Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio

A Deviation from the Bipolar-Tetrapolar Mating Paradigm in an Early Diverged Basidiomycete

In fungi, sexual identity is determined by specialized genomic regions called MAT loci which are the equivalent to sex chromosomes in some animals and plants. Usually, only two sexes or mating types exist, which are determined by two alternate sets of genes (or alleles) at the MAT locus (bipolar system). However, in the phylum Basidiomycota, a unique tetrapolar system emerged in which four different mating types are generated per meiosis. This occurs because two functionally distinct molecular recognition systems, each encoded by one MAT region, constrain the selection of sexual partners. Heterozygosity at both MAT regions is a pre-requisite for mating in both bipolar and tetrapolar basidiomycetes. Tetrapolar mating behaviour results from the absence of genetic linkage between the two regions bringing forth up to thousands of mating types. The subphylum Pucciniomycotina, an early diverged lineage of basidiomycetes encompassing important plant pathogens such as the rusts and saprobes like Rhodosporidium and Sporidiobolus, has been so far poorly explored concerning the content and organization of MAT loci. Here we show that the red yeast Sporidiobolus salmonicolor has a mating system unlike any previously described because occasional disruptions of the genetic cohesion of the bipolar MAT locus originate new mating types. We confirmed that mating is normally bipolar and that heterozygosity at both MAT regions is required for mating. However, a laboratory cross showed that meiotic recombination may occur within the bipolar MAT locus, explaining tetrapolar features like increased allele number and evolution rates of some MAT genes. This pseudo-bipolar system deviates from the classical bipolar–tetrapolar paradigm and, to our knowledge, has never been observed before. We propose a model for MAT evolution in the Basidiomycota in which the pseudo-bipolar system may represent a hitherto unforeseen gradual form of transition from an ancestral tetrapolar system to bipolarity

Sex in the PAC: A hidden affair in dark septate endophytes?

<p>Abstract</p> <p>Background</p> <p>Fungi are asexually and sexually reproducing organisms that can combine the evolutionary advantages of the two reproductive modes. However, for many fungi the sexual cycle has never been observed in the field or <it>in vitro </it>and it remains unclear whether sexual reproduction is absent or cryptic. Nevertheless, there are indirect approaches to assess the occurrence of sex in a species, such as population studies, expression analysis of genes involved in mating processes and analysis of their selective constraints. The members of the <it>Phialocephala fortinii </it>s. l. - <it>Acephala applanata </it>species complex (PAC) are ascomycetes and the predominant dark septate endophytes that colonize woody plant roots. Despite their abundance in many ecosystems of the northern hemisphere, no sexual state has been identified to date and little is known about their reproductive biology, and how it shaped their evolutionary history and contributes to their ecological role in forest ecosystems. We therefore aimed at assessing the importance of sexual reproduction by indirect approaches that included molecular analyses of the mating type (<it>MAT</it>) genes involved in reproductive processes.</p> <p>Results</p> <p>The study included 19 PAC species and > 3, 000 strains that represented populations from different hosts, continents and ecosystems. Whereas <it>A. applanata </it>had a homothallic (self-fertile) <it>MAT </it>locus structure, all other species were structurally heterothallic (self-sterile). Compatible mating types were observed to co-occur more frequently than expected by chance. Moreover, in > 80% of the populations a 1:1 mating type ratio and gametic equilibrium were found. <it>MAT </it>genes were shown to evolve under strong purifying selection.</p> <p>Conclusions</p> <p>The signature of sex was found in worldwide populations of PAC species and functionality of <it>MAT </it>genes is likely preserved by purifying selection. We hypothesize that cryptic sex regularely occurs in the PAC and that further field studies and <it>in vitro </it>crosses will lead to the discovery of the sexual state. Although structurally heterothallic species prevail, it cannot be excluded that homothallism represents the ancestral breeding system in the PAC.</p

Passive samplers for chemical substance monitoring and associated toxicity assessment in water

The European legislation, and in particular the Water Framework Directive requires the development of cost efficient monitoring tools that can provide the required information for the assessment of water contamination. Passive sampling methods represent one of the novel tools that have a potential to be used in various regulatory monitoring programmes aimed at assessing the levels of chemical pollutants. These methods are particularly interesting for sampling polar organic pollutants in water because they provide representative information of the water quality over extended time periods (days to weeks) in environments with fluctuating contaminant concentrations. This is achieved by integrative sampling of pollutants over the whole sampler deployment period. These tools can be coupled to toxicity testing using bioassays that give information on toxic and ecotoxic hazards associated to substances that are present, these substances being identified or not. In this study the polar organic chemical integrative sampler (POCIS) was used in surface water to evaluate the water contamination by polar organic compounds and their potential toxicity

A multibiomarker approach to the assessment of pollution impacts in two Baltic Sea coastal areas in Sweden using caged mussels (Mytilus trossulus)

Blue mussels (Mytilus trossulus) were transplanted in cages for three months in two Swedish coastal areas in the Bothnian Sea (northern Baltic Sea) to investigate the interactions between analysed environmental chemicals and biological responses. A wide array of biological parameters (biomarkers) including antioxidant and biotransformation activity, geno-, cyto- and neurotoxic effects, phagocytosis, bioenergetic status and heart rate were measured to detect the possible effects of contaminants. Integrated Biomarker Response index and Principal Component Analysis performed on the individual biological response data were able to discriminate between the two study areas as well as the contaminated sites from their respective local reference sites. The two contaminated sites outside the cities of Sundsvall (station S1) and Gävle (station G1) were characterised by different biomarker response patterns. Mussels at station S1 showed a low condition index, increased heart rate recovery time and phagocytosis activity coinciding with the highest tissue concentrations of some trace metals, polycyclic aromatic hydrocarbons and organotins. At station G1 the highest organochlorine pesticide concentration was recorded as well as elevations in glutathione S-transferase activity, thiamine content and low lysosomal membrane stability. Significant variability in the geno- and cytotoxic responses and bioenergetic status was also observed at the different caging stations. The results obtained suggest that different chemical mixtures present in the study areas cause variable biological response patterns in organisms

Assessment of the effects of discontinuous sources of contamination through biomarker analyses on caged mussels

International audienc

Genotoxicant accumulation and cellular defence activation in bivalves chronically exposed to waterborne contaminants from the Seine River

International audienc

Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens

Chantier qualité GAInternational audienceNumerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced c. 17 000–32 000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non-model organisms for which candidate genes for diversifying selection are needed

Contamination externe des agriculteurs et contamination environnementales par les produits phytosanitaires en arboriculture : de la compréhension des pratiques à la prévention des cancers (projet CANEPA)

International audienceLa France, dont la moitié du territoire est dédiée à l'agriculture, se situe au premier rang européen des utilisateurs de produits de protection des plantes (PPP). La question des PPP sur la santé est un sujet de préoccupation croissante pour les professionnels agricoles, qui sont plus d'1 millions à être au contact direct ou indirect de pesticides, mais également du point de vue environnemental. En effet, s'ils ont permis un grand progrès en augmentant les rendements de la production alimentaire, leurs conséquences sur l'environnement ou la santé humaine sont désormais avérées. Le projet pluridisciplinaire CANEPA constitue une opportunité unique de rassembler les thématiques Environnement et Santé autour de la question des impacts liés à l'exposition aux pesticides. Il se propose de comprendre les déterminants de la contamination des travailleurs agricoles et des écosystèmes et d'envisager comment une réduction des usages des produits phytosanitaires est susceptible de s'accompagner à la fois d'une diminution de l'impact sur les écosystèmes et d'une réduction des expositions des travailleurs. Pour cela, l'étude CANEPA a été menée sur deux années consécutives (2016-2017) dans le but de renseigner les expositions des personnes travaillant dans les vergers de pommiers. Au total, plus de 150 observations ont été effectuées sur le terrain (31 observations de traitement, 66 observations de réentrées et 51 récoltes) dans 30 exploitations agricoles sur trois zones de production (Normandie, Rhône-Alpes et Sud-Ouest). L'exposition professionnelle a été étudiée par la pose de patches (au nombre de 11) au contact de la peau et par l'utilisation de gants en coton pour les mains, afin de recueillir les expositions cutanées des travailleurs en condition normale de travail. Pour les traitements, des pompes ont été placées pour collecter les expositions respiratoires. Au total, plus de 3000 patches ont été collectés au cours de ces deux années d'étude. Des vidéos ont été prises pour chaque observation afin de renseigner au mieux les sources d'expositions. En parallèle, un volet agronomique a été mis en place à l'aide d'enquêtes auprès des pomiculteurs, d'organismes professionnels et de centres techniques expérimentaux, afin de connaître les systèmes de production, les pratiques culturales et les règles de décision en matière de protection phytosanitaire du verger. Les sources potentielles d'exposition ont été recherchées par le prélèvement de nombreux échantillons. Les résidus de pesticides à la surface des pommes et des feuilles ont été déterminés. Des prélèvements à l'aide de lingettes ont également été effectués pour échantillonner le matériel manipulé par les travailleurs. Enfin, des préleveurs atmosphériques bas-débits ont été utilisés pour contrôler la qualité de l'air à l'intérieur de la salle de préparation de pesticides et à l'intérieur de la cabine du tracteur. La contamination environnementale a également été étudiée par la mise en place d'échantillonneurs passifs atmosphériques et aquatiques (périodicité mensuelle) et par des prélèvements ponctuels d'eaux et de sols. Enfin, des échantillons d'urine et des mèches de cheveux ont été collectés en tant que témoin d'exposition. L'analyse des échantillons par des nouvelles méthodologies analytiques très sensibles, développées au laboratoire, permettra de mettre en évidence les quantités de PPPs sur les différents échantillons collectés (principalement Captane et Dithianon qui sont les deux fongicides les plus utilisés contre la tavelure en vergers de pommiers). Le but in fine est de mieux comprendre les déterminants de la contamination des travailleurs et des écosystèmes et de proposer des mesures concrètes aux agriculteurs pour une réduction de leur exposition aux PPPs. Les indicateurs d'exposition élaborés au cours de ce projet seront utiles pour les futures études épidémiologiques