CIGENE seminars 2017-2020


Spring 2021


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.

 

Date: 19.05.2021

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.

 

Date: 02.06.2021

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.


Autumn 2020


CRISPR at NMBU: a tribute to the Nobel prize winners

Thursday, 10th December 2020 at 13:00 – 15:15

Link to Agenda

 

 


Spring 2020


Date: 12th February 2020Boyartchuk Victor

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.


Autumn 2019


Date: Wednesday 18th September 2019Sandvik Guro Katrine

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

Pernille-Bronken-Eidesen.jpg

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 2019Olga Pulouskaya

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 2019Trevor Krabbenhoft

Presenter: Trevor Krabbenhoft
Title: Sequening the suckers: a new teleost resource for understanding the evolution following whole genome duplication’


Date: Wednesday 6th November 2019Hanne Dvergedal

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 DecemberSusan Johnston

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


Spring 2019


Date: May 22nd, NB new time: 11:00-11:45

Speakers: Ivar Grytten, Geir Kjetil Sandve og Knut Rand, UiO

Knut RandGeir Kjetil SandveIvar grytten

Title: Graph-based genome representations

Abstract: See the seminar schedule


Date: May 8thSiri Fjellheim, førsteamanuensis, NMBU.

Speaker: Siri Fjellheim, IPV/CIGENE, NMBU

Title: Evolution of cold acclimation and its role in niche transition in the temperate grass


Date: April 10thPhilineDec2018

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

Morten Limborg

Tom Gilbert

Speakers: Tom Gilbert and Morten Limborg

Topics:

  • Life through the hologenomic window
  • Applied hologenomics

Date: March 20thBildet viser Nicola Barson NMBU

Speaker: Nicola Barson, CIGENE, NMBU

Title: The rainbow genome reveals genetic basis for sex-dependent migratory behavior


Date: March 6thMats Albertsen

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 20thAmine Namouchi

Speaker: Amine Namouchi, CIGENE, NMBU

Title: Tracing the plague through Medieval times using metagenomics and phylogenomics of ancient DNA


Date: February 6thYann and Julien beskjært

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)


Autumn 2018


Date: November 21stMichel Moser

Speaker: Dr. Michel Moser – postdoctor at CIGENE | BIOVIT |NMBU

Title: Genomic insighs into pollinator adaptation in Petunia

Abstract can be found here.


Date: October 24thCBerthelot_square

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 MO

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 SeptemberAlexSuh

Speaker: Dr. Alexander Suh (lab webpage), Dept. of Evolutionary Biology (EBC), Uppsala University

Title: Filling assembly gaps and knowledge gaps with transposable elements


Spring 2018


Date: Wednesday 8th May

Speaker: Prof. Jorge Fernandes

Title: Growth-related epigenetic changes during domestication of Nile tilapia


Date: Wednesday 25th April.Bildet viser Gustav Vaaje-Kolstad, Post-doc / forsker

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)


Time: 12.15-13.00

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

Time: 09:15-10.00

SKP auditorium


Date: Wednesday 7th of February

Fabian Grammes, researcher IHA/BIOVIT, NMBU

Talk title: Epigenomic impact on sea lice resistance in Atlantic salmon


Autumn 2017


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 Octoberknutrudi

Presenter: Knut Rudi, Professor in Microbiology. KMB, NMBU

Talk title: Gut microbiota of Atlantic salmon


Date: Wednesday 18th of OctoberTorgeir2015_Vasser

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 OctoberAnnaWargeliusmindre.small

Presenter: Anna Wargelius. Group leader at the Norwegian Institute for Marine Research.

Talk title: Gene editing-addressing major sustainability issues in Atlantic salmon farming