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

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

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

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

Etude des potentialités de transfert des transgènes des plantes transgéniques aux bactéries du sol et de l'impact sur la communauté bactérienne

Le transfert de gènes à partir de PGM vers les bactéries de sol a été détecté dans des conditions optimales en laboratoire, mais de tels évènements n ont pas été rapportés pour les bactéries dans leur milieu naturel en plein champ. Ces résultats pourraient être dus à la faible fréquence de ces événements et au manque de sensibilité des techniques de détection. Une approche métagénomique a été utilisée dans ce travail afin de détecter les événements de transfert de gènes de PGM vers les bactéries de sol et d évaluer l'impact possible de la culture PGM sur les bactéries dans les conditions du champ à l aide d outils novateurs et de grande sensibilité. La technologie Illumina n a pas identifié de transfert d ADN à partir de la vigne transgénique. Les techniques RISA et Microarrays taxonomiques ont révélé un effet léger des cultures PGM sur la composition des communautés bactériennes isolées du sol des parcelles, mais aucun impact n a été détecté sur celles isolées des sols des serres.Laboratory and greenhouse conducted experiments have shown that gene transfer events from transgenic plants to bacteria can happen but field trials failed to detect any in situ evidence. This may be due to the low frequency of these events but also to the lack of sensitivity of detection techniques. In our study, a metagenomic approach was used to detect gene transfer events from GMPs to soil bacteria and evaluate the possible impact of the cultivation of these plants on microbial communities under field conditions by using high sensitivity innovative tools. No molecular evidence of DNA transfer from transgenic grapevine was detected by Illumina sequencing. To evaluate the impact of transgenic grapevine on the bacterial community in greenhouse and field trials soils, RISA and taxonomic microarrays technologies were performed. A slight effect of GMPs crops on field bacterial communities was detected, but no impact was detected in greenhouse bacterial communities.VERSAILLES-BU Sciences et IUT (786462101) / SudocSudocFranceF

Organisation moleculaire et expression du genome mitochondrial d'une plante superieure, le ble: etude des recombinaisons au niveau de la sequence primaire de l'ADN

SIGLECNRS AR 12562 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc