The CIGENE seminar series Spring 2022 has invited speakers representing different areas within genomics, microbiology and evolution. We look forward to see you again and welcome new attendees to subscribe to the email notification list.
Next speaker: Wednesday, June 1st, 12-13 CET
Kaur Alasoo, Lecturer of Bioinformatics, University of Tartu
Title: A compendium of uniformly processed human gene expression and splicing quantitative trait loci
Abstract:Many gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue (https://www.ebi.ac.uk/eqtl), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues.
This will be an online event. Contact us to receive the meeting link.
ABSTRACTS speakers Spring 2022
Wednesday, May 4th, 12-13 CET
Lindsay Hall, Professor, Quadram Institute
Title: Exploring the delicate balance of the early life gut microbiota
Abstract: Initial colonisation of the gut by pioneer bacterial species is the first key step for host well-being. The process of initial gut microbiota colonisation in preterm babies is radically interrupted due to a variety of factors including mode of delivery and antibiotics. This aberrant colonisation of premature infants appears pivotal to the development of a number of diseases, including necrotising enterocolitis (NEC). I will discuss how the microbiota ‘balance’ in the preterm gut impacts NEC outcomes – exploring the role of both beneficial and pathogenic microbiota members.
Wednesday, April 27th, 12-13 CET
Leif Andersson, Professor, Dept of Medical Biochemistry and Microbiology, Uppsala University
Title: Low mutation load in a supergene underpinning alternative male mating strategies in ruff.
Abstract: Ruffs are shorebirds with an elaborate lekking behavior involving three male morphs with different mating strategies: Independents, Satellites, and Faeders. The latter two are heterozygous for different versions of a supergene maintained by an inversion that were estimated to have occurred about 4 million years ago. Faeders carry an intact inversion while the Satellite allele is recombinant, both of which are expected to accumulate high mutational load because they are recessive lethals. Here we have constructed a highly contiguous genome assembly of the inversion region for both the Independent and Satellite haplotypes. The recombination event(s) between an inverted and non-inverted chromosome creating the Satellite allele must have occurred recently (within the last 100,000 years) based on the minute sequence divergence between the Satellite and Independent alleles in the recombinant regions. Contrary to expectations, we find no expansion of repeats and only a very modest mutation load on the Satellite allele in the nonrecombinant region despite high sequence divergence (1.46%). The essential centromere protein CENPN gene is disrupted by the inversion, and surprisingly is as well conserved on the inversion haplotypes as on the noninversion haplotype. The results suggest that the inversion may be much younger than previously thought.
Eaaswarkhanth Muthukrishnan, Research Scientist, New York University Abu Dhabi
Title: Insights into the fine-scale population structure and contributions of ancient genetic adaptations to metabolic traits in modern-day Kuwaiti Arabs.
Abstract: Being at the crossroads between Africa and Eurasia, the Arabian Peninsula has experienced several waves of human migrations despite the prevailing extreme and varying environmental conditions; therefore, the resident populations have a high genetic diversity. In this talk, I will present our recent works that explored the regional genetic heterogeneities and admixture history of populations inhabiting the Peninsula. In addition, I will highlight interesting ancient genetic adaptations once key to survival for Kuwaiti ancestors in the harsh desert environment that predispose their descendants to debilitating metabolic diseases.
Wednesday, April 6th, 12-13 CET
Sabina Leanti La Rosa, researcher NMBU
Title: Decrypting the mechanism for xanthan gum processing by human gut bacteria through multi-omics and enzymology
Abstract: Microbial communities and their enzymes process many of the “typical” dietary nutrients accessible in the human gastrointestinal tract and play an essential role in host health and nutrition. Eating habits of industrialized countries and gluten-free diets reflect an increasing consumption of processed foods, hence concomitant increased intakes of “atypical” nutrients such as food additives. While often believed to be inert, little is known about the interactions of food additives with the human gut microbiota and their fate in the gut. In this talk, I will present results showing that the human gut microbiota can process xanthan gum, a common food additive used in bakery products, beverages and in gluten-free foods. Metagenomic and metatranscriptomic analyses revealed the presence of a common uncultured Ruminococcaceae genus (R. UCG13) equipped with a gene cluster responsive to xanthan gum. Detailed biochemical studies supported a model whereby extracellular hydrolysis of xanthan gum generates oligosaccharides that are subsequently depolymerized to monosaccharides by a cocktail of intracellular enzymes. In some cases, oligosaccharides produced by the primary degrader R. UCG13 also cross-feed other bacterial populations equipped with their own specific catabolic pathway. A survey of 2441 public human gut metagenomes revealed the broad, diet-specific, distribution of these xanthan utilization loci across the world. Overall, we show that this food additive is not inert and has driven the evolution of interlinked trophic relationships between at least two populations within the human gut microbiota, an adaptation that reflects the incorporation of xanthan gum into human diets in the past 50 years.
Wednesday, March 30th, 12-13 CET
José Cerca, researcher, NTNU
Title: A chromosome-resolved genome of Darwin’s giant daisy trees (Scalesia; Galápagos endemics) shows the genomic basis of the plant island syndrome
Abstract: Oceanic archipelagos comprise multiple disparate environments in small areas, and home few species per area. These elements set in motion some of the most spectacular adaptive radiations, thus offering a unique chance to characterise the genomic basis underlying changes in morphology, ecology and physiology. Plants in oceanic archipelagos often undergo changes in leaf morphology, acquire perennial life habits, readjust their chemical ecology, and change their ploidy (i.e. island syndromes). In this talk, I will present the genome of the critically endangered Scalesia atractyloides, a member of Darwin’s giant daisy tree radiation in the Galápagos. We obtained a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate genes. We identified the two ancestral (sub)genomes coming together in the allopolyploidization event, and date their divergence. We found signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, finding evidence for genomic adaptation associated with transitions to insular life (island syndromes).
Wednesday, March 16th, 12-13 CET
Stefan Lüpold, Prof. Dr., University of Zurich
Title: Post-mating sexual selection depends on many players
Abstract: When a female mate with multiple males, paternity success may depend on complex interactions between both the female and the competing sperm of her mates. Such interactions have been identified as potential sources of genetic variation in sexually selected traits but are also expected to inhibit trait diversification. Unlike widely studied genotypic interactions, little is known about how phenotypic variation in sexually selected traits may contribute to their outcome. Using fruit flies as an example, I will disentangle the complex interactions between both male and female traits known to influence competitive fertilization. And I will demonstrate that these interactions do not limit the ability of multivariate systems to respond to directional sexual selection, including the evolution of gigantic sperm.
Wednesday, March 3rd, 12-13 CET
Arianna Servili, Ifremer, Université de Brest, CNRS, IRD, LEMAR, Plouzané, France
Title: Global change impacts reproduction and stress response of fish
Abstract: Anthropogenic emissions of carbon dioxide in the atmosphere generate rapid variations in atmospheric composition which drives major climate changes. This includes variations in physicochemical proprieties of sea and freshwater, such as water temperature, salinity, pH/pCO2 and oxygen content, which can impact fish critical physiological functions. We will discuss how climate change related effects would impact reproduction of fish affecting the neuroendocrine axes, with a special focus on the effect of ocean acidification on reproduction and stress response of the marine teleost the European sea bass.
This will be an online event. Contact us to receive the meeting link.
Wednesday, February 16th, 12-13 CET
Martin Kuhlwilm, Assistant Professor, University of Vienna
Title: Admixture in apes and humans and its consequences
Abstract: Admixture is an important topic in many species, including humans and our extinct relatives. Great apes also show patterns of admixture, and the exchange of genetic material did have an impact on these species as well. Studying their genomes guides our understanding of adaptation and speciation.