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

International audienc

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

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

High quality genome sequence reveals important events during domestication of White Lupin

International audienceWhite lupin (Lupinus albus; 2n=50) is the only crop producing cluster roots, an outstanding developmental adaptation to low phosphate soils. We report a high-quality chromosome-scale assembly of white lupin genome, together with an extensive transcriptome data from ten different organs. We used singlemolecule real-time technology, in combination with short-reads sequencing and optical and genetic maps to have a successful assembly. The final assembly size is 443 Mb with a N50 of 17 Mb. About 98% of the assembled genome is included on the 25 pseudo-chromosomes. The structural annotation identified 38258 coding genes and 3,129 ncRNA, being 97.3% genes anchored on the pseudo-chromosomes. Genome of white lupin is laden with gene duplications and repetitive elements, which represent ~55% of the genome. A comparative evolutionary analysis of white lupin with other legumes revealed that it experienced a whole genome triplication in about 10 M years ago. We resequenced other 15 white lupin accessions, including a landrace and a non-domesticated variety. This has shown a highly polymorphic genome that has been impacted by domestication in different ways. Some transposons families present on the non-domesticated variety have disappeared in modern accessions, as well as the protein content of the seed has changed. Interestingly, the domestication has also modified cluster root formation. The cluster roots are formed earlier on time and closer to topsoil in the cultivated varieties. Altogether, this genome is a valuable resource and represents a keystone for legume genomics research

FAK Inhibitor-Based Combinations with MEK or PKC Inhibitors Trigger Synergistic Antitumor Effects in Uveal Melanoma

Uveal Melanoma (UM) is a rare and malignant intraocular tumor with dismal prognosis. Even if radiation or surgery permit an efficient control of the primary tumor, up to 50% of patients subsequently develop metastases, mainly in the liver. The treatment of UM metastases is challenging and the patient survival is very poor. The most recurrent event in UM is the activation of Gαq signaling induced by mutations in GNAQ/11. These mutations activate downstream effectors including protein kinase C (PKC) and mitogen-activated protein kinases (MAPK). Clinical trials with inhibitors of these targets have not demonstrated a survival benefit for patients with UM metastasis. Recently, it has been shown that GNAQ promotes YAP activation through the focal adhesion kinase (FAK). Pharmacological inhibition of MEK and FAK showed remarkable synergistic growth-inhibitory effects in UM both in vitro and in vivo. In this study, we have evaluated the synergy of the FAK inhibitor with a series of inhibitors targeting recognized UM deregulated pathways in a panel of cell lines. The combined inhibition of FAK and MEK or PKC had highly synergistic effects by reducing cell viability and inducing apoptosis. Furthermore, we demonstrated that these combinations exert a remarkable in vivo activity in UM patient-derived xenografts. Our study confirms the previously described synergy of the dual inhibition of FAK and MEK and identifies a novel combination of drugs (FAK and PKC inhibitors) as a promising strategy for therapeutic intervention in metastatic UM

The hidden legume roots: cluster root development in white lupin

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Genome sequence of the cluster root forming white lupin;

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify the APETALA2 transcription factor LaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture

High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

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Population genomics of apricots unravels domestication history and adaptive events

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.Organisation et montée en puissance d'une Infrastructure Nationale de Génomiqu