The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Genotyping Durum Wheat using specific allelic capture: an application to detect QTL for WSSMV resistance

International audienc

Broadening the genetic basis of durum wheat

International audienc

Genotyping by sequencing transcriptomes in an evolutionary pre-breeding durum wheat population

The genetic diversity in durum wheat, Triticum turgidum durum, has been strongly reduced since the domestication of the wild Triticum turgidum dicoccoides. Monitoring durum wheat composite crosses incorporating related tetraploid taxa, such as wild and domesticated emmer wheat, is a suitable evolutionary pre-breeding method. Transcriptome sequencing paves the way for a genomic survey of single nucleotide polymorphisms (SNPs) segregating in such populations, offering the possibility of genotyping by sequencing to use these resources in genome-wide association studies (GWAS) and genomic selection (GS) programs. Evolutionary Pre-breeding pOpulation (EPO) is an evolutionary durum wheat pre-breeding population. Sequencing the transcriptome of 179 durum wheat lines (175 from EPO) led to the detection of 103,262 SNPs on two reference transcriptomes: one from the International Wheat Genome Sequencing Consortium and one assembled de novo on durum wheat. Using strict filtering to remove dubious heterozygous SNPs, EPO genetic diversity was eventually described with 76,188 high-confidence SNPs. The percentage of missing genotyping data depended on the expression level, and 88 individuals out of 175 were genotyped per SNP on average. Using the 3B pseudo-molecule of bread wheat, the transcription and diversity levels were shown to be higher in distal regions than in proximal regions, but SNPs were available throughout the chromosomes. Assuming good synteny with Hordeum, the trend was similar on the 14 chromosomes of the durum wheat genome. EPO hosts a high level of diversity, has a number of SNPs in low linkage disequilibrium (< 40 Mb) and would be well suited for GWAS and GS programs

Broadening the genetic bases of durum wheat. Proceedings of the International Symposium on Genetics and Breeding of Durum Wheat

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Epistatic determinism of durum wheat resistance to the wheat spindle streak mosaic virus

UMR AGAP : équipe GE2popUMR BGPI : équipe 6KEY MESSAGE: The resistance of durum wheat to the Wheat spindle streak mosaic virus (WSSMV) is controlled by two main QTLs on chromosomes 7A and 7B, with a huge epistatic effect. Wheat spindle streak mosaic virus (WSSMV) is a major disease of durum wheat in Europe and North America. Breeding WSSMV-resistant cultivars is currently the only way to control the virus since no treatment is available. This paper reports studies of the inheritance of WSSMV resistance using two related durum wheat populations obtained by crossing two elite cultivars with a WSSMV-resistant emmer cultivar. In 2012 and 2015, 354 recombinant inbred lines (RIL) were phenotyped using visual notations, ELISA and qPCR and genotyped using locus targeted capture and sequencing. This allowed us to build a consensus genetic map of 8568 markers and identify three chromosomal regions involved in WSSMV resistance. Two major regions (located on chromosomes 7A and 7B) jointly explain, on the basis of epistatic interactions, up to 43% of the phenotypic variation. Flanking sequences of our genetic markers are provided to facilitate future marker-assisted selection of WSSMV-resistant cultivars

Macrophage- and Neutrophil-Derived TNF-α Instructs Skin Langerhans Cells To Prime Antiviral Immune Responses

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Low incidence of SARS-CoV-2, risk factors of mortality and the course of illness in the French national cohort of dialysis patients

International audienceThe aim of this study was to estimate the incidence of COVID-19 disease in the French national population of dialysis patients, their course of illness and to identify the risk factors associated with mortality. Our study included all patients on dialysis recorded in the French REIN Registry in April 2020. Clinical characteristics at last follow-up and the evolution of COVID-19 illness severity over time were recorded for diagnosed cases (either suspicious clinical symptoms, characteristic signs on the chest scan or a positive reverse transcription polymerase chain reaction) for SARS-CoV-2. A total of 1,621 infected patients were reported on the REIN registry from March 16th, 2020 to May 4th, 2020. Of these, 344 died. The prevalence of COVID-19 patients varied from less than 1% to 10% between regions. The probability of being a case was higher in males, patients with diabetes, those in need of assistance for transfer or treated at a self-care unit. Dialysis at home was associated with a lower probability of being infected as was being a smoker, a former smoker, having an active malignancy, or peripheral vascular disease. Mortality in diagnosed cases (21%) was associated with the same causes as in the general population. Higher age, hypoalbuminemia and the presence of an ischemic heart disease were statistically independently associated with a higher risk of death. Being treated at a selfcare unit was associated with a lower risk. Thus, our study showed a relatively low frequency of COVID-19 among dialysis patients contrary to what might have been assumed