This semester, three master students at CIGENE have completed their thesis with excellent results. We congratulate Dominiki Manousi, Hanna Magdalena Sahlström and Jostein Arntsen with their great accomplishments and wish you all the best in your future work.
Domniki Manousi
Assessing the effects of genotype imputation in the new Atlantic salmon (Salmo salar) genome assembly
Supervisors: Simen Rød Sandve and Tim Martin Knutsen.
Genotype imputation is an in silico inference method that increases the
genotyping density of large populations. We believe that the success of this method in Atlantic salmon is hindered by assembly errors in the specie’s reference genome, resulting from high sequence similarity and past sequencing technologies. Using long-read sequencing, an improved genome assembly for salmon has recently been released. We tested the power of the new reference genome in terms of genotype imputation accuracy and compared results against the previous assembly version. We report large genomic rearrangements and increase in chromosome length in the new genome assembly, followed by drastic improvement on imputation accuracy for regions of sequence similarity. Testing the applicability of currently available genotyping panels, we show good overall imputation performance but also heterogeneity in genotyping coverage, locally decreasing imputation accuracy performance
Click here to read Domniki’s thesis
Figure: Local imputation accuracy comparison between the new (red line) and old (blue line) genome assembly in selected chromosomes. Local performance was assessed as the mean r2 accuracy in groups of 100 markers (points in line).The density in points across each line indicates the genotyping density for the respective regions.
Hanna Magdalena Sahlström
Transposable Elements as a Source of Novel Gene Regulation in Atlantic Salmon (Salmo salar)
Supervisors: Simen Rød Sandve and Alex Kojo Datsomor
Transposable elements (TEs) are mobile genetic elements that can “jump” from one place in the genome to another. Specific TEs have been linked to genes with increased expression in liver cells in Atlantic salmon. We functionally tested these TEs and determined if they impact gene expression. Our results clearly show that the TEs do not lead to increased gene expression, and may even act as repressive elements.
Click here to read Hanna’s thesis
Figure: The graph included shows a negative control, two positive control and the TEs presenting with lower expression than the negative control. Sadly I do not have any pictures of myself in the lab.
Jostein Arntsen
Cloning and characterization of Cas9 in IPEC-J2 cells for CRISPR screens against porcine E. coli pathogen
Supervisors: Victor Boyartchuk and Thomas Nelson Harvey
Whole genome CRISPR screens have recently emerged as powerful tools for discovery of key genes that determine susceptibility to infectious diseases. Such screens can be greatly facilitated by creating cell lines that stably produce defined levels of Cas9 nuclease. During the course of the project we used IPEC J2 cell line, derived from the pig intestine, to create a series of clones that produce different levels of Cas9. We have subsequently tested theses lines for their ability to support targeted gene editing. We identified two lines in which had nearly 100% efficient deletion mutagenesis of MUC4, a host gene that mediates adhesion of pathogenic bacteria to intestinal cells.
Figure: Western blot of IPEC J2 clones lysates that illustrating different levels of endogenous Cas9 protein