Exploration de données génomiques haut-débit pour l’étude de l’histoire évolutive des Oléacées

Oleaceae is a cosmopolitan plant family gathering several species of interest such as the olive, ash tree, lilac or jasmine. In addition, this family exhibits a large diversity, particularly in traits linked to reproduction. It thus constitutes a great study system, both in terms of fundamental implications to decipher evolutionary processes and economical applications for olive culture notably. In this dissertation, we took advantages of new possibilities offered by the increasing sequencing data to undertake the study of this non-model family evolution at the genomic scale. We investigated several puzzling questions in the family that have been little explored with genomics data. In particular, this work led to the identification of the genomic locus underlying self-incompatibility in olive which brings new insights on the evolution of OleaceaeLes Oléacées sont une famille de plantes cosmopolites incluant plusieurs espèces d’intérêt telles que l’olivier, le frêne, le lilas ou le jasmin. Cette famille présente en plus une large diversité, notamment au niveau de traits liés à la reproduction. Elle constitue donc un modèle d’étude particulièrement intéressant autant sur le plan fondamental pour déchiffrer les processus évolutifs, que sur un plan plus appliqué, pour l’oléiculture notamment. Dans le cadre de cette thèse, nous avons tiré profit de la disponibilité croissante de données de séquençage pour entreprendre l’étude de l’évolution de cette famille d’espèces non modèles à l’échelle génomique. Nous avons étudié différentes questions majeures dans l’évolution de cette famille, jusqu’ici peu explorées à l’aide de données génomiques. Ce travail a notamment abouti à l’identification de la région déterminant l’auto-incompatibilité chez l’olivier, apportant de nouvelles informations pour comprendre l'évolution des Oléacée

Exploration de données génomiques haut-débit pour l’étude de l’histoire évolutive des Oléacées

Oleaceae is a cosmopolitan plant family gathering several species of interest such as the olive, ash tree, lilac or jasmine. In addition, this family exhibits a large diversity, particularly in traits linked to reproduction. It thus constitutes a great study system, both in terms of fundamental implications to decipher evolutionary processes and economical applications for olive culture notably. In this dissertation, we took advantages of new possibilities offered by the increasing sequencing data to undertake the study of this non-model family evolution at the genomic scale. We investigated several puzzling questions in the family that have been little explored with genomics data. In particular, this work led to the identification of the genomic locus underlying self-incompatibility in olive which brings new insights on the evolution of OleaceaeLes Oléacées sont une famille de plantes cosmopolites incluant plusieurs espèces d’intérêt telles que l’olivier, le frêne, le lilas ou le jasmin. Cette famille présente en plus une large diversité, notamment au niveau de traits liés à la reproduction. Elle constitue donc un modèle d’étude particulièrement intéressant autant sur le plan fondamental pour déchiffrer les processus évolutifs, que sur un plan plus appliqué, pour l’oléiculture notamment. Dans le cadre de cette thèse, nous avons tiré profit de la disponibilité croissante de données de séquençage pour entreprendre l’étude de l’évolution de cette famille d’espèces non modèles à l’échelle génomique. Nous avons étudié différentes questions majeures dans l’évolution de cette famille, jusqu’ici peu explorées à l’aide de données génomiques. Ce travail a notamment abouti à l’identification de la région déterminant l’auto-incompatibilité chez l’olivier, apportant de nouvelles informations pour comprendre l'évolution des Oléacée

Mining high-throughput genomic datasets to investigate the evolutionary history of Oleaceae

Les Oléacées sont une famille de plantes cosmopolites incluant plusieurs espèces d’intérêt telles que l’olivier, le frêne, le lilas ou le jasmin. Cette famille présente en plus une large diversité, notamment au niveau de traits liés à la reproduction. Elle constitue donc un modèle d’étude particulièrement intéressant autant sur le plan fondamental pour déchiffrer les processus évolutifs, que sur un plan plus appliqué, pour l’oléiculture notamment. Dans le cadre de cette thèse, nous avons tiré profit de la disponibilité croissante de données de séquençage pour entreprendre l’étude de l’évolution de cette famille d’espèces non modèles à l’échelle génomique. Nous avons étudié différentes questions majeures dans l’évolution de cette famille, jusqu’ici peu explorées à l’aide de données génomiques. Ce travail a notamment abouti à l’identification de la région déterminant l’auto-incompatibilité chez l’olivier, apportant de nouvelles informations pour comprendre l'évolution des OléacéesOleaceae is a cosmopolitan plant family gathering several species of interest such as the olive, ash tree, lilac or jasmine. In addition, this family exhibits a large diversity, particularly in traits linked to reproduction. It thus constitutes a great study system, both in terms of fundamental implications to decipher evolutionary processes and economical applications for olive culture notably. In this dissertation, we took advantages of new possibilities offered by the increasing sequencing data to undertake the study of this non-model family evolution at the genomic scale. We investigated several puzzling questions in the family that have been little explored with genomics data. In particular, this work led to the identification of the genomic locus underlying self-incompatibility in olive which brings new insights on the evolution of Oleacea

Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes

The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae’s diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae

Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes

The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae’s diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae

Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage

International audienceSummary Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta ). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32–100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6–28 per Ma) and subsequent losses (11–24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02–0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation

Contrasting Genetic Footprints among Saharan Olive Populations: Potential Causes and Conservation Implications

International audienceThe Laperrine’s olive is endemic to the Saharan Mountains. Adapted to arid environments, it may constitute a valuable genetic resource to improve water-stress tolerance in the cultivated olive. However, limited natural regeneration coupled with human pressures make it locally endangered in Central Sahara. Understanding past population dynamics is thus crucial to define management strategies. Nucleotide sequence diversity was first investigated on five nuclear genes and compared to the Mediterranean and African olives. These data confirm that the Laperrine’s olive has a strong affinity with the Mediterranean olive, but it shows lower nucleotide diversity than other continental taxa. To investigate gene flows mediated by seeds and pollen, polymorphisms from nuclear and plastid microsatellites from 383 individuals from four Saharan massifs were analyzed. A higher genetic diversity in Ahaggar (Hoggar, Algeria) suggests that this population has maintained over the long term a larger number of individuals than other massifs. High-to-moderate genetic differentiation between massifs confirms the role of desert barriers in limiting gene flow. Yet contrasting patterns of isolation by distance were observed within massifs, and also between plastid and nuclear markers, stressing the role of local factors (e.g., habitat fragmentation, historical range shift) in seed and pollen dispersal. Implications of these results in the management of the Laperrine’s olive genetic resources are discusse

Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity

International audienceThe betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected more than 100 years ago

Expedient Bayesian prediction of subfossil bone protein content using portable ATR-FTIR data

Rapid and minimally destructive methods for estimating the endogenous organic content of subfossil bone save time, lab consumables, and valuable ancient materials. Fourier transform infrared (FTIR) spectroscopy is an established method to estimate bone protein content, and portable spectroscopes enable field applications. We review the ability of benchtop and portable FTIR indices to predict %N and %collagen from 137 bone specimens drawn from eight taxa. We also explore associations of these indices with the endogenous DNA content estimated for 105 specimens. Bulk bone elemental abundance and crystallinity index data reflect diagenetic alteration of these specimens, which come from a variety of depositional environments in four countries (Madagascar, Greece, Monaco, and Germany). Infrared (IR) indices from benchtop and portable units perform similarly well in predicting observed sample N content and collagen yields. Samples that include little collagen (0–5 wt%) tend to have similar IR index values, and we present a Bayesian approach for the prediction of collagen yields. Bone type best explains variation in target species DNA content (endogenous DNA being particularly abundant in petrosals), but low IR index values were consistently associated with minimal DNA content. We conclude that, although portable FTIR fails to distinguish collagen preservation among poorly preserved samples, a simple approach with minimal sample preparation can effectively screen bone from a variety of taxa, elements, and environments for the extraction of organics

A hemizygous supergene controls homomorphic and heteromorphic self-incompatibility systems in Oleaceae

International audienceSelf -incompatibility (SI) has evolved independently multiple times and prevents self -fertilization in hermaphrodite angiosperms. Several groups of Oleaceae such as jasmines exhibit distylous flowers, with two compatibility groups each associated with a specific floral morph. 1 Other Oleaceae species in the olive tribe have two compatibility groups without associated morphological variation. 2-5 The genetic basis of both homomorphic and dimorphic SI systems in Oleaceae is unknown. By comparing genomic sequences of three olive subspecies ( Olea europaea ) belonging to the two compatibility groups, we first locate the genetic determinants of SI within a 700 -kb hemizygous region present only in one compatibility group. We then demonstrate that the homologous hemizygous region also controls distyly in jasmine. Phylogenetic analyses support a common origin of both systems, following a segmental genomic duplication in a common ancestor. Examination of the gene content of the hemizygous region in different jasmine and olive species suggests that the mechanisms determining compatibility groups and floral phenotypes (whether homomorphic or dimorphic) in Oleaceae rely on the presence/absence of two genes involved in gibberellin and brassinosteroid regulation