Deciphering the genome structure and paleohistory of _Theobroma cacao_

We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution

Dynamic modelling of ammonia biofiltration from waste gases

A dynamic model to describe ammonia removal in a gas-phase biofilter was developed. The math-ematical model is based on discretized mass balances and detailed nitrification kinetics that includeinhibitory effects caused by free ammonia (FA) and free nitrous acid (FNA). The model was able to pre-dict experimental results operation under different loading rates (from 3.2 to 13.2 g NH3h-1m-3). In par-ticular the model was capable of reproducing inhibition caused by high inlet ammonia concentrations. Alsoelimination capacity was accurately predicted. Experimental data was also used to optimize certain modelparameters such as the concentration of ammonia- and nitrite-oxidizing biomass.Peer ReviewedPostprint (published version

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes-and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement. (Résumé d'auteur

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes-and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement

Translational research in plants and animals

International audienc

Paleogenomics as a Guide for Traits Improvement: Volume 1. Managing, sequencing and mining genetic resources

International audienc

Recherche translationnelle entre espèces modèles et cultivées :la génomique comparative pour la sélection végétale

International audienceThe concept of translational research, which originated in the medical field in the 1980s,consists in improving the efficient transfer of research results obtained in a species (which can be considered as a model or pivot) to all the species for which these results are of interest for its improvementin Agriculture. In this context, comparative genomics is an important tool for translational research,effectively identifying genes controlling common functions between species. Editing and phenotypingtools must thus allow the functional validation of the gene conserved within the species for which theknowledge has been extrapolated, that is to say transferred, and the identification of the best allelesand associated genotypes for exploitation in current breeding programsé. Le concept de recherche translationnelle, issu du domaine médical dans les années 80,consiste à améliorer le transfert efficace des résultats de recherche obtenus chez une espèce (pouvantêtre considéré comme modèle ou pivot) à l’ensemble des espèces pour lesquelles ces résultats sontd’intérêt pour son amélioration en agriculture. Dans ce contexte, la génomique comparée constitueun outil important de la recherche translationnelle en identifiant efficacement les gènes contrôlantdes fonctions communes entre espèces. Les outils d’édition génomique, de criblage de diversitégénétique et de phénotypage doivent ainsi permettre la validation fonctionnelle du gène conservé ausein de l’espèce chez laquelle la connaissance a été extrapolée à partir de l’espèce pivot, c’est-à-diretransférée, ainsi que l’identification des meilleurs allèles et génotypes associés pour leur exploitationdans les programmes actuels de sélectio

Unveiling Species Evolution from Extinct Ancestral Genomes

International audienc

Translational research in Plants

National audienc

In silico archeogenomics unveils modern plant genome organisation, regulation and evolution

Increasing access to plant genome sequences as well as high resolution gene-based genetic maps have recently offered the opportunity to compare modern genomes and model their evolutionary history from their reconstructed founder ancestors on an unprecedented scale. In silico paleogenomic data have revealed the evolutionary forces that have shaped present-day genomes and allowed us to gain insight into how they are organised and regulated today