ABIeS: A database for softwood identification

International audienceSoftwoods constitute an important part of the plant macro-remains that are found within the Carboniferous to the most recent fossil deposits. Their taxonomical study is mostly made possible thanks to classical references (Philips 1948, Greguss 1955, Esteban 2004, Philippe & Bamford 2008). As for hardwoods, in addition to similar standard publications, a dedicated database has started being developed seven years ago (Insidewood - Wheeler 2011). Today Insidewood constitutes a very useful and indispensable tool, in constant development, which allows online identification for extant and fossil hardwoods. Despite their abundance in fossil deposits, no tool dedicated to softwoods has been developed yet. To fill this gap, we initiated the implementation of a softwood database, ABIeS, on the biodiversity collaborative management platform Xper3 (Ung et al. 2010). The descriptive model is mainly based on IAWA list of softwood features (IAWA committee 2004) but we also propose original features linked for instance to cell size and cross-field characteristics. As a first step, we tried as much as possible to illustrate the softwoods diversity using local resources. Therefore, extant species were chosen among the one hosted at the MNHN-xylarium, Paris, whereas fossil species where chosen from the collection Boureau (UPMC, Paris). We finally carried a global analysis of the database in order to better understand the softwood variability regarding systematics and ecology. This project, although initiated in our laboratory in Paris has a collaborative aim. We invite all the researchers who are interested by the wood anatomy of extant and fossil conifers to join us. Esteban, L. G., de Palacios, P. D. P., Casasús, A. G., & Fernández, F. G. (2004). Characterisation of the xylem of 352 conifers. Forest Systems, 13(3): 452-478.Greguss, P. (1955). Identification of living gymnosperms on the basis of xylotomy. Akademiai Kiado, Budapest. 263 pp.IAWA committee (2004). IAWA list of microscopic features for softwood identification. IAWA J, 25(1): 1-70.Philippe, M., & Bamford, M. K. (2008). A key to morphogenera used for Mesozoic conifer-like woods. Review of Palaeobotany and Palynology, 148(2-4): 184-207.Phillips, E.W.J. 1948. Identification of Softwoods. Forest Products Research Bulletin 22, 56 p.Ung, V., Dubus, G., Zaragüeta-Bagils, R., Vignes-Lebbe, R. 2010. Xper2: introducing e-taxonomy. Bioinformatics, 26 (5): 703-704.Wheeler, E.A. (2011). InsideWood - a web resource for hardwood anatomy. IAWA J. 32 (2): 199-211

Softwood from the Boureau’s collection: re-examination in the light of the ABIeS database

International audienceThe ABIeS database aims to become the equivalent for softwood anatomy of what Insidewood database represents today for hardwoods. This project, begun two years ago, was intended for producing a knowledge database on the anatomy of extant and fossil coniferous woods. In a first time, we initiated a work on softwood features. Although the main nomenclature of these features is the one proposed by the IAWA, a review of other features was realized using key references on softwood anatomy. A number of original features were also proposed. Emphasis has been placed on the qualitative features related to radial and cross-field pits, which are particularly important for softwood identification but also on quantitative traits linked to fibers, rays and pits. All these characters were then tested in order 1) to assess their effectiveness and usability, 2) to evaluate their relationships and 3) to establish their efficiency to discriminate different taxa (at the specific, genera or family level). A short list of features that seemed the most judicious but also the most commonly used by the wood anatomist community was then set up. Finally, a thesaurus was compiled to define, illustrate and explain the coding methodology for these selected features.In a second step of our project, we chose to illustrate extant genera diversity by including all material available in each family in the xylotheque of diverse institutions (MNHN in Paris, CIRAD in Montpellier and in the Royal Museum for Central Africa in Tervuren). For the largest genera, that is those with more than 10 species, we chose to code at least 20% of their species. The latter were selected from recent phylogenies in the aim of illustrating the diversity of the genera. Data on biological habit and ecological requirements of the different species were also provided.The third phase of this work was dedicated to the inclusion of some of the fossil woods from the Boureau’s collection. This work allows us to re-examine many type specimens in the light of extant conifer anatomy, to evaluate their anatomical proximity but also to detect potential impact of ecological or bio-geographical parameters on fossil wood anatomy.This project, although initiated within the CR2P in Paris has a collaborative aim. We invite all the researchers who are interested by the wood anatomy of extant and fossil conifers to join us

Association of two co-occurring mutations at the AvrMlp7 avirulence locus in poplar rust during the breakdown of RMlp7 resistance gene: [Poster]

International audienceThe deployment of plant varieties carrying resistance (R) genes exerts strong selection pressures towards pathogen populations. Several studies reported the rapid evolution of avirulence (Avr) genes to escape R-mediated plant immunity and identified a variety of mechanisms leading to virulence. The poplar rust fungus Melampsora larici-populina is the most damaging pathogen of poplars. A major adaptive event occurred in 1994 with the breakdown of RMlp7 resistance gene in poplar in Europe. Population genomics studies identified a locus in the genome of M. larici-populina, which likely corresponds to the AvrMlp7 candidate avirulence gene. We used a population genetics approach combined with dedicated qPCR assays on a comprehensive set of 281 isolates, covering 27 years (encompassing the resistance breakdown event), to validate the candidate locus and to assess its polymorphism. We found two mechanisms, a point mutation and a deletion, that allowed the pathogen to escape RMlp7-mediated resistance. Six diploid genotypes were thus characterized at the candidate locus (three avirulent and three virulent). In addition, a temporal analysis revealed that the two virulence alleles pre-existed (harbored as avirulent heterozygous genotypes) since the early samplings and were found in association (as virulent genotypes) at the time of the resistance breakdown. Our study documented that, in a diploid pathogen, combining virulence determinisms is adaptive

A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown

International audienceThe deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown

Association of two co-occurring mutations at the AvrMlp7 avirulence locus in poplar rust during the breakdown of RMlp7 resistance gene: [Poster]

International audienceThe deployment of plant varieties carrying resistance (R) genes exerts strong selection pressures towards pathogen populations. Several studies reported the rapid evolution of avirulence (Avr) genes to escape R-mediated plant immunity and identified a variety of mechanisms leading to virulence. The poplar rust fungus Melampsora larici-populina is the most damaging pathogen of poplars. A major adaptive event occurred in 1994 with the breakdown of RMlp7 resistance gene in poplar in Europe. Population genomics studies identified a locus in the genome of M. larici-populina, which likely corresponds to the AvrMlp7 candidate avirulence gene. We used a population genetics approach combined with dedicated qPCR assays on a comprehensive set of 281 isolates, covering 27 years (encompassing the resistance breakdown event), to validate the candidate locus and to assess its polymorphism. We found two mechanisms, a point mutation and a deletion, that allowed the pathogen to escape RMlp7-mediated resistance. Six diploid genotypes were thus characterized at the candidate locus (three avirulent and three virulent). In addition, a temporal analysis revealed that the two virulence alleles pre-existed (harbored as avirulent heterozygous genotypes) since the early samplings and were found in association (as virulent genotypes) at the time of the resistance breakdown. Our study documented that, in a diploid pathogen, combining virulence determinisms is adaptive

: [Oral presentation]

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