Translating the cod genome for aquaculture

In this period (6 months) we have essentially worked on the completion of papers base don results from the three WPs WP 1: We have written a paper on the new cod genome assembly (cod 2). The new version of the genome assembly is roughly 50-fold improved with respect to contingency. A new annotation showing more complete genes, but essentially the same repertoire, had been made. The improved genome assembly also show an unusual high content of simple repeated sequences, and comparing the original genome and cod 2 it is evident that these repeats are to a large extent causing the fragmentation of cod 1. Further, a large fraction of the simple repeats are heterozygous, and among trinucleotide repeats they are frequently found within coding regions of genes or within regulatory regions. The paper presenting the new genome assembly will be submitted within one or two weeks (Tørresen et al. 2016). In addition we have written two chapters for the book Genomics in Aquaculture edited by Simon MacKenzie and Sissel Jentoft. The first chapter deals with the first version of the cod genome and is an introduction to high throughput sequencing (Tørresen, Star et al. 2016), the other chapter is summarizing a large number of results obtained with the genome information from cod and presents the new assembly (Tørresen, Rise et al. 2016). The book will be published in late 2016. WP 2: We have carried out a number of different genome scans using the SNP chip. Recently we have published an investigation of the differences between Barents Sea cod (NEAC) and coastal cod (NCC) showing that NEAC and NCC essentially differ in three large inversions (3 different linkage groups) in the genome (Berg et al. 2016). Outside these inversions the two ecotypes only differ to a small extent. In collaboration with IMR (Flødevigen) we have published a paper describing the differences between pelagic North Sea/Skagerak cod and coastal cod in Southern Norway (Sodeland et al. 2016). Also this investigation detected inversions. Further, we have performed a large-scale investigation of east-Atlantic, Icelandic and west-Atlantic (Canadian) cod. This article is in preparation (Berg et al. in prep). WP 3: The aforementioned manuscript addressing the Toll-like receptor (TLR) repertoire in cod has now been published (Solbakken et al. 2016). We are just about to submit a manuscript on organisation of TLRs in teleosts (Solbakken et al 2016 ready for subm.). Here it is shown that the TLR repertoire varies considerably between bony fished and that the codfishes clearly have the most deviating innate immune system. The changes in TLRs seen in codfishes coincide with paleoclimatic and geological processes (continental drift). In addition, we have shown that the loss of the Mx immune gene (Myxovirus resistance) has been lost form the gadiformes prior to the loss of MHC II (Solbakken et al. ? manuscript ready for subm.) ? implying that loss of MX could be a precursor to MHC II loss. Finally, the analyses of the transcriptome profiles of challenge experiments with Francisella and Vibrio vaccine experiments are finished, and two papers are being written up (Solbakken et al in prep a and b). These papers will also be included in Solbakken?s PhD thesis.

We have completed a first - full genome - reference sequence of Atlantic cod (Gadus morhua) that will become publicly available within the next 6 months. In order to exploit this genome providing explicit benefit to the Norwegian community, we propose to take the cod genome sequence to the next level and translate this sequence into genomic tools for cod aquaculture. First, we will improve the cod reference sequence by refined bioinformatic analyses - including annotation and taking the heterozygosity int o account, and by constructing superscaffolds using existing BAC end sequence information. An extended annotation will improve the biological relevance of the genome, making it a more useful tool for cod aquaculture. Second, using this improved version of the genome, we will re-sequence and scan the genomes of multiple individuals of cod, characterizing genome-wide functional genomic variation. We will focus on traits important for cod aquaculture; among others, age at maturity, growth rates and disease r esistance. Third, our analysis of the cod reference genome has revealed that cod lack MHC class II genes. So far, cod is the only known vertebrate that lacks this important set of genes. This discovery may have profound implications for the development of vaccines and medications that are important in cod aquaculture. We aim to fully characterize the unique MHC system in cod, which will simultaneously stimulate the targeted development of vaccines preventing bouts of disease in cod aquaculture.