High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

International audienceIn the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed

Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species

Caractérisation d'hybrides intergénériques entre pomoïdées fruitières

*INRA Centre d'Angers. Unité d'Améliotation des Espèces Fruitières et Ornementales Diffusion du document : INRA Centre d'Angers. Unité d'Améliotation des Espèces Fruitières et Ornementales Diplôme : Maîtris

Xylomic, plateforme de génomique et de phénotypage des arbres

La plateforme technologique Xylomic est une des six composantes de l'Equipement d'Excellence Xyloforest. Elle est spécialisée dans la génomique des arbres et l'étude fine des caractères mesurables du bois. Au moyen d'outils technologiques de dernière génération, les généticiens cherchent à comprendre les déterminants environnementaux et génétiques de la variabilité du bois, ainsi que les processus biologiques et écologiques impliqués dans son élaboration. Scientifiques, professionnels et organismes de formation sont invités à utiliser les équipements de Xylomic dans le cadre de projets R&D ou de prestations

Xylomic, plateforme de génomique et de phénotypage des arbres

La plateforme technologique Xylomic est une des six composantes de l'Equipement d'Excellence Xyloforest. Elle est spécialisée dans la génomique des arbres et l'étude fine des caractères mesurables du bois. Au moyen d'outils technologiques de dernière génération, les généticiens cherchent à comprendre les déterminants environnementaux et génétiques de la variabilité du bois, ainsi que les processus biologiques et écologiques impliqués dans son élaboration. Scientifiques, professionnels et organismes de formation sont invités à utiliser les équipements de Xylomic dans le cadre de projets R&D ou de prestations

Xylomic, plateforme de génomique et de phénotypage des arbres

La plateforme technologique Xylomic est une des six composantes de l'Equipement d'Excellence Xyloforest. Elle est spécialisée dans la génomique des arbres et l'étude fine des caractères mesurables du bois. Au moyen d'outils technologiques de dernière génération, les généticiens cherchent à comprendre les déterminants environnementaux et génétiques de la variabilité du bois, ainsi que les processus biologiques et écologiques impliqués dans son élaboration. Scientifiques, professionnels et organismes de formation sont invités à utiliser les équipements de Xylomic dans le cadre de projets R&D ou de prestations

Cryopreservation of Prunus cerasus through vitrification and replacement of cold hardening with preculture on medium enriched with sucrose and/or glycerol

Cryopreservation is the only alternative, safe and cost-effective method for long-term storage of plant genetic resources, particularly for stone fruits (Prunus spp.). In this study, an efficient cryopreservation protocol was developed for sour cherry (Prunus cerasus L.). In vitro shoot tips of two varieties (Montmorency and Schattenmorelle) were successfully cryopreserved using the vitrification technique. Our study showed the possibility of replacing the 3-week cold hardening treatment of mother-plants with preculture of apices on medium enriched with sucrose and/or glycerol. The highest recovery percentages after liquid nitrogen exposure were obtained after a cold hardening treatment followed by a 3-day preculrure on 0.8 M sucrose medium or by replacing cold hardening with a 7-day preculture on the following media: 0.4 M glycerol or sucrose, 0.4 M sucrose + 0.4 M glycerol or 0.8 M glycerol. Under these conditions, recovery after cryopreservation ranged between 41 and 63%, These results complement the range of Prunus species successfully cryopreserved using in vitro explants. Our protocol, which is simplified in comparison with the original one, since cold hardening of mother-plants in a cold chamber is replaced by pretreatment of apices on medium with high sugar concentration, may facilitate the application of vitrification for cryopreservation of additional Prunus specie

Selective pressures between oaks and their obligate fungal parasite causing powdery mildew

International audienc