waterbirds that are exposed to the pesticides used and therefore can be valuable indicators of their risk for wildlife. To evaluate integrated management success we examined exposure of Black-winged Stilts (Himantopus himantopus) to cholinesterase-inhibiting pesticides in rice fields under different types of management by measuring plasma cholinesterase activity. Cholinesterase activity was lower in birds sampled in (a) 2008 after a period of intense pesticide application, than in (b) 2005-2007 and 2011 in rice fields subject to integrated management in Doñana (SW Spain) and (c) in control natural wetlands in Spain and Morocco. During 2009 and 2010, cholinesterase activity was lower in rice fields in Doñana than in rice fields in Larache and Sidi Allal Tazi (NW Morocco). Our results suggest that integrated management successfully reduced the exposure of Black-winged Stilts to pesticides in most of the years. Care should be taken to implement mosquito and pest crop controls on time and with environmentally friendly products in order to reduce its impact on wildlife., The Junta de Andalucía funded this study through the project “Las aves acuáticas de Doñana y el cultivo del arroz: la interacción entre la agricultura y la conservación de las zonas húmedas”. This study was possible thanks to the INRA administration and CNRST-CSIC collaboration program (P2007MA01 and P2009MA01). GMT was funded by an I3P-CSIC grant for the formation of Researchers. MMH is supported by a Marie Curie Intra-European Fellowship for Career Development (PIEF-GA-2011-299747) within the 7th Framework Programme (FP7 2007-2013) of the European Commission.

International audience; A highly thermostable and alkaline lichenase was isolated from the newly isolated strain Bacillus UEB-S. Single step purification was achieved by heating the enzyme extract for 30 min at 90 degrees C. The enzyme was a monomeric protein with a molecular weight of 28 kDa. The optimal temperature and pH for UEB-S lichenases activity were 60 degrees C and 6.0, respectively. More remarkably, the purified lichenase was stable over a broad range of temperature and pH. It retained more than 60% of its activity after incubation at 90 degrees C for 30min. Substrate specificity studies revealed that the enzyme is a true lichenase. A genomic library was screened. It allows the identification of a gene that encodes a putative lichenase showing 98% identity with the lichenase from Bacillus subtilis 168. Sequence comparison revealed that the two enzymes differed by two mutations at positions 69 and 83, where Va169 and Ser83 are replaced by Met and Ala amino acids, respectively. Therefore, a theoretical structural model was built using the lichenase from B. subtilis 168 Pdb code (3 o5sA) structure as template. Comparison of the two 3D structures suggested that Va169 stabilizes a calcium-binding site and could be involved in the higher stability of the enzyme.

For nearly 3 decades, listeriologists and immunologists have used mainly three strains of the same serovar (1/2a) to analyze the virulence of the bacterial pathogen Listeria monocytogenes. The genomes of two of these strains, EGD-e and 10403S, were released in 2001 and 2008, respectively. Here we report the genome sequence of the third reference strain, EGD, and extensive genomic and phenotypic comparisons of the three strains. Strikingly, EGD-e is genetically highly distinct from EGD (29,016 single nucleotide polymorphisms [SNPs]) and 10403S (30,296 SNPs), and is more related to serovar 1/2c than 1/2a strains. We also found that while EGD and 10403S strains are genetically very close (317 SNPs), EGD has a point mutation in the transcriptional regulator PrfA (PrfA*), leading to constitutive expression of several major virulence genes. We generated an EGD-e PrfA*mutant and showed that EGD behaves like this strain in vitro, with slower growth in broth and higher invasiveness in human cells than those of EGD-e and 10403S. In contrast, bacterial counts in blood, liver, and spleen during infection in mice revealed that EGD and 10403S are less virulent than EGD-e, which is itself less virulent than EGD-e PrfA*. Thus, constitutive expression of PrfA-regulated virulence genes does not appear to provide a significant advantage to the EGD strain during infection in vivo, highlighting the fact that in vitro invasion assays are not sufficient for evaluating the pathogenic potential of L. monocytogenes strains. Together, our results pave the way for deciphering unexplained differences or discrepancies in experiments using different L. monocytogenes strains. © 2014 Bécavin et al., European Research Council (advanced grant 233348), the French Agence Nationale de la Recherche (grants BACNET 10-BINF-02-01, IBEID ANR-10-LABX-62-01, and ERA-NET ANR-2010-PATH), the Institut Pasteur, the Institut National de la Santé et de la Recherche Médicale, and the Institut National de la Recherche Agronomique. A.K

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.-- et al., The diversity of Babesia species infecting cervids in parts of central and southern Spain was analyzed by collecting blood from farmed red deer (Cervus elaphus). Babesia sp. was isolated in vitro from two red deer herds in Cádiz and Ciudad Real. The number of Babesia sp. carriers differed between the two herds: 36/77 in Cádiz and 1/35 in Ciudad Real. Hyalomma lusitanicum was the most prevalent tick species identified on the Cádiz farm vegetation and on sampled animals, and is therefore a candidate vector. The molecular characteristics of 21 isolates were determined by complete (8 isolates) or partial (13 isolates) 18S rRNA gene sequencing. The sequences were highly similar (over 99.4% identity) and 6 sequence types were identified at the level of one herd only, demonstrating a rather high genetic diversity. They formed a monophyletic clade, and members of the three main sequence types shared a similar morphology and the same erythrocyte susceptibility pattern. This clade also included Babesia sp. Xinjiang isolated from sheep in China and Babesia sp. identified in giraffe in South Africa, with identities higher than 98.3% and statistically relevant phylogenetic support. None of the biological properties analyzed for both Babesia from red deer and Babesia sp. Xinjiang allowed their differentiation (ability to develop in vitro in erythrocytes from cattle and sheep, as well as in erythrocytes from different cervids, unsuccessful infection of calves). We propose the Babesia isolated from red deer as a new species named B. pecorum. Whether Babesia sp. Xinjiang and the Babesia characterized in South Africa belong to the same species is debated., This research was supported by funds from the Institut National de la Recherche Agronomique, the European Union Cooperation Project PIROVAC (KBBE-3-245145) and from the project “Zoonosis transmitidas por vectores hematófagos en Castilla-La Mancha: Mapa de riesgos” (JCCM POII09-0141-8176) and CDTI/Medianilla. F. Ruiz-Fons and I.G. Fernández de Mera are supported by a Juan de la Cierva contract from the Spanish Ministry for Economy and Competitiveness.

Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N50 = 694 kb, including contigs with N50 = 20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43 384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (Ks) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. © 2012 Blackwell Publishing Ltd.

Este artículo forma parte de la tesis de clara Roces. Mecanismos moleculares de respuesta al estrés sobre la pared celular en Lactococcus lactis. http://hdl.handle.net/10261/109851, Lactococcin 972 (Lcn972) is a nonlantibiotic bacteriocin that inhibits cell wall biosynthesis by binding to lipid II. In this work, two mutants resistant to Lcn972, Lactococcus lactis D1 and D1-20, with high (>320 arbitrary units [AU]/ml) and low (80 AU/ml) susceptibilities, respectively, have been isolated. Resistance to Lcn972 did not impose a burden to growth under laboratory conditions, nor did it substantially alter the physicochemical properties of the cell surface. However, the peptidoglycan of the mutants featured a higher content of muropeptides with tripeptide side chains than the wild-type strain, linking for the first time peptidoglycan remodelling to bacteriocin resistance. Moreover, L. lactis lacking a functional D, D-carboxypeptidase DacA (i.e., with a high content of pentapeptide side chain muropeptides) was shown to be more susceptible to Lcn972. Cross-resistance to lysozyme and nisin and enhanced susceptibility to penicillin G and bacitracin was also observed. Intriguingly, the Lcn972-resistant mutants were not infected by the lytic phage c2 and less efficiently infected by phage sk1. Lack of c2 infectivity was linked to a 22.6-kbp chromosomal deletion encompassing the phage receptor protein gene pip. The deletion also included maltose metabolic genes and the two-component system (TCS) F. However, a clear correlation between these genes and resistance to Lcn972 could not be clearly established, pointing to the presence of as-yet-unidentified mutations that account for Lcn972 resistance. © 2012, American Society for Microbiology., The work has been funded by grants BIO2007-65061 and BIO2010-17414 of the Ministerio de Ciencia e Innovación (Spain). C.R. is a recipient of a predoctoral JAE-CSIC fellowship. Work of M.-P.C.-C. and S.K. was supported by an INRA Jeune Equipe grant.

The knowledge of tree age is important for understanding tree growth and forest dynamics. It may be estimated by 'direct' methods involving growth ring counts, or by 'indirect' methods involving field measurements of growth rates. Direct methods are considered more accurate, but it is not clear if they are appropriate for all species, notably from the humid tropics. In this paper we assess the occurrence of annual growth rings and their utility for age estimation in three tropical tree species, Acrocarpus fraxinifolius, Dalbergia latifolia (Fabaceae) and Syzygium cumini (Myrtaceae), growing in traditional shade coffee plantations of the southern Western Ghats, India. These species previously were described as having "indistinct or absent" growth rings. We used anatomical studies, field measurements and computational methods to characterise growth rings and assess similarities between directly and indirectly estimated tree ages. Our study revealed that annual growth rings were characterised by different sets of anatomical features per species and were most distinct in the fast-growing deciduous A. fraxinifolius. Growth rates measured in the field showed annual periodicity in all three species, and reflected annual rainfall-drought cycles in D. latifolia and S. cumini. Direct age estimates were most similar to indirect estimates in D. latifolia, and least so in S. cumini. The results of direct age estimation by counting rings are consistent with them being annual in nature in tropical species with distinct and reliable annual growth ring formation. However, for species with poorly defined growth rings, indirect age estimation methods might be more useful.

International audience; Root-knot nematodes. Meloidogyne spp., are sedentary biotrophic parasites which are able to infest > 2000 plant species. After root invasion they settle sedentarily inside the vascular cylinder and maintain a compatible interaction for up to 8 weeks. Plant cells respond to pathogen attacks by producing reactive oxygen species (ROS). These ROS, in particular hydroperoxides, are important regulators of host-parasite interactions and partly govern the success or failure of disease. ROS producing and ROS scavenging enzymes from both the pathogen and the host finely tune the redox state at the host-pathogen interface. We have analysed the gene structure and organization of peroxiredoxins (prx) in Meloidogyne incognita and analysed their role in the establishment of the nematode in its host. Meloidogyne incognita has seven prx genes that can be grouped with other nematode prx into three clades. Clade B prx genes are more actively transcribed in parasitic stages compared with free-living pre-parasitic juveniles. We confirmed in vitro the activity of one of these. Mi-prx2.1, on hydrogen peroxide and butylhydroperoxide. We showed by ultrastructural immunocytochemistry the expression of clade B PRX proteins in the hypodermis and pseudocoelum beneath the tissues directly in contact with the environment, both in free-living and parasitic stages. Finally, knock-down of clade B prx genes led to a significant reduction in the ability of the nematodes to complete their life cycle in the host. The expression of clade B PRX proteins in the tissues in close contact with plant cells during parasitism and the impaired development of nematodes inside the host after clade B prx knock-down suggest an important role for these genes during infection. (C) 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

International audience; Understanding the processes that have led to the recent prevalence of necrotic genotypes in PVY populations is an important challenge for research programs studying this virus. Non-necrotic PVY(O)-139, necrotic PVY(N)-605 and point mutated versions of PVY(N)-605 (PVY(KRED), PVY(KR) and PVY(ED)) were used in mixtures to inoculate two Nicotiana hosts which express (N. tabacum cv. Xanthi) or not (N. clevelandii) necrosis symptoms in response to infection by PVY(N) group members. The comparison during serial passage experiments of proportions of PVY genotypes produced in mixed infected plants with those of the inocula was used to describe: (i) complementation between PVY(KR) and PVY(N) and between PVY(KRED) and PVY genotypes: (ii) exclusion of the PVY(KRED) genotype, previously described as fitter, during mixed infections in the presence of one of the less fit PVY(N), PVY(ED) and PVY(KR) genotypes and (iii) the prevalence of the non-necrotic PVY(KR) genotype in the presence of PVY(N) parental sequence. These results indicate that the role of both A/G(2213) and A/C(2271) nucleotides in the fitness of PVY genotypes depends on other genetic information in the viral genome that has not yet been identified. Moreover, the collected data indicate that mutation of the nucleotide 2213 in the PVY(N)-605 sequence could lead to the prevalence, both in N. tabacum cv. Xanthi and in N. clevelandii, of the non-necrotic PVY(KR) genotype. (C) 2010 Elsevier B.V. All rights reserved.

We have characterized the genetic and molecular origin of the reiterated reproductive meristem (RRM) somatic variant phenotype of grapevine cultivar Carignan. Here, we show that the extreme cluster proliferation and delayed anthesis observed in this somatic variant is caused by a single dominant mutation. Transcriptional profiling of Carignan and RRM plants during early stages of inflorescence development demonstrated the overexpression of a few regulatory genes, including VvTFL1A, a close TFL1 Arabidopsis homolog, in RRM inflorescences. Genetic and molecular analyses correlated the insertion of a class-II transposable element, Hatvine1-rrm, in the VvTFL1A promoter, with upregulation of the corresponding VvTFL1A allele in reproductive and vegetative organs of the shoot apex. These results suggest a role for this TFL1 grapevine homolog in the determination of inflorescence structure, with a critical effect on the size and branching pattern of grapevine fruit clusters. Our results demonstrate the existence of spontaneous cis-activation processes caused by class-II transposable elements in grapevine plants, and point to their possible role as a mechanism to generate somatic cell variation in perennial plants. This mechanism is expected to generate dominant phenotypes in chimeric sectors that can be readily exposed to natural selection., This research was supported by grants BIO2005-07612 and BIO2008-03892 from the Spanish Ministry for Science and Innovation, and by funds from the INRA Plant Breeding and Genetics Department.

Bile salts are natural detergents that facilitate the digestion and absorption of the hydrophobic components of the diet. However, their amphiphilic nature makes them very inhibitory for bacteria and strongly influences bacterial survival in the gastrointestinal tract. Adaptation to and tolerance of bile stress is therefore crucial for the persistence of bacteria in the human colonic niche. Bifidobacterium animalis subsp. lactis, a probiotic bacterium with documented health benefits, is applied largely in fermented dairy products. In this study, the effect of bile salts on proteomes of B. animalis subsp. lactis IPLA 4549 and its bile-resistant derivative B. animalis subsp. lactis 4549dOx was analyzed, leading to the identification of proteins which may represent the targets of bile salt response and adaptation in B. animalis subsp. lactis. The comparison of the wild-type and the bile-resistant strain responses allowed us to hypothesize about the resistance mechanisms acquired by the derivative resistant strain and about the bile salt response in B. animalis subsp. lactis. In addition, significant differences in the levels of metabolic end products of the bifid shunt and in the redox status of the cells were also detected, which correlate with some differences observed between the proteomes. These results indicate that adaptation and response to bile in B. animalis subsp. lactis involve several physiological mechanisms that are jointly dedicated to reduce the deleterious impact of bile on the cell's physiology., This work was financed by European Union FEDER funds and the Spanish Plan Nacional de I + D (project AGL2004-06727-C02-01/ALI). B. Sánchez was the recipient of an FPI predoctoral fellowship from the Spanish Ministerio de Ciencia y Tecnología and from the MICA Department of the National Institute for Research in Agronomy (INRA).

This article is available from: http://www.biomedcentral.com/1471-2229/7/34, [Background] Translation initiation factors of the 4E and 4G protein families mediate resistance to several RNA plant viruses in the natural diversity of crops. Particularly, a single point mutation in melon eukaryotic translation initiation factor 4E (eIF4E) controls resistance to Melon necrotic spot virus (MNSV) in melon. Identification of allelic variants within natural populations by EcoTILLING has become a rapid genotype discovery method., [Results] A collection of Cucumis spp. was characterised for susceptibility to MNSV and Cucumber vein yellowing virus (CVYV) and used for the implementation of EcoTILLING to identify new allelic variants of eIF4E. A high conservation of eIF4E exonic regions was found, with six polymorphic sites identified out of EcoTILLING 113 accessions. Sequencing of regions surrounding polymorphisms revealed that all of them corresponded to silent nucleotide changes and just one to a non-silent change correlating with MNSV resistance. Except for the MNSV case, no correlation was found between variation of eIF4E and virus resistance, suggesting the implication of different and/or additional genes in previously identified resistance phenotypes. We have also characterized a new allele of eIF4E from Cucumis zeyheri, a wild relative of melon. Functional analyses suggested that this new eIF4E allele might be responsible for resistance to MNSV., [Conclusion] This study shows the applicability of EcoTILLING in Cucumis spp., but given the conservation of eIF4E, new candidate genes should probably be considered to identify new sources of resistance to plant viruses. Part of the methodology described here could alternatively be used in TILLING experiments that serve to generate new eIF4E alleles., This work was supported by grants from Ministerio de Educación y Ciencia (ref. AGL2003-02739) (Spain) and GENOPLANTE (France). Cristina Nieto was in receipt of a Marie Curie Fellowship.