Online – Wednesday, December 8th 12-13 CET
Felicity Jones, Max Planck Institute for Developmental Biology
Title: Finding the mutations and molecular mechanisms underlying adaptation in naturally evolving populations.
Abstract: The genome contains an organism’s complete set of instructions for development, survival and reproduction. “Decoding” these instructions remains one of the biggest challenges in biology with enormous implications for medicine, agriculture, and conservation. Leveraging the unique advantages of the threespine stickleback fish system, I’ll describe the approaches we’ve been using to identify the molecular basis and common molecular mechanisms underlying gene regulation, trait variation, physiological and disease phenotypes and survival in different marine and freshwater environments. Combining diverse genomic, transcriptomic and epigenomic datasets I’ll discuss the importance of cis-regulation of the non-coding regulatory genome as mechanisms underlying divergent adaptation to different habitats.
Online – Wednesday, December 1st 12-13 CET
Anthony Mathelier, Researcher, University of Oslo, Norway.
Title: Towards high-quality maps of TF-DNA interactions
Abstract: Transcription Factors (TFs) are key proteins regulating when and where genes are expressed through their interaction with the DNA at specific binding sites. Hence, the identification of these TF binding sites (TFBSs) is essential to further our understanding of transcriptional regulation. In this talk, I will present our recently developed methodology to identify high-quality direct TF-DNA interactions by combining experiment and computational evidence.
Online – Wednesday, November 17th, 12-13 CET
Hie Lim Kim, Assistant Professor at Asian School of the Environment, Nanyang Technological University, Singapore
Title: Human back migration out of Sundaland driven by sea-level rise during the last deglaciation
Abstract: The rapid sea-level rise since the Last Glacial Maximum (LGM) flooded Sundaland changed Southeast Asian coastal landscapes dramatically and impacted the human demography. We reconstructed sea level and paleogeography and infer the population history in Southeast and South Asia since the LGM to present, using 742 whole-genome sequencing datasets generated by GenomeAsia 100K. We show that rapid sea-level rise reduced land area by > 50% since the LGM and segregated human populations and drove Southeast Asians to migrate into South Asia.
Online – Wednesday, November 10th, 12-13 CET
Professor Ross Houston, Personal Chair of Aquaculture Genetics, The Roslin Institute, University of Edinburgh
Title: Probing domesticated animal genomes to investigate history and phenotype
Abstract: Applications of genomics to expedite genetic improvement in aquaculture species
The potential to grow aquaculture production via informed use of selective breeding and genomic technologies is huge, due to the relatively recent domestication and high fecundity of most species. In the more advanced, high value aquaculture sectors such as Atlantic salmon, genomic selection is routinely applied to increase selection accuracy and therefore cumulative genetic gain. This has been enabled by the development of high density SNP arrays and genotyping by sequencing technologies. To translate these benefits to many other aquaculture species, lower cost solutions are required, such as combined-purpose low density SNP panels with genotype imputation.
In parallel, high quality annotated reference genomes and functional genomic assays to profile transcriptional regulation can now be utilised to prioritise putative causative variants in genomic regions associated with traits of economic interest. Such variants can potentially be harnessed to improve the accuracy of genomic prediction, and persistency of that accuracy in more distant relatives. Genome editing (e.g. CRISPR/Cas9) can be used to demonstrate the causality of these variants, and also has potential for the ‘introgression’ of favourable alleles from other strains or species, or the informed generation of de novo alleles, including via the application of genome-wide CRISPR screens.
This presentation will describe some examples of applied genomic and genome editing research aiming to take steps towards improvements in aquaculture breeding and production, with a focus on disease resistance.
Biography: Ross is Personal Chair of Aquaculture Genetics and the Deputy Director for Translation and Commercialisation at The Roslin Institute. His research team focusses on genetics and genome editing technologies in aquaculture species. His primary research interests include (i) development and application of genomic tools for aquaculture species, including sequencing and functional annotation of genomes; (ii) genomic selection for commercially relevant traits in breeding programmes, with a focus on disease resistance; and (iii) optimising and applying CRISPR/Cas9 genome editing in vitro and in vivo to pinpoint functional disease resistance alleles. You can read more about Roslin’s Aquaculture team here.
Link to Google Scholar
Online – Wednesday, November 3rd, 12-13 CET
Dr. Pam Wiener, the Roslin Institute, University of Edinburgh
Title: Probing domesticated animal genomes to investigate history and phenotype
Abstract: The work I will describe relates to the application of selection mapping, the use of genetic diversity patterns to infer historical processes and dissect genetic architecture, to domesticated animal species. I will describe examples of this approach to map genes associated with animal production, morphological features and environmental adaptation. I will also discuss how these studies provide insights into the selection pressures that have been imposed on the studied populations and, more generally, contribute to the understanding of convergent evolution.
Online – Wednesday, October 27th, 12-13 CET
Kathryn Elmer, Professor at Institute of Biodiversity Animal Health & Comparative Medicine, University of Glasgow.
Title: Parallel evolution of adaptive divergences in a freshwater salmonid
Abstract: The repeated diversification of postglacial fishes into ecotype specialists in northern freshwaters is a major source of temperate biodiversity and a long-standing model for studying evolution. I will present some of our recently published work on the evolutionary, genomic, and transcriptomic underpinnings of ecotype specialists in Arctic charr. This work is geographically broad, as it compares within regions and also across distinct lineages spanning Scotland and Siberia. We find extensive variation in historical and demographic background yet parallel evolution of ecologically relevant forms.
Online – Wednesday, October 20th, 12-13 CET
Odd Arne Olsen, Department of plant sciences, NMBU
Daniel Lang, Plant Genome and Systems Biology, Helmholtz Zentrum Munchen
Title: Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions
Abstract: We initially studied the Dek1 (Defective kernel 1) gene due to its essential function in forming the aleurone layer of the cereal endosperm. The gene encodes a Ca2+activated cysteine protease termed calpain (Lid et al., PNAS 2002). Soon after, it became clear that the DEK1 protein serves a fundamental role in land plants, ranging from the earliest diverging land plants formed 500 million years ago to flowering plants. Although subsequent studies during the following twenty years have associated diverse cellular and developmental functions with the Dek1 gene, a mechanistic and integrative understanding of its molecular function and role in these diverse developmental and biological processes has been missing. In animals, including humans, calpains are viewed as modulatory proteases displaying severe, pleiotropic phenotypes. Calpain cleavage targets were recently shown to be directed to the N-end rule degradatory pathway. Several of these destabilized targets are transcription factors, hinting at a gene regulatory role of the cysteine protease. Here, we analyze the gene regulatory networks of the moss Physcomitrium patens and characterize the regulons that are deregulated in Dek1 calpain mutants. Predicted cleavage patterns of the regulatory hierarchies in the five DEK1-controlled subnetworks are consistent with the gene’s pleiotropy and the regulatory role in cell fate transitions targeting a broad spectrum of functions. Network structure suggests DEK1-gated sequential transition between cell fates in 2D to 3D development. We anticipate that both our method combining phenotyping, transcriptomics and data science to dissect phenotypic traits and our model explaining the calpain’s role as a switch gatekeeping cell fate transitions will inform biology beyond plant development.
Wednesday, October 6th
Doruk Beyter, Research Scientist at deCODE genetics
Title: Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits
Abstract: Long-read sequencing (LRS) promises to improve the characterization of structural variants (SVs). Upon generating LRS data from 3,622 Icelanders, we identified a median of 22,636 SVs per individual, and investigated their impacts in human diseases and other traits. We discovered an association of a rare 14kb deletion in PCSK9 with lower low-density lipoprotein (LDL) cholesterol levels, and of a multiallelic SV in a tandem repeat region within ACAN and height, where a higher number of repeats carried indicated increase in height. These results show that SVs can be accurately characterized at the population scale using LRS data in a genome-wide non-targeted approach and demonstrate how SVs impact phenotypes.
This seminar will be online.
Date: 10th February 2021
Presenter: Rishi De-Kayne
Title: Genomic insights into the evolution of the Alpine whitefish radiation
Abstract: Within the Alpine whitefish (Coregonus spp.) species complex, the independent diversification into six or more sympatric whitefish species in multiple lakes across Switzerland are thought to have been facilitated by ecological and reproductive strategy differentiation with sympatric species varying in diet, body length, gill-raker number, and spawning depth and time. Using a large whole-genome re-sequencing dataset including 97 whitefish individuals, spanning 22 species from five independent lake systems, we investigated the evolutionary mechanisms that have driven Alpine whitefish diversification within Switzerland. Our results indicate that, despite strong lake-specific differentiation between whitefish ecomorphs, the repeated diversification of ecologically distinct species within lake systems is underpinned to some degree by parallel genetic changes distributed along the genome. Additionally, rare ecomorphs show evidence of contemporary introgression between lake systems, likely as a result of the anthropogenic movement of fish between lake systems. This suggests that the postglacial whitefish diversification was facilitated by both wide-spread standing genetic variation enabling the rapid built up of somewhat parallel genome-wide differentiation, and admixture-derived variation.
Presenter: Danang Crysnanto
Date: 3rd March 2021
Title: Assessing the complete genetic repertoire of a species using a pangenome graph
Abstract: Reference genome is generated from a single or few individuals and thus, it is a poor representation of the full species diversity. This pitfall has led to the development of the pangenome; the use of multiple genomes for genomic analysis. In this study, we integrated six cattle reference-quality genome assemblies into a pangenome graph, and we found 70 Mb sequences are not included in the existing cattle reference genome. We further demonstrated that these non-reference sequences contain functionally active bases and thousands of polymorphic sites that remain undetected with a single linear genome. Our findings call the need for a more representative reference genome that captures the entire diversity of a species.
Date: 17th March 2021
Presenter: Annaliese Mason
Title: Making new crop species
Abstract: By investigating how hybrid species form, we hope to work out how to utilise these natural evolutionary processes for human agricultural benefit, making new Brassica crop types for food, oil and biofuel. Hybridisation and genome doubling are processes which often result in increased vigour and ability to exploit different environmental niches in nature. Hence, if we can harness these processes to produce new hybrid species, such species may have a wider tolerance of environmental conditions such as heat, drought and disease, which would be beneficial to human agriculture.
Date: 24th March 2021
Presenter: Kentaro Shimizu
Title: Genome duplication affected patterns of selection in polyploid Arabidopsis and wheat species
Abstract: In 1970, Susumu Ohno proposed that genome duplication is an important source of novelty in vertebrates. Recent advances in polyploid genomics enabled population genomic studies of initial stages of genome duplication. Our data supported that parental adaptive traits were combined thanks to allopolyploidization in natural Arabidopsis and crop wheat allopolyploid species.
Date: 14th April 2021
Presenter: Kara Layton
Title: Using genomics to untangle marine mimicry systems
Abstract: Mimicry has evolved multiple times across the tree of life, it is maintained by both evolutionary and ecological mechanisms and it contributes to speciation through the generation of adaptive phenotypic diversity. While these processes have been extensively studied in terrestrial taxa, less is known about mimicry in marine systems. Here, I present a novel mimicry system in a group of aposematic and toxic nudibranchs (sea slugs) where multiple polychromatic species have recently been discovered. I use exon capture data to provide evidence for multiple scenarios of mimicry evolution in this group and discuss how future work will look to identify the genomic basis of mimicry.
Date: 21st April 2021
Presenter: Fernando Racimo
Title: Dynamic and descriptive models for spatiotemporal population genomics
Abstract: Ancient genome sequencing provides the opportunity to study population genomic processes as they unfolded in time and space. We can now directly observe how and when alleles moved across a landscape over succeeding generations with unprecedented detail. Here, I will describe several methods developed in our group to relate these spatiotemporal observations to informative parameters about migration, admixture and species ranges. First, I will present new way to model the spread of ancestry in ancient genomes through time and space. We have recently applied this method to a dataset containing thousands of ancient human genomes and inferred the geographic spread of major population movements in the past 13 millennia of Western Eurasian history. Our group has also developed a new dynamic framework for inferring the diffusion of a positively selected allele in a landscape, and a new wrapper to a forwards simulation framework, which makes it easy for users to readily generate spatiotemporal genetic processes programmatically. Finally, I will present a model to jointly infer changes in species distributions, using a combination of fossil records, sedimentary DNA data and paleo-climate records. We have applied this model to an arctic Pleistocene mega-fauna dataset and demonstrate that incorporating different types of data allows us to evince patterns that would not be visible if these were studied in isolation.
Date: 5th May 2021
Presenter: Daniel Machado
Title: Genome-scale models of microbial communities and their application to biotechnology
Abstract: From controlling our gut-brain axis to regulating the planetary geochemical cycles, the role of microbes in our lives seems endless. Microbes are everywhere, and they are usually not alone, but rather operating as part of complex microbial ecosystems. It thus becomes fundamental to understand how microbes interact with each other and with their environment. Next-generation sequencing technologies are shedding a light on the vast taxonomic and functional diversity of microbial communities. In this talk, I will discuss how we are using these data to build genome-scale models of single species and communities, and how we use such models to simulate the metabolic phenotype of microbial communities and their response to different kinds of perturbations. These are some of our preliminary steps towards the design and control of synthetic communities for application in industrial biotechnology.
Presenter: Mark Ravinet
Title: The evolution of human commensalism in Passer sparrows.
Abstract: From early civilization to the development of modern cities, human activity has shaped the evolution of other species. Some taxa are able to survive, adapt and even thrive in an anthropogenic niche. Human commensal species are a special case, having evolved a dependency on human resources without our direct influence. Intriguingly, human commensal relationships have arisen multiple times across many different species and even in parallel within the same genus. What factors drive the evolution of human commensalism? Is it a case of being in the right place at the right time? Or are there particular (pre)adaptations, traits and genes that mean some species are better able to exploit human resources than others? To explore these questions, I will focus on the repeated evolution of human commensalism in a single genus – Passer sparrows. I will show that we are able to use genomic data to reconstruct when and where human commensalism arose in each species. In particular, I will demonstrate that major human cultural transitions, i.e. the development of agriculture, have led to range expansions in these widespread and well-known birds. Finally, I will show that by combining phenotypic and genomic data, we are able to investigate the genetic basis for key traits involved in adapting to a human commensal life history.
Presenter: Michael Matschiner,
Title: The adaptive radiation of cichlid fishes in Lake Tanganyika
Abstract: Adaptive radiation – the explosive diversification of a group adapting to various niches within the same environment – may have generated a large part of Earth’s biodiversity. A prime example of this process are cichlid fishes of Lake Tanganyika, which diversified into over 250 species of great morphological and ecological variation. In this talk I will present insights into this radiation that were gained from whole-genome sequencing and phenotypic characterization of all species in the lake. These extensive datasets allowed us to reconstruct the unfolding of the radiation in unprecedented detail, revealing how several discrete stages of morphological evolution produced the spectacular current cichlid diversity of Lake Tanganyika.
Date: 16th June 2021
Presenter: Cristobal Uauy
Title: Unlocking the Polyploid Potential of Wheat Through Genomics
Abstract: Developments over the past few years have radically changed the way we work with polyploid wheat. These developments have dramatically lowered the barriers to undertake biological research in polyploid wheat. For many purposes, wheat can now be treated (almost) like a model crop species. The next phase will be to start understanding the biological mechanisms underlying the most important traits in polyploid wheat and to design strategies to ensure this knowledge is quickly transferred to the field. I will argue that given polyploidy, breeders have exploited only a fraction of the potential genetic variation in the wheat genome. The recent breakthroughs in wheat genomics now allow us to make a decisive effort towards exploiting this under-utilised variation, thereby unleashing the full potential of the polyploid wheat genome.
CRISPR at NMBU: a tribute to the Nobel prize winners
Thursday, 10th December 2020 at 13:00 – 15:15
Date: 12th February 2020
Presenter: Victor Boyartchuk, CIGENE
Title: Remodeling of intracellular lipidome defines the inflammatory state of immune cells
Abstract: A superfamily of nuclear receptor (NR) transcription factors mediate cross-talk between inflammatory and metabolic pathways. Activity of NRs is controlled by lipid ligands and therefore the makeup of the endogenous lipid pool determines their basal activity. Scavenger receptor like molecule CD5L has been proposed to act as a key regulator of the intracellular lipidome content. Using genome editing of macrophage like cells we generated data supporting the importance of this regulator in defining basal inflammatory state of human immune cells.
Date: Wednesday 18th September 2019
Presenter: Guro K. Sandvik, CIGENE
Title: CRISPR: designer babies and dehorned cows
How to encourage the public to reject a revolutionizing technique with unlimited potential for science, environment and human welfare
Abstract: CRISPR is a fantastic new technique, and can be used to manipulate the DNA and RNA in ways we could only dream of a couple of years ago. In this talk, I will present some new exciting techniques and use some examples from my previous postdoc working with CRISPR in live mouse brain. Despite the huge potential this technique has for improving food production and medical treatment, the public view of this method is not always so positive, in part because eager scientists and companies use the technique prematurely. I will discuss some recent happenings that is increasing the public’s skepticism towards the CRISPR technique.
Date: Thursday 26th September 2019
Presenter: Pernille Bronken Eidesen
Title: Double up to succeed? Understanding mechanisms and evolutionary consequences of autopolyploidy
Abstract: The arctic flora is dominated by polyploids, and diversification through polyploidy seems particularly beneficial in extreme environments. Still, the direct effect of polyploidy, autopolyploidy in particular, on evolutionary development and success of a species is largely unknown. In this project we aim at reducing knowledge gaps regarding formation, establishment and niche divergence of autopolyploid lineages in natural systems. We have recently established a field-laboratory that include a set-up for autopolyploidy-research on the mixed ploidy species Saxifraga oppositifolia. Through combined molecular and field-based investigations we are adding new pieces to this fascinating puzzle.
Date: Wednesday 9th October 2019
Presenter: Olga Pawłowska, CIGENE
Title: Adaptation to transposable elements in Drosophila simulans
Abstract: Transposable elements (TEs) are genomic parasites that proliferate within host genomes, and can also invade new species. The P-element, a DNA-based transposable element, recently invaded two Drosophila species: D. melanogaster in the 20th century, and D. simulans, in the 21st. In this talk I present analyses of D. simulans collected early and late in the invasion of the P-element that shed light on the role of silencing RNA molecules (piRNAs) during invasion of TEs.
Date: Tuesday 22nd October 2019
Presenter: Trevor Krabbenhoft
Title: Sequening the suckers: a new teleost resource for understanding the evolution following whole genome duplication’
Date: Wednesday 6th November 2019
Presenter: Hanne Dvergedal
Title: Towards an understanding of the genetics and physiology underlying variation in feed efficiency in salmon (Salmo salar)
Abstract An important trait for animal production is how efficiently animals convert their feed into muscle (referred to as feed efficiency). Even small improvements in feed efficiency could save large costs and improve sustainability of the animal production system. In salmon breeding however, individual records of fed efficiency have been lacking due to difficulties in measuring this trait. In this talk I present a new method to measure salmon feed efficiency using stable isotopes and use this method to perform QTL and gene expression analyses to identify genes and genomic regions associated with variation in this important production trait.
H. Dvergedal, J. Ødegård, M. Øverland, L.T. Mydland and G. Klemetsdal
Date: Wednesday 4th of December
Presenter: Susan Johnston
Title: The evolution of recombination rate variation in wild populations
Abstract: Meiotic recombination is often essential for proper chromosome segregation and is an important driver of genetic diversity. The relative benefits and costs of recombination vary with selection and demography: if recombination rate itself is heritable, then it has the potential to evolve. Our research investigates the evolution of recombination rates in wild populations in Soay sheep (Ovis aries) and Red deer (Cervus elaphus) by identifying genes associated with recombination rate and examining their relationship with reproductive success and survival. I will also discuss the implications of these findings for understanding the evolutionary importance of recombination rate variation more broadly across taxa.
S.E. Johnston, C. Bérénos, J. Huisman, P. Ellis, J. Slate, J.M. Pemberton
Date: May 22nd, NB new time: 11:00-11:45
Speakers: Ivar Grytten, Geir Kjetil Sandve og Knut Rand, UiO
Title: Graph-based genome representations
Abstract: See the seminar schedule
Date: May 8th
Speaker: Siri Fjellheim, IPV/CIGENE, NMBU
Title: Evolution of cold acclimation and its role in niche transition in the temperate grass
Date: April 10th
Speaker: Philine Feulner, Centre for Ecology, Evolution and Biogeochemistry, Switserland
Title: Federal Institute of Aquatic Science and Technology. Genomics of the Alpine whitefish radiation
Date: April 3rd
Speakers: Tom Gilbert and Morten Limborg
- Life through the hologenomic window
- Applied hologenomics
Date: March 20th
Speaker: Nicola Barson, CIGENE, NMBU
Title: The rainbow genome reveals genetic basis for sex-dependent migratory behavior
Date: March 6th
Speaker: Mads Albertsen, Aalborg University
Title: Genomic-centric metagenomics in the long-read era
Time: 10:15-11:00 (for this seminar only)
Date: February 20th
Speaker: Amine Namouchi, CIGENE, NMBU
Title: Tracing the plague through Medieval times using metagenomics and phylogenomics of ancient DNA
Date: February 6th
Speaker: Yann Guigen and Julien Bobe, INRA, France
Title: Novel teleost whole-genome sequences for studying genome evolution after whole genome duplication (Julien) and sex determination (Yann)
Date: November 21st
Speaker: Dr. Michel Moser – postdoctor at CIGENE | BIOVIT |NMBU
Title: Genomic insighs into pollinator adaptation in Petunia
Abstract can be found here.
Date: October 24th
Speaker: Dr. Camille Berthelot, Research Associate (CR2) at INSERM, Paris, France.
Title: Regulatory evolution of mammalian genomes
Abstract can be found here.
Date: October 10th
Speaker: Dr. Marie-Odile Baudement, postdoctor at CIGENE | BIOVIT |NMBU
Talk title: “Mapping the functional genomic landscape through sequencing of High-salt Recovered Sequences”
Date: 5th of September
Speaker: Dr. Alexander Suh (lab webpage), Dept. of Evolutionary Biology (EBC), Uppsala University
Title: Filling assembly gaps and knowledge gaps with transposable elements
Date: Wednesday 8th May
Speaker: Prof. Jorge Fernandes
Title: Growth-related epigenetic changes during domestication of Nile tilapia
Date: Wednesday 25th April.
Speaker: Ass. prof. Gustav Vaaje-Kolstad, KBM/NMBU
Title: Proteomic properties of the Atlantic salmon skin-mucus and its microbiota
Date: Wednesday 4th of April
Speaker: Prof. Yves Van de Peer
Talk title: The evolutionary significance of polyploidy.
Place: Festspisesalen på samfunnet (see map: Kart_festspisesal)
Date: Wednesday 21st of March
Speaker: Associate prof. Ola Westengen, Noragric, NMBU
Talk title: Crops and cultures – a co-evolutionary perspective on domestication
Date: Wednesday 8th of March
Speaker: Prof. Susan McCouch, Cornell University, USA
Talk title: The history of rice domestication: genetic isolation punctuated by genetic exchange
Date: Wednesday 7th of February
Fabian Grammes, researcher IHA/BIOVIT, NMBU
Talk title: Epigenomic impact on sea lice resistance in Atlantic salmon
Date: Wednesday 29 November, 12.15-13.00
Speaker: Tatiana Belova, researcher IPV, NMBU
Talk title: Putting the bread wheat genome sequence to work: analysing Norwegian bread wheat quality cultivars and wheat allergenicity epitopes
Date: Wednesday 15th November
Speaker: Ass. Prof. Simen Rød Sandve
Talk title: The grayling genome reveals insights into gene expression evolution following genome duplication
Where: Husdyrfagbygningen, room H109, 12.15-13.00
Date: Wednesday 1st of October
Presenter: Knut Rudi, Professor in Microbiology. KMB, NMBU
Talk title: Gut microbiota of Atlantic salmon
Date: Wednesday 18th of October
Presenter: Torgeir R Hvidsten. Professor in Bioinformatics. KMB, NMBU
Talk title: Gene regulatory networks involved in wood development (find paper here)
Date: Monday 2nd of October
Presenter: Anna Wargelius. Group leader at the Norwegian Institute for Marine Research.
Talk title: Gene editing-addressing major sustainability issues in Atlantic salmon farming