Génomique comparative entre Muscadinia rotundifolia et Vitis vinifera pour faciliter l'identification de gènes de résistance

Muscadinia rotundifolia est une espèce de la famille des Vitaceae. C est un sous-genre du genre Vitis, le deuxième sous-genre étant celui des Euvitis qui comprend l espèce cultivée Vitis vinifera (2n=38). M. rotundifolia (2n=40) est une source de résistance aux maladies très importante pour l amélioration de la vigne. Son génome commence seulement à être décrit avec deux cartes génétiques récemment publiées. Ma thèse a consisté à utiliser des ressources génomiques chez M. rotundifolia cv Regale (banque BAC, collection de séquence d extrémités de BAC ou BES et séquences de BACs) pour caractériser le génome de cette espèce en comparaison avec celui de V. vinifera. Les résultats obtenus ne montrent pas de différence importante entre les génomes des deux espèces en termes de composition du génome en bases (GC%), en séquences codantes ou en éléments répétés. De même, à une échelle globale, la famille de gènes NBS-LRR semble être similaire en termes de nombre et de balance entre les sous-familles. A une échelle plus fine cependant (carte physique et séquences de BAC), des remaniements relativement importants sont observés dans des régions portant cette famille de gènes, aboutissant parfois à des contenus différents en gènes, de région normalement homologues: duplication différentielles de gènes, présence/absence de gènes.Muscadinia Rotundifolia is a species of the Vitaceae family. It is a sub-genus of the Vitis genus along with the Euvitis sub-genus, which the cultivated species Vitis vinifera belongs to. M. rotundifolia (2n=40) is a very important source of resistance to diseases in grapevine breeding programs. Its genome is only starting to be described with the recent publication of two genetic maps. The present study aimed at using M. rotundifolia cv Regale genomic resources (BAC library, BAC end sequences or BES, BAC sequences) in order to characterize the genome of this species in comparison with the genome of V. vinifera. The results showed that there is no striking difference between the two species in term of base composition (GC %), repeats frequency and gene space. The NBS LRR gene family also seems to be globally quite similar between the two species in terms of numbers and balance between subfamilies. At a finer scale (physical map and BAC sequence), frequent rearrangements are observed in genomic regions carrying the NBS-LRR gene family sometimes clearly associated with a different gene content between the two species in homologous regions: differential gene duplication, presence/absence of genes.EVRY-Bib. électronique (912289901) / SudocSudocFranceF

Does maternal environmental condition during reproductive development induce genotypic selection in Picea abies ?

In forest trees, environmental conditions during reproduction can greatly influence progeny performance. This phenomenon probably results from adaptive phenotypic plasticity but also may be associated with genotypic selection. In order to determine whether selective effects during the reproduction are environment specific, single pair-crosses of Norway spruce were studied in two contrasted maternal environments (warm and cold conditions). One family expressed large and the other small phenotypic differences between these crossing environments. The inheritance of genetic polymorphism was analysed at the seed stage. Four parental genetic maps covering 66 to 78% of the genome were constructed using 190 to 200 loci. After correcting for multiple testing, there is no evidence of locus under strong and repeatable selection. The maternal environment could thus only induce limited genotypic-selection effects during reproductive steps, and performance of progenies may be mainly affected by a long-lasting epigenetic memory regulated by temperature and photoperiod prevailing during seed productio

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation

Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2\u2009Mb and 62.9\u2009Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in low-gene density regions of the poplar genome and were, for the majority, associated with the activity of transposable elements. Genes affected by SV showed lower-than-average expression levels and higher levels of dN/dS, suggesting that they are subject to relaxed selective pressure or correspond to pseudogenes.Functional annotation of genes affected by INDELs showed over-representation of categories associated with transposable elements activity, while genes affected by genic CNVs showed enrichment in categories related to resistance to stress and pathogens. This study provides a genome-wide catalogue of SV and the first insight on functional and structural properties of the poplar pan-genome

The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis

Genetic determination of gender is a fundamental developmental and evolutionary process in plants. Although it appears that dioecy in [i]Populus[/i] is genetically controlled, the precise gender-determining systems remain unclear. The recently released second draft assembly and annotated gene set of the [i]Populus[/i] genome provided an opportunity to revisit this topic. We hypothesized that over evolutionary time, selective pressure has reformed the genome structure and gene composition in the peritelomeric region of the chromosome XIX, which has resulted in a distinctive genome structure and cluster of genes contributing to gender determination in [i]Populus trichocarpa[/i]. Multiple lines of evidence support this working hypothesis. First, the peritelomeric region of the chromosome XIX contains significantly fewer single nucleotide polymorphisms than the rest of [i]Populus[/i] genome and has a distinct evolutionary history. Second, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding site–leucine-rich repeat (NBS–LRR) class of disease resistance genes in the entire [i]Populus[/i] genome. Third, there is a high occurrence of small microRNAs on chromosome XIX, which is coincident to the region containing the putative gender-determining locus and the major cluster of NBS–LRR genes. Further, by analyzing the metabolomic profiles of floral bud in male and female [i]Populus[/i] trees using a gas chromatography-mass spectrometry, we found that there are gender-specific accumulations of phenolic glycosides. Taken together, these findings led to the hypothesis that resistance to and regulation of a floral pathogen and gender determination coevolved, and that these events triggered the emergence of a nascent sex chromosome. Further studies of chromosome XIX will provide new insights into the genetic control of gender determination in [i]Populus[/i]

Resilience of genetic diversity in forest trees over the Quaternary

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

<p>Abstract</p> <p>Background</p> <p>One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it>Quercus robur</it>, its characterization and an analysis of BAC end sequences.</p> <p>Results</p> <p>The <it>Eco</it>RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it>ab initio </it>repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it>Arabidopsis thaliana</it>, <it>Vitis vinifera </it>and <it>Populus trichocarpa</it>. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it>V. vinifera.</it></p> <p>Conclusions</p> <p>This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p

Between but not within species variation in the distribution of fitness effects

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact