PROGAMME
10.00 – 10.10 Welcome and opening remarks by Nils Chr. Stenseth, Centre for Ecological & Evolutionary Synthesis, University of Oslo
10.10 – 11.00 “Fish in the cold: Antarctic fish, spotted gar, and the teleost genome” by Dr. John H. Postlethwait, University of Oregon (http://uoneuro.uoregon.edu/ionmain/htdocs/faculty/postlethwait.html)
An ancestor to teleost fish experienced a whole genome duplication event about 350 million years ago. An interesting hypothesis is that the subsequent diversification of the extra genes helped contribute to the success of this taxon, which now includes half of all vertebrate species. Understanding the mechanisms that guided teleost genome evolution requires comparison to the lineage that diverged most recently before the teleost genome duplication. We found that spotted gar, an ancient air breathing ray-fin fish, provides a useful outgroup for comparison. The use of gar as outgroup helps to understand, for example, the evolution of reduced bone mineral density in Antarctic icefish that accompanied the chilling of Antarctica, a phenotype that mimics osteoporosis, a health threat to our aging population. Identification of genes, gene pathways, and genetic regulatory elements responsible for the origin of osteopenia in Antarctic icefish over evolutionary time may help in understanding the origin of bone loss diseases that occur over in humans over a lifetime.
11.00 – 11.30 “A different kettle of fish entirely: bioinformatic challenges and solutions for whole de novo genome assembly of Atlantic cod and Atlantic salmon” by Dr. Alexander J. Nederbragt, University of Oslo/NSC (/about/people/lex-nederbragt.html)
The genomes of the Atlantic cod and Atlantic salmon each have their own difficulties when it comes to sequencing and assembly. The Atlantic cod chosen for sequencing is a highly heterozygous individual, resulting in fragmented assemblies when sequenced with short read technologies. The Atlantic salmon has a pseudotetraploid genome, meaning that parts of the genome are duplicated. In addition, this genome is rich in very long repeats, much longer than can be covered by short reads. Both genomes therefore pose unique bioinformatic challenges for de novo genome assembly. The Norwegian Sequencing Centre is providing extra long reads of the Pacific Biosciences platform (PacBio RS) for both projects. This talk will discuss the status of both projects, focusing on how the long PacBio reads will contribute to high quality reference genomes for these important fishes.
11.30 – 12.20 “Building better genomes, transcriptomes, and metagenomes with improved techniques for de novo assembly - an easier way to do it” by Dr. C. Titus Brown, Michigan State University (http://ged.msu.edu/)
De novo sequence assembly - the computational process by which new genomes, transcriptomes, and metagenomes are assembled from shotgun sequencing - is a very complex and fragile process. Our ability to make sense of genomic data is often limited by the quality of our assemblies, making the improvement of de novo assembly an important bioinformatic problem. Motivated by the need to analyze some extremely large Illumina shotgun metagenome samples from agricultural soil, we have developed several computational techniques that can be applied to data sets prior to assembly to improve the data; these techniques yield sometimes surprising improvements in the both the quality and completeness of the assembly. They have the additional positive effect of dramatically simplifying the computational requirements for assembly. I will discuss our techniques and the results of applying them to highly polymorphic genome assembly, non-model transcriptome assembly, and the assembly of very large environmental shotgun metagenomes.
12.20 – 12.30 Discussion
12.30 – 13.30 Lunch
13.30 – 14.00 “High-throughput sequencing and human genetics” by Dr. Robert Lyle, Oslo University Hospital/NSC (/about/people/robert-lyle.html)
High-throughput sequencing is having a large impact on human genetics, in research and increasingly clinical applications. Many challenges remain, not just in terms of sequencing technology and variant identification, but also for data management and security, ethics and patients rights. This presentation will discuss some of these topics and how they are being addressed, and also present some success stories from clinical sequencing.
14.00 – 14.50 “Evolution of major histocompatibility complex class I genes in humans and other placental mammals” by Dr. Peter Parham, Stanford University School of Medicine (http://med.stanford.edu/profiles/Peter_Parham/)
Major histocompatibility complex class I and II genes are the most polymorphic genes in mammalian genomes and the ones most commonly and strongly associated with human disease. Whereas the MHC class II genes are dedicated to the adaptive immune response, MHC class I genes contribute to innate immunity, adaptive immunity and reproduction. Our research has focused on determining the nature of MHC-A, -B and -C I polymorphism, its evolution and the extent it has been needed for survival and expansion of human populations. Currently, we are exploring the possibility of expanding the approach to whole MHC haplotypes.
14.50 – 15.00 Discussion and closing remarks by Dag E. Undlien, Department of Medical Genetics, Oslo University Hospital and University of Oslo