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

EuGene-PP: a next generation automated annotation pipeline for prokaryotic genomes.

International audienceIt is now easy and increasingly usual to produce oriented RNA-Seq data as a prokaryotic genome is being sequenced. However, this information is usually just used for expression quantification. EuGene-PP is a fully automated pipeline for structural annotation of prokaryotic genomes integrating protein similarities, statistical information and any oriented expression information (RNA-Seq or tiling arrays) through a variety of file formats to produce a qualitatively enriched annotation including coding regions but also (possibly antisense) non-coding genes and transcription start sites

Genome sequence of white lupin, a model to study root developmental adaptations.

International audienc

Effector polymorphisms of the sunflower downy mildew pathogen <em>Plasmopara Halstedii</em> and their use to identify pathotypes from field isolates

The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved

Effector polymorphisms of the sunflower downy mildew pathogen <em>Plasmopara Halstedii</em> and their use to identify pathotypes from field isolates

The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved

An Improved Assembly of the Diploid ‘Regina’ Sweet Cherry Genome

Sweet cherry (Prunus avium L.) is a diploid species with an estimated genome size of 338 MB (Arumuganathan et al. 1991) and an heterozygous genetic background.We have sequenced and assembled the genome of the ‘Regina’ sweet cherry variety, using FALCON UNZIP and optical mapping. Our de novo genome assembly resulted in a genome of 279 Mb (83 % of estimated genome size), 92 scaffolds and a largest scaffold of 16,3 Mb. The assembly has high contiguity (contig N50=1.23Mb, scaffold N50=5.96Mb) and good completeness with 95,9% BUSCO genes complete (scaffolds+ unscaffolded contigs + haplotigs).Here we present the construction of pseudomolecules using GBS markers, synteny between sweet cherry and peach genomes, and the preliminary results of structural annotation of the genome using a set of RNASeq assemblies of prunus avium

Genome sequence of white lupin, a model to study root developmental adaptations

White lupin ( Lupinus albus ; 2n=50) stands out as a model legume species since it is the only crop producing cluster roots, one of the most outstanding developmental adaptations to nutrient‐scarce environments. We report a high‐quality chromosome‐scale assembly of white lupin genome, together with an extensive transcriptome data from ten different organs of that species. We took advantage of single‐molecule real‐time technology, in combination with short‐reads sequencing and optical and genetic maps in order to have a successful assembly. The final assembly size is 451Mb with a N50 of 17Mb. About 96% (434Mb) of the assembled genome is included on the 25 pseudo‐chromosomes. The structural annotation identified 38 258 coding genes and 3129 ncRNA, being 97.3% genes anchored on the pseudo‐chromosomes. A majority (94.6%) of the 1440 genes in the Plantae BUSCO dataset were identified in the annotation, which is suggestive of a complete assembly and annotation. White lupin genome revealed to be laden with gene duplications and repetitive elements. It presents extensive duplication blocks inside its own genome and also a high degree of synteny with the close legumes species Lupinus angustifolious and Medicago truncatula . This genome is a valuable resource and represents a keystone for legumes genomics research