Ole Kristian Tørresen

• Klemetsen, Terje; Endresen, Dag; Johnsen, Arild; Boer, Hugo de; Fossøy, Frode & Ekrem, Torbjørn [Show all 11 contributors for this article] (2026). Strengthening molecular biodiversity research and monitoring in Norway – connecting tools, data and people. F1000 Research. 15, p. (ELIXIR)–(ELIXIR). doi: 10.12688/f1000research.179210.1. Full text in Research Archive Show summary

  Background Norway’s diverse ecosystems and strong research community are well-positioned to leverage molecular approaches (DNA barcoding, eDNA, whole-genome sequencing) for biodiversity research and monitoring. However, progress is constrained by gaps in data accessibility, standardisation, and interoperability across molecular, ecological, and biobank datasets. Methods ELIXIR’s Norwegian Molecular Biodiversity Working Group mapped national actors and networks through a desk review (2024–2025) and conducted a national survey (58 questions; open from 18 February to 8 March 2024) targeting data management, standards, tooling, infrastructures, and training. The survey was implemented in Nettskjema and received 58 responses from biodiversity-related researchers. Results We identified 19 Norwegian institutes active in molecular biodiversity and 28 relevant networks, with 11 networks involving three or more institutes. The survey results highlight gaps between policy and practice: 60% of respondents were familiar with the FAIR principles, but only 29% consistently made data fully open or FAIR-compliant. Data linkage with physical specimens was often reported as missing (38% of respondents), and taxonomic assignment was frequently challenging (39.3%). Most researchers reuse published datasets (90%), but data discovery and reuse are hindered: only 41% find it easy to locate relevant data, 32% struggle to find appropriate sequence databases, 54% cite insufficient metadata, and 72% need to harmonise combined datasets. Tool discoverability and documentation were limited (32% knew bio.tools; 5% WorkflowHub; 32% agreed tools are well documented and user-friendly). Data publication is not straightforward (63.8% find it hard or answered neutral). Conclusions Norway can strengthen molecular biodiversity research by 1) connecting molecular and ecological data, collections, and biobanks using persistent identifiers; 2) adhering to international metadata standards (e.g., DwC, MIxS) and rewarding data stewardship; 3) consolidating national collaborative networks; and 4) building capacity through targeted training and dedicated data steward roles. Implementing these measures will enhance interoperability, FAIR data sharing, and Norway’s leadership in biodiversity research and conservation.

• Strand, Marius André; To, Thu-Hien; Tørresen, Ole Kristian; Fullmer, Sarah; Ferrari, Giada & Skage, Morten [Show all 9 contributors for this article] (2026). The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events. Journal of Heredity. ISSN 0022-1503. 117(4), p. 822–833. doi: 10.1093/jhered/esag028. Full text in Research Archive
• Baalsrud, Helle T; Tørresen, Ole K; Danneels, Bram; Ferrari, Giada; Tooming-Klunderud, Ave & Skage, Morten [Show all 12 contributors for this article] (2026). Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758). Journal of Heredity. ISSN 0022-1503. 117(4), p. 750–760. doi: https:/academic.oup.com/jhered/article/117/4/750/8497176. Full text in Research Archive Show summary

  The phylum Bryozoa is an understudied, yet commonly occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in eight autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

• Solbakken, Monica Hongrø; Tørresen, Ole Kristian; Tooming-Klunderud, Ave; Skage, Morten; Bakken, Torkild & Jakobsen, Kjetill Sigurd (2026). Loss of Major Histocompatibility Complex I and II Function in the Genome of Glacier Lanternfish Provides Insight Into Evolution of Vertebrate Immune Systems. Genome Biology and Evolution (GBE). 18(7). doi: 10.1093/gbe/evag154. Full text in Research Archive
• Cerca, José; Ravinet, Mark; Flagstad, Øystein; Rolandsen, Christer Moe; Strand, Olav & Tørresen, Ole Kristian [Show all 8 contributors for this article] (2026). Hybridization with wild individuals fuels reindeer feralization. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 293(2075), p. 1–11. doi: 10.1098/rspb.2026.1226. Full text in Research Archive Show summary

  Domestication has profoundly influenced the development of human agriculture, and is characterized by intense artificial selection. Feralization occurs when domestic animals return to the wild. Although feralization does not fully reverse domestication traits, the selective pressures and evolutionary mechanisms driving it remain poorly understood. In northern Europe and Asia, wild, semi-domesticated and feral reindeer (Rangifer tarandus) populations coexist, offering a unique opportunity to study feralization. We studied genomic signatures of selection in semi-domesticated, feral and wild reindeer populations in Norway. Analysis of population structure confirmed historical records indicating the feral population formed a monophyletic clade that originated from neighbouring semi-domesticated reindeer. However, we also found evidence for excess allele-sharing between wild and feral reindeer, indicating hybridization between these lineages. Signatures of selection were identified using a top-down approach (orthologues of domestication candidate genes) and a bottom-up approach (FST and extended haplotypes). We found that candidate regions under selection have higher rates of excess allele-sharing between wild and feral populations. This provides the first evidence of reversed selection pressures during feralization in reindeer and reveals a link between selection and hybridization. Together, our findings suggest that hybridization likely promoted adaptive introgression during feralization. We discuss the implications of our findings for conserving the genetic integrity of endangered wild reindeer populations.

• Baalsrud, Helle Tessand; Garmann-Aarhus, Benedicte; Enevoldsen, Emily Louise Gilbert; Krabberød, Anders Kristian; Dominik, Fischer, & Tooming-Klunderud, Ave [Show all 13 contributors for this article] (2026). Centromeric satellite expansion drives genome evolution in the snowy owl. Genome Biology. ISSN 1474-7596. doi: 10.1186/s13059-026-04175-y. Full text in Research Archive Show summary

  Comparative genomic studies in birds have revealed that bird genomes are relatively repeat-poor and stable in terms of karyotype, size, and gene synteny/collinearity compared to other vertebrates. One notable exception is the owls, with cytogenetic studies demonstrating large variations in karyotypes and the evolution of unusual centromeric satellite repeats in some species. However, there has so far not been an investigation into genome architecture and repeat landscape of owls. Here, we present a chromosome-level genome assembly for the snowy owl (Bubo scandiacus). We find that the repeat DNA content in the relatively large snowy owl genome (1.6 Gb) is among the highest reported for any bird genome to date (28.34% compared to an average of ~ 10% in other birds). The bulk of the snowy owl genomic repeat landscape consists of extensive centromeric satellite arrays that form large contiguous blocks across multiple chromosomes. These arrays represent one of the largest centromeric satellite expansions reported in birds and are consistent with rapid turnover and amplification of centromeric repeats. Using gene collinearity analyses we show that the position of the centromeres are not homologous with chicken centromeres, and are located in regions with collinearity breaks to other bird genomes due to chromosomal rearrangements. Our results support rapid satellite turnover at lineage-specific centromeres, which could have played a role in centromeric drive, reproductive isolation and speciation of the snowy owl. The extensive centromeric satellite arrays uncovered in this genome highlight centromere evolution as a potentially important driver of genome evolution in owls.

• Hoff, Siv Nam Khang; Maurstad, Marius Filomeno; Tørresen, Ole K.; Araya, Robin Aasegg; Berg, Paul R. & Præbel, Kim [Show all 8 contributors for this article] (2026). Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species. Genome Biology. ISSN 1474-7596. 27. doi: 10.1186/s13059-026-03975-6. Full text in Research Archive Show summary

  Genome evolvability involves activation of transposable elements (TEs) that result in novel genomic rearrangements, including translocations, deletions, duplications, as well as larger structural reorganizations, such as chromosomal inversions and fusions. These genomic modifications contribute to raw genetic variability in which selection can act upon, and thus, promote local adaptation. Results Using a comparative genomics framework combined with the generation of six chromosome-level gadid reference genomes, including the cold-water adapted polar cod ( Boreogadus saida ) and Arctic cod ( Arctogadus glacialis ), we uncover an array of larger and smaller chromosomal reorganizations within this lineage. For the two Arctic codfishes, we detect lineage-specific chromosomal fusions, i.e., five in polar cod vs. eight in Arctic cod, resulting in a reduced number of chromosomes found to be associated with their geographical distribution. For the same species, we identify a high number of partly overlapping chromosomal inversions where a majority (especially within breakpoint regions) display an overrepresentation of specific TE families, accompanied by signatures of high degree of conservation. We further demonstrate involvement of miniature inverted-repeat transposable elements (MITEs) in the expansion of the well-known antifreeze glycoprotein genes in polar cod, and that the three gene clusters were localized in association with chromosomal rearrangements on chromosomes 1, 2, and 14. Conclusions We characterize how the Gadidae lineage has undergone massive genomic modifications — potentially via activation of TEs — throughout their evolutionary history, and particularly for the more Arctic species. These genomic reorganizations have likely played an important role in divergence processes and adaptation to freezing environmental conditions.

• Tørresen, Ole K; Tooming-Klunderud, Ave; Skage, Morten; Streitlien, Anne Eline; Strand, Olav & Rolandsen, Christer Moe [Show all 10 contributors for this article] (2025). Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus). Journal of Heredity. ISSN 0022-1503. doi: 10.1093/jhered/esaf094. Full text in Research Archive Show summary

  We describe a chromosome-level genome assembly from a wild alpine reindeer individual (Rangifer tarandus tarandus) from the Rondane area in Southern Norway. The assembly is resolved into two pseudo-haplotypes: hap 1 spanning 3,081 Mb and hap 2 spanning 2,633 Mb. Contig N50 and scaffold N50 lengths are in the range of 31 to 41 and 66 to 69 Mb, respectively. A large part of these two haplotypes (83.8% and 90.4%, respectively) are scaffolded into 34 autosomal chromosomal pseudomolecules, and in sex chromosomes X and Y for hap 1. The BUSCO completeness scores are 98.0% and 95.2%, respectively, and gene annotations of the assemblies identified 37,998 and 36,977 protein-coding genes. We also present an updated and improved genome assembly for Svalbard reindeer (Rangifer tarandus platyrhynchus; contig N50 46 to 48 Mb, scaffold N50 67 to 71 Mb, BUSCO 95.4% to 98.0%) and a comparison with previously published genome assemblies of reindeer.

• Araya, Robin Aasegg; Reinar, William Brynildsen; Tørresen, Ole K; Goubert, Clément; Daughton, Tara Jane & Hoff, Siv Nam Khang [Show all 12 contributors for this article] (2025). Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements. Genome Biology and Evolution (GBE). 17(8). doi: 10.1093/gbe/evaf131. Full text in Research Archive Show summary

  Chromosomal inversions play a crucial role in evolution by influencing phenotypes through the linkage of coadapted alleles. While inversions have been found across a large number of taxa, mapping and characterizing inversion breakpoint regions remain challenging, often due to the presence of complex tandem repeats and transposable elements. Here, we identify and quantify transposable elements in the breakpoints of the four large-scale inversions previously reported in Atlantic cod, leveraging on three high-quality long-read-based reference genome assemblies for the Norwegian Coastal cod, the Northeast Arctic cod, and Celtic cod ecotypes. We detected a significant enrichment of transposable element orders and superfamilies with terminal inverted repeats within the inversion breakpoint regions of chromosomes 1, 7 and 12. Notably, we discovered a tandem accumulation of miniature inverted-repeat transposable elements belonging to a family of hAT transposons, exclusively residing in the breakpoints of the inverted haplotype on chromosomes 1 and 7 found in the Northeast Arctic cod. The accumulation of tandemly arranged transposable elements with high sequence similarity in breakpoint regions suggests that they have driven the appearance of inversions through ectopic recombination, further supporting the potential of transposable elements in facilitating chromosomal reorganizations with large evolutionary implications.

• Tellini, Nicolo; Tørresen, Ole K.; Edwards, David; Rieseberg, Loren H.; Jakobsen, Kjetill Sigurd & Cerca, José (2025). Pangenomes as a framework for adaptive radiation, speciation, and adaptation. American Journal of Botany. ISSN 0002-9122. 112(12), p. 1–4. doi: 10.1002/ajb2.70130. Full text in Research Archive Show summary

  Understanding the genomic basis of diversification is a central goal in evolutionary biology. In recent years, the development and use of pangenomes, a genomic representation of multiple individuals within a lineage (a set of related populations, subspecies, ecotypes, or species), has enabled researchers to differentiate between DNA sequences shared by all individuals of a given lineage (core regions) from those present only in some individuals (accessory or variable regions). Differentiating between core and accessory regions has highlighted a key limitation of relying on a single reference genome: It captures the genetic code of only one individual and this biases genomic analyses and our understanding of diversification. Here, we propose that by identifying genes associated with both core and accessory regions, we can deepen our understanding of the processes underlying diversification. We suggest that analyzing pangenomes and accessory regions will provide deeper insights into diversification, hybridization, and the genetic basis of adaptation and speciation.

• Solbakken, Monica Hongrø; Tørresen, Ole K.; Tooming-Klunderud, Ave; Skage, Morten; Bakken, Torkild & Jakobsen, Kjetill Sigurd (2025). The genome of the Glacier lanternfish shows loss of MHC I and II function and provides insight into evolution of lanternfish immune systems. bioRxiv - the preprint server for biology. doi: https:/www.biorxiv.org/content/10.1101/2025.08.28.672920v1. Full text in Research Archive Show summary

  Lanternfishes (Myctophidae) are one of the most abundant and species diverse orders inhabiting the mesopelagic zone. Exploitation of marine resources has recently attracted increased interest. It is therefore essential to improve our understanding of the meso- and deep pelagic ecosystems with respect to conservation and management strategies. Genomic resources are paramount to enable in-depth studies of population structuring and understanding the inherent genetic diversity, but also to enable studies of processes such as local adaptation and selection. Here we present a genome assembly of the Glacier lanternfish (Benthosema glaciale) generated with long-read PacBio and Hi-C contact map data. By comparing additional available genomes from the Myctophiformes order we explore their adaptive immune strategies. Our findings reveal that multiple lineages within this order have lost a significant proportion of genes related to adaptive immunity (Electrona, Protomyctophum and Benthosema). We find simultaneous loss of both classical MHC class I and class II function coinciding with reduction in genetic diversity with respect to immunoglobulin and T-cell receptors. In contrast, the sister branch represented by Gymnoscopelus and Nannobrachium appear to have maintained the standard configuration of the jawed vertebrate adaptive immune system apart from large gene expansions in MHC class II. Our results demonstrate that the Benthosema-belonging lineage (Myctophinae) has completely lost the core functions of the adaptive immune system. How, when and why this occurred warrants further investigations.

• Martin, Sarah Louise; Torre, Renato La; Danneels, Bram; Tooming-Klunderud, Ave; Skage, Morten & Kollias, Spyridon [Show all 12 contributors for this article] (2025). Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids. GigaScience. doi: 10.1093/gigascience/giaf160. Full text in Research Archive Show summary

  Background Arctic and alpine insects experience extreme environmental stressors, yet the genomic basis of their adaptation is poorly understood. Diamesa midges (Diptera: Chironomidae) are cold-adapted insects inhabiting glacial and high-altitude freshwater ecosystems, but no chromosome-level genomes have been available to date. Findings We present the first haplotype-resolved, chromosome-level genomes for four Diamesa species (D. hyperborea, D. lindrothi, D. serratosioi and D. tonsa), assembled using PacBio HiFi sequencing and Hi-C scaffolding. The assemblies show high completeness and k-mer representation. Phylogenomic analyses place Diamesinae as sister to other Chironomidae except Podonominae, and comparisons suggest introgression between the distinct species D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species identified significant gene family contractions in Diamesa related to oxygen transport and metabolism, consistent with adaptation to high-altitude, low-oxygen environments. Expansions were observed in histone-related and Toll-like receptor gene families, suggesting roles in chromatin remodeling and immune regulation under cold stress. A glucose dehydrogenase gene family was significantly expanded across all cold-adapted species studied, implicating it in cryoprotectant synthesis and oxidative stress mitigation. Diamesa exhibited the largest gene family contraction at any phylogenetic node, with limited overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation. Conclusions Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These new genome assemblies provide a valuable resource for studying adaptation, speciation, and conservation in cold-specialist insects. Future integration of gene expression and population genomics will further clarify the evolutionary resilience of Diamesa in a warming world.

• Tørresen, Ole Kristian; Garmann-Aarhus, Benedicte; Hoff, Siv Nam Khang; Jentoft, Sissel; Svensson, Mikael & Schartum, Eivind Sandvik [Show all 11 contributors for this article] (2025). Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri). Journal of Heredity. ISSN 0022-1503. 117, p. 96–106. doi: 10.1093/jhered/esaf036. Full text in Research Archive
• Strand, Marius André; To, Thu-Hien; Tørresen, Ole Kristian; Fullmer, Sarah; Skage, Morten & Tooming-Klunderud, Ave [Show all 8 contributors for this article] (2025). Chromosome-level assembly of the octoploid cloudberry (Rubus chamaemorus). BioRxiv. ISSN 0362-4331. doi: 10.1101/2025.07.07.663483. Full text in Research Archive
• Pesqueira, Laura Marian Valencia; Hoff, Siv Nam Khang; Tørresen, Ole Kristian; Jentoft, Sissel & Nilsson, Sjannie Lefevre (2025). Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius. Scientific Data. 12. doi: 10.1038/s41597-025-04813-3. Full text in Research Archive Show summary

  Crucian carp (Carassius carassius), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.

• Baalsrud, Helle Tessand; Garmann-Aarhus, Benedicte; Enevoldsen, Emily Louise Gilbert; Krabberød, Anders Kristian; Fischer, Dominik & Tooming-Klunderud, Ave [Show all 13 contributors for this article] (2024). Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element. BioRxiv. ISSN 0362-4331. doi: 10.1101/2024.07.05.602039. Full text in Research Archive
• Weist, Peggy; Kusche, H.; Tørresen, Ole K.; Hermida, M.; Lopes, E.P. & Jentoft, Sissel [Show all 7 contributors for this article] (2024). Genomic differentiation and interoceanic population structure of two large pelagic scombrid species. Global Ecology and Conservation. 54. doi: 10.1016/j.gecco.2024.e03117. Full text in Research Archive Show summary

  Tunas of the family Scombridae are of paramount importance for fisheries and the international seafood trade. In order to ensure a sustainable use of these valuable resources, it is crucial that stock delineation and management plans are in accordance. Here, we examined the population genetic structure of the two data-poor scombrid species wahoo (Acanthocybium solandri) and bigeye tuna (Thunnus obesus), both of growing significance in tuna fisheries. Our study employed whole-genome sequencing methods to conduct the most extensive genomic analysis of wahoo and bigeye tuna samples to date, collected from the Atlantic, Indian and Pacific Oceans. For both species, we observe genome-wide differentiation between samples from the Atlantic and the Indo-Pacific regions with little or no genetic structure within each of the ocean basins, indicative of high gene flow. However, by applying a set of extreme outlier tests, genomic differentiation between locations was identified within the Pacific Ocean for both species, as well as for wahoo within the Atlantic Ocean. Additionally, for bigeye tuna, we uncovered a putative chromosomal inversion with patterns of highly linked loci and strong population divergence, that may be involved in adaptive divergence across the distributional range of the species. Taken together, despite considerable gene flow, the detected substructures – most likely driven by local adaptation – challenge previously held assumptions of panmixia in both species. Our findings show that future stock assessment should consider genetic differences at both neutral and divergent loci to develop sustainable conservation and management actions for these valuable marine resources.

• Tørresen, Ole K.; Kersten, Oliver Sven; Garmann-Aarhus, Benedicte; Helberg, Morten; Tooming-Klunderud, Ave & Skage, Morten [Show all 8 contributors for this article] (2024). A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758). Journal of Heredity. ISSN 0022-1503. doi: 10.1093/jhered/esae042. Full text in Research Archive Show summary

  The common eider, Somateria mollissima mollissima (Chordata; Aves; Anseriformes; Anatidae), is a large sea duck with a circumpolar distribution. We here describe a chromosome-level genome assembly from an individual female. The haplotype-resolved assembly contains one pseudo-haplotype spanning 1,205 megabases (with both Z and W sex chromosomes) and one pseudo-haplotype spanning 1,080 megabases. Most of these two assemblies (91.13% and 93.18%, respectively) are scaffolded into 32 autosomal chromosomal pseudomolecules plus Z and W for pseudo-haplotype one. The BUSCO completeness scores are 94.0% and 89.9%, respectively, and gene annotations of the assemblies identified 17,479 and 16,315 protein coding genes. Annotation of repetitive sequences classify 17.84% and 14.62% of pseudo-haplotype one and two, respectively, as repeats. The genome of the common eider will be a useful resource for the widely distributed northern species in light of climate change and anthropogenic threats.

• Jentoft, Sissel; Tørresen, Ole K.; Tooming-Klunderud, Ave; Skage, Morten; Kollias, Spyridon & Jakobsen, Kjetill Sigurd (2024). The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758). Wellcome Open Research. 9. doi: 10.12688/wellcomeopenres.21122.1. Full text in Research Archive Show summary

  We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.

• Dussex, Nicolas; Tørresen, Ole Kristian; Valk, Tom van der; Moullec, Mathilde Le; Veiberg, Vebjørn & Tooming-Klunderud, Ave [Show all 17 contributors for this article] (2023). Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer. iScience. 26(10). doi: 10.1016/j.isci.2023.107811. Full text in Research Archive Show summary

  Typically much smaller in number than their mainland counterparts, island populations are ideal systems to investigate genetic threats to small populations. The Svalbard reindeer (Rangifer tarandus platyrhynchus) is an endemic subspecies that colonized the Svalbard archipelago ca. 6,000–8,000 years ago and now shows numerous physiological and morphological adaptations to its arctic habitat. Here, we report a de-novo chromosome-level assembly for Svalbard reindeer and analyze 133 reindeer genomes spanning Svalbard and most of the species’ Holarctic range, to examine the genomic consequences of long-term isolation and small population size in this insular subspecies. Empirical data, demographic reconstructions, and forward simulations show that long-term isolation and high inbreeding levels may have facilitated the reduction of highly deleterious—and to a lesser extent, moderately deleterious—variation. Our study indicates that long-term reduced genetic diversity did not preclude local adaptation to the High Arctic, suggesting that even severely bottlenecked populations can retain evolutionary potential.

• Kersten, Oliver Sven; Star, Bastiaan; Krabberød, Anders Kristian; Atmore, Lane; Tørresen, Ole K. & Anker-Nilssen, Tycho [Show all 12 contributors for this article] (2023). Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change. Science Advances. 9(40). doi: 10.1126/sciadv.adh1407. Full text in Research Archive Show summary

  The Arctic is experiencing the fastest rates of global warming,leading to shifts in the distribution of its biota and increasing the potential for hybridization. However, genomic evidenc eof recent hybridization events in the Arctic remains unexpectedly rare. Here, we use whole-genome sequencing of contemporary and 122-year-old historical specimens to investigate the origin of an Arctic hybrid population of Atlantic puffins(Fratercula arctica) on Bjørnøya, Norway. We show that the hybridization between the High Arctic, large-bodied subspecies F.a. naumanni and the temperate, smaller-sized subspecies F.a. arctica began as recently as six generations ago due to an unexpected southward range expansion of F.a. naumanni. Moreover, we find a significant temporal loss of genetic diversity across Arctic and temperate puffin populations.Our observations provide compelling genomic evidence of the impacts of recent distributional shifts and loss of diversity in Arctic communities during the 20th century.

• Reinar, William Brynildsen; Tørresen, Ole K.; Nederbragt, Lex; Matschiner, Michael; Jentoft, Sissel & Jakobsen, Kjetill Sigurd (2023). Teleost genomic repeat landscapes in light of diversification rates and ecology. Mobile DNA. 14(1), p. 1–12. doi: 10.1186/s13100-023-00302-9. Full text in Research Archive Show summary

  Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

• Reinar, William Brynildsen; Greulich, Anne; Stø, Ida Myhrer; Knutsen, Jonfinn Mordekai Blix; Reitan, Trond & Tørresen, Ole K. [Show all 9 contributors for this article] (2023). Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. Science Advances. 9(12), p. 1–10. doi: 10.1126/sciadv.add6960. Full text in Research Archive Show summary

  Intrinsically disordered protein regions are of high importance for biotic and abiotic stress responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations because of expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2514 length variable tracts in 770 whole-genome sequenced Arabidopsis thaliana, we show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bioclimatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations affect protein function and are likely adaptive. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.

• Weist, Peggy; Jentoft, Sissel; Tørresen, Ole K.; Schade, Franziska M.; Pampoulie, Christophe & Krumme, Uwe [Show all 7 contributors for this article] (2022). The role of genomic signatures of directional selection and demographic history in the population structure of a marine teleost with high gene flow. Ecology and Evolution. 12(12). doi: 10.1002/ece3.9602. Full text in Research Archive Show summary

  Recent studies have uncovered patterns of genomic divergence in marine teleosts where panmixia due to high gene flow has been the general paradigm. These signatures of divergent selection are often impacted by structural variants, acting as “supergenes” facilitating local adaptation. The highly dispersing European plaice (Pleuronectes platessa)—in which putative structural variants (i.e., inversions) have been identified—has successfully colonized the brackish water ecosystem of the Baltic Sea. Thus, the species represents an ideal opportunity to investigate how the interplay of gene flow, structural variants, natural selection, past demographic history, and gene flow impacts on population (sub)structuring in marine systems. Here, we report on the generation of an annotated draft plaice genome assembly in combination with population sequencing data—following the salinity gradient from the Baltic Sea into the North Sea together with samples from Icelandic waters—to illuminate genome-wide patterns of divergence. Neutral markers pointed at large-scale panmixia across the European continental shelf associated with high gene flow and a common postglacial colonization history of shelf populations. However, based on genome-wide outlier loci, we uncovered signatures of population substructuring among the European continental shelf populations, i.e., suggesting signs of ongoing selection. Genome-wide selection analyses (xp-EHH) and the identification of genes within genomic regions of recent selective sweeps—overlapping with the outlier loci—suggest that these represent the signs of divergent selection. Our findings provide support for genomic divergence driven by local adaptation in the face of high gene flow and elucidate the relative importance of demographic history versus adaptive divergence in shaping the contemporary population genetic structure of a marine teleost. The role of the putative inversion(s) in the substructuring—and potentially ongoing adaptation—was seemingly not substantial.

• Matschiner, Michael; Barth, Julia Maria Isis; Tørresen, Ole K.; Star, Bastiaan; Baalsrud, Helle Tessand & Brieuc, Marine Servane Ono [Show all 10 contributors for this article] (2022). Supergene origin and maintenance in Atlantic cod. Nature Ecology and Evolution. 6(4), p. 469–481. doi: 10.1038/s41559-022-01661-x. Full text in Research Archive Show summary

  Abstract Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation.

• Sætre, Camilla Lo Cascio; Rönkä, Katja; Ravinet, Mark; Vitulano, Severino; Caldarella, Matteo & Procházka, Petr [Show all 13 contributors for this article] (2022). Genomic consequences of range expansion and colonisation in the reed warbler (Acrocephalus scirpaceus). BioRxiv. ISSN 0362-4331. doi: 10.1101/2022.11.28.518135. Full text in Research Archive
• Sætre, Camilla Lo Cascio; Eroukhmanoff, Fabrice; Rönkä, Katja; Kluen, Edward; Thorogood, Rose & Torrance, James [Show all 12 contributors for this article] (2021). A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus). Genome Biology and Evolution (GBE). 13(9), p. 1–7. doi: 10.1093/gbe/evab212. Full text in Research Archive Show summary

  Abstract The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behavior in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here, we present a high-quality reference genome for the reed warbler, based on PacBio, 10×, and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of BUSCO genes were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, and a BUSCO analysis of the protein sequences indicated 97.5% completeness. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.

• Nilsson, Pernille; Solbakken, Monica Hongrø; Schmid, Boris Valentijn; Orr, Russell; Lv, Ruichen & Cui, Yujun [Show all 15 contributors for this article] (2020). The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biology and Evolution (GBE). 12(2), p. 3832–3849. doi: 10.1093/gbe/evaa008. Full text in Research Archive Show summary

  Abstract The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.

• Jin, Xingkun; Morro, Bernat; Tørresen, Ole K.; Moiche, Visila; Solbakken, Monica Hongrø & Jakobsen, Kjetill Sigurd [Show all 8 contributors for this article] (2020). Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System. Frontiers in Immunology. 11. doi: 10.3389/fimmu.2020.609456. Full text in Research Archive
• Barth, Julia Maria Isis; Gubili, Chrysoula; Matschiner, Michael; Tørresen, Ole K.; Watanabe, Shun & Egger, Bernd [Show all 11 contributors for this article] (2020). Stable species boundaries despite ten million years of hybridization in tropical eels. Nature Communications. 11. doi: 10.1038/s41467-020-15099-x. Full text in Research Archive Show summary

  Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla) and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past introgression across a time-calibrated phylogeny. We show that the seven species have remained distinct for up to 10 million years and find that the current frequencies of hybridization across species pairs contrast with genomic signatures of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we suggest cytonuclear incompatibilities, hybrid breakdown, and purifying selection as mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of clades.

• Roth, Olivia; Solbakken, Monica Hongrø; Tørresen, Ole K.; Bayer, Till; Matschiner, Michael & Baalsrud, Helle Tessand [Show all 12 contributors for this article] (2020). Evolution of male pregnancy associated with remodeling of canonical vertebrate immunity in seahorses and pipefishes. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 117(17), p. 9431–9439. doi: 10.1073/pnas.1916251117. Full text in Research Archive Show summary

  A fundamental problem for the evolution of pregnancy, the most specialized form of parental investment among vertebrates, is the rejection of the nonself-embryo. Mammals achieve immunological tolerance by down-regulating both major histocompatibility complex pathways (MHC I and II). Although pregnancy has evolved multiple times independently among vertebrates, knowledge of associated immune system adjustments is restricted to mammals. All of them (except monotremata) display full internal pregnancy, making evolutionary reconstructions within the class mammalia meaningless. Here, we study the seahorse and pipefish family (syngnathids) that have evolved male pregnancy across a gradient from external oviparity to internal gestation. We assess how immunological tolerance is achieved by reconstruction of the immune gene repertoire in a comprehensive sample of 12 seahorse and pipefish genomes along the “male pregnancy” gradient together with expression patterns of key immune and pregnancy genes in reproductive tissues. We found that the evolution of pregnancy coincided with a modification of the adaptive immune system. Divergent genomic rearrangements of the MHC II pathway among fully pregnant species were identified in both genera of the syngnathids: The pipefishes (Syngnathus) displayed loss of several genes of the MHC II pathway while seahorses (Hippocampus) featured a highly divergent invariant chain (CD74). Our findings suggest that a trade-off between immunological tolerance and embryo rejection accompanied the evolution of unique male pregnancy. That pipefishes survive in an ocean of microbes without one arm of the adaptive immune defense suggests a high degree of immunological flexibility among vertebrates, which may advance our understanding of immune-deficiency diseases.

• Cayuela, Hugo; Rougemont, Quentin; Laporte, Martin; Mérot, Claire; Normandeau, Eric & Dorant, Yann [Show all 15 contributors for this article] (2020). Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish. Molecular Ecology. ISSN 0962-1083. 29, p. 2379–2398. doi: 10.1111/mec.15499. Full text in Research Archive
• Musilova, Zuzana; Cortesi, Fabio; Matschiner, Michael; Davies, Wayne I. L.; Patel, Jagdish Suresh & Stieb, Sara M. [Show all 18 contributors for this article] (2019). Vision using multiple distinct rod opsins in deep-sea fishes. Science. ISSN 0036-8075. 364(6440), p. 588–592. doi: 10.1126/science.aav4632. Full text in Research Archive
• Tørresen, Ole K.; Star, Bastiaan; Mier, Pablo; Andrade-Navarro, Miguel A.; Bateman, Alex & Jarnot, Patryk [Show all 13 contributors for this article] (2019). Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(21), p. 10994–11006. doi: 10.1093/nar/gkz841. Full text in Research Archive Show summary

  The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.

• Varadharajan, Srinidhi; Sandve, Simen Rød; Gillard, Gareth Benjamin; Tørresen, Ole K.; Mulugeta, Teshome Dagne & Hvidsten, Torgeir Rhoden [Show all 11 contributors for this article] (2018). The grayling genome reveals selection on gene expression regulation after whole-genome duplication. Genome Biology and Evolution (GBE). 10(10), p. 2785–2800. doi: 10.1093/gbe/evy201. Full text in Research Archive Show summary

  Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein–protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.

• Hoff, Siv Nam Khang; Baalsrud, Helle Tessand; Tooming-Klunderud, Ave; Skage, Morten; Richmond, Todd & Obernosterer, Gregor [Show all 10 contributors for this article] (2018). Long‐read sequence capture of the haemoglobin gene clusters across codfish species. Molecular Ecology Resources. ISSN 1755-098X. 19(1), p. 245–259. doi: 10.1111/1755-0998.12955. Full text in Research Archive
• Lie, Kai Kristoffer; Tørresen, Ole K.; Solbakken, Monica Hongrø; Rønnestad, Ivar; Tooming-Klunderud, Ave & Nederbragt, Alexander Johan [Show all 8 contributors for this article] (2018). Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish. BMC Genomics. 19(186), p. 1–17. doi: 10.1186/s12864-018-4570-8. Full text in Research Archive Show summary

  Background: The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach loss has occurred independently multiple times in the course of evolution. By assembling the ballan wrasse genome and transcriptome we aimed to determine the genetic basis for its digestive system function and appetite regulation. Among other, this knowledge will aid the formulation of aquaculture diets that meet the nutritional needs of agastric species. Results: Long and short read sequencing technologies were combined to generate a ballan wrasse genome of 805 Mbp. Analysis of the genome and transcriptome assemblies confirmed the absence of genes that code for proteins involved in gastric function. The gene coding for the appetite stimulating protein ghrelin was also absent in wrasse. Gene synteny mapping identified several appetite-controlling genes and their paralogs previously undescribed in fish. Transcriptome profiling along the length of the intestine found a declining expression gradient from the anterior to the posterior, and a distinct expression profile in the hind gut. Conclusions: We showed gene loss has occurred for all known genes related to stomach function in the ballan wrasse, while the remaining functions of the digestive tract appear intact. The results also show appetite control in ballan wrasse has undergone substantial changes. The loss of ghrelin suggests that other genes, such as motilin, may play a ghrelin like role. The wrasse genome offers novel insight in to the evolutionary traits of this large family. As the stomach plays a major role in protein digestion, the lack of genes related to stomach digestion in wrasse suggests it requires formulated diets with higher levels of readily digestible protein than those for gastric species.

• Malmstrøm, Martin; Britz, Ralf; Matschiner, Michael; Tørresen, Ole K.; Hadiaty, Renny Kurnia & Yaakob, Norsham [Show all 10 contributors for this article] (2018). The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biology and Evolution (GBE). 10(4), p. 1088–1103. doi: 10.1093/gbe/evy058. Full text in Research Archive Show summary

  The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

• Eide, Marta; Rydbeck, Halfdan; Tørresen, Ole K.; Lille-Langøy, Roger; Puntervoll, Pål & Goldstone, Jared V. [Show all 10 contributors for this article] (2018). Independent losses of a xenobiotic receptor across teleost evolution. Scientific Reports. 8, p. 1–13. doi: 10.1038/s41598-018-28498-4. Full text in Research Archive Show summary

  Sensitivity to environmental stressors largely depend on the genetic complement of the organism. Recent sequencing and assembly of teleost fish genomes enable us to trace the evolution of defense genes in the largest and most diverse group of vertebrates. Through genomic searches and in-depth analysis of gene loci in 76 teleost genomes, we show here that the xenosensor pregnane X receptor (Pxr, Nr1i2) is absent in more than half of these species. Notably, out of the 27 genome assemblies that belong to the Gadiformes order, the pxr gene was only retained in the Merluccidae family (hakes) and Pelagic cod (Melanonus zugmayeri). As an important receptor for a wide range of drugs and environmental pollutants, vertebrate PXR regulate the transcription of a number of genes involved in the biotransformation of xenobiotics, including cytochrome P450 enzymes (CYP). In the absence of Pxr, we suggest that the aryl hydrocarbon receptor (Ahr) have evolved an extended regulatory role by governing the expression of certain Pxr target genes, such as cyp3a, in Atlantic cod (Gadus morhua). However, as several independent losses of pxr have occurred during teleost evolution, other lineages and species may have adapted alternative compensating mechanisms for controlling crucial cellular defense mechanisms.

• Mattingsdal, Morten; Jentoft, Sissel; Tørresen, Ole K.; Knutsen, Halvor; Hansen, Michael Möller & Robalo, Joana I. [Show all 9 contributors for this article] (2018). A continuous genome assembly of the corkwing wrasse (Symphodus melops). Genomics. ISSN 0888-7543. 110(6), p. 399–403. doi: 10.1016/j.ygeno.2018.04.009. Full text in Research Archive
• Tørresen, Ole K.; Brieuc, Marine Servane; Solbakken, Monica Hongrø; Sørhus, Elin; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd [Show all 9 contributors for this article] (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics. 19(240), p. 1–17. doi: 10.1186/s12864-018-4616-y. Full text in Research Archive Show summary

  Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group.

• Machado, Andrè M.; Tørresen, Ole K.; Kabeya, Naoki; Couto, Alvarina; Petersen, Bent & Felício, Mónica [Show all 17 contributors for this article] (2018). “Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus. Genes. 9(10), p. 1–13. doi: 10.3390/genes9100485. Full text in Research Archive Show summary

  Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first omics dataset from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation.

• Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2017). Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Scientific Data. 4, p. 1–13. doi: 10.1038/sdata.2016.132. Full text in Research Archive Show summary

  Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts.

• Elgvin, Tore Oldeide; Trier, Cassandra Nicole; Tørresen, Ole Kristian; Hagen, Ingerid; Lien, Sigbjørn & Nederbragt, Alexander Johan [Show all 9 contributors for this article] (2017). The genomic mosaicism of hybrid speciation. Science Advances. 3, p. 1–16. doi: 10.1126/sciadv.1602996. Full text in Research Archive Show summary

  Hybridization is widespread in nature and, in some instances, can result in the formation of a new hybrid species. We investigate the genetic foundation of this poorly understood process through whole-genome analysis of the hybrid Italian sparrow and its progenitors. We find overall balanced yet heterogeneous levels of contribution from each parent species throughout the hybrid genome and identify areas of novel divergence in the hybrid species exhibiting signals consistent with balancing selection. High-divergence areas are disproportionately located on the Z chromosome and overrepresented in gene networks relating to key traits separating the focal species, which are likely involved in reproductive barriers and/or species-specific adaptations. Of special interest are genes and functional groups known to affect body patterning, beak morphology, and the immune system, which are important features of diversification and fitness. We show that a combination of mosaic parental inheritance and novel divergence within the hybrid lineage has facilitated the origin and maintenance of an avian hybrid species.

• Baalsrud, Helle Tessand; Voje, Kjetil L.; Tørresen, Ole Kristian; Solbakken, Monica Hongrø; Matschiner, Michael & Malmstrøm, Martin [Show all 10 contributors for this article] (2017). Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Scientific Reports. 7, p. 1–10. doi: 10.1038/s41598-017-08286-2. Full text in Research Archive Show summary

  Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments.

• Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Reinar, William Brynildsen; Grove, Harald & Miller, Jason R. [Show all 16 contributors for this article] (2017). An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics. 18(1), p. 1–23. doi: 10.1186/s12864-016-3448-x. Full text in Research Archive Show summary

  Background The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. Results By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. Conclusions The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

• Baalsrud, Helle Tessand; Tørresen, Ole Kristian; Solbakken, Monica Hongrø; Salzburger, Walter; Hanel, Reinhold & Jakobsen, Kjetill Sigurd [Show all 7 contributors for this article] (2017). De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 35(3), p. 593–606. doi: 10.1093/molbev/msx311. Full text in Research Archive Show summary

  New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13–18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.

• Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Star, Bastiaan; Snipen, Lars-Gustav & Hansen, Thomas F [Show all 13 contributors for this article] (2016). Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics. ISSN 1061-4036. 48(10), p. 1204–1210. doi: 10.1038/ng.3645. Full text in Research Archive Show summary

  Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in the entire Gadiformes lineage and thus was lost once in their common ancestor. In contrast, we find that MHC I gene expansions have occurred multiple times, both inside and outside this clade. Moreover, we identify an association between high MHC I copy number and elevated speciation rates using trait-dependent diversification models. Our results extend current understanding of the plasticity of the adaptive immune system and suggest an important role for immune-related genes in animal diversification.

• Star, Bastiaan; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd; Pampoulie, Christophe & Jentoft, Sissel (2016). Genomic characterization of the Atlantic cod sex-locus. Scientific Reports. 6, p. 1–9. doi: 10.1038/srep31235. Full text in Research Archive Show summary

  A variety of sex determination mechanisms can be observed in evolutionary divergent teleosts. Sex determination is genetic in Atlantic cod (Gadus morhua), however the genomic location or size of its sex-locus is unknown. Here, we characterize the sex-locus of Atlantic cod using whole genome sequence (WGS) data of 227 wild-caught specimens. Analyzing more than 55 million polymorphic loci, we identify 166 loci that are associated with sex. These loci are located in six distinct regions on fve diferent linkage groups (LG) in the genome. The largest of these regions, an approximately 55Kb region on LG11, contains the majority of genotypes that segregate closely according to a XX-XY system. Genotypes in this region can be used genetically determine sex, whereas those in the other regions are inconsistently sex-linked. The identifed region on LG11 and its surrounding genes have no clear sequence homology with genes or regulatory elements associated with sex-determination or diferentiation in other species. The functionality of this sex-locus therefore remains unknown. The WGS strategy used here proved adequate for detecting the small regions associated with sex in this species. Our results highlight the evolutionary fexibility in genomic architecture underlying teleost sexdetermination and allow practical applications to genetically sex Atlantic cod.

• Tørresen, Ole Kristian; Rise, Matthew L.; Jin, Xingkun; Star, Bastiaan; MacKenzie, Simon & Jakobsen, Kjetill Sigurd [Show all 8 contributors for this article] (2016). An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming. In MacKenzie, Simon & Jentoft, Sissel (Ed.), Genomics in Aquaculture. Elsevier. ISSN 9780128014189. p. 45–72. doi: 10.1016/B978-0-12-801418-9.00003-2. Full text in Research Archive
• Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2016). The new era of genome sequencing using high-throughput sequencing technology: Generation of the first version of the Atlantic cod genome. In MacKenzie, Simon & Jentoft, Sissel (Ed.), Genomics in Aquaculture. Elsevier. ISSN 9780128014189. p. 1–20. doi: 10.1016/B978-0-12-801418-9.00001-9. Full text in Research Archive
• Solbakken, Monica Hongrø; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Seppola, Marit; Gregers, Tone Fredsvik & Jakobsen, Kjetill Sigurd [Show all 7 contributors for this article] (2016). Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. Scientific Reports. 6. doi: 10.1038/srep25211. Full text in Research Archive Show summary

  Genome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity.

• Cortesi, Fabio; Musilováa, Zuzana; Stieb, Sara M.; Hart, Nathan S.; Siebeck, Ulrike E. & Malmstrøm, Martin [Show all 12 contributors for this article] (2015). Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 112(5), p. 1493–1498. doi: 10.1073/pnas.1417803112. Full text in Research Archive
• Minge, Marianne Aastebøl; Shalchian-Tabrizi, Kamran; Tørresen, Ole Kristian; Takishita, Kiyotaka; Probert, Ian & Inagaki, Yuji [Show all 8 contributors for this article] (2010). A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum. BMC Evolutionary Biology. 10. doi: 10.1186/1471-2148-10-191. Full text in Research Archive Show summary

  Background Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.

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• Tørresen, Ole K. (2026). Gene annotations for copse snail (Arianta arbustorum). doi: 10.5281/ZENODO.22025065. Full text in Research Archive
• Martin, Sarah Louise; Torre, Renato La; Danneels, Bram; Tooming-Klunderud, Ave; Skage, Morten & Kollias, Spyridon [Show all 12 contributors for this article] (2025). Genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance adaptations and species boundaries. Full text in Research Archive
• Baalsrud, Helle Tessand; Arnyasi, Mariann; To, Thu-Hien; Shapaval, Volha; Byrtusova, Dana & Andersstuen, Terese [Show all 13 contributors for this article] (2025). Chromosomal Chaos: Exploring a Dramatic Shift in the Evolution of Genome Organization in Mucoromycota. Full text in Research Archive
• Baalsrud, Helle Tessand; Arnyasi, Mariann; To, Thu-Hien; Shapaval, Volha; Byrtusova, Dana & Andersstuen, Terese [Show all 13 contributors for this article] (2024). Different modes of chromosomal evolution in fungi revealed by long-read sequencing. Full text in Research Archive
• Hoff, Siv Nam Khang; Tørresen, Ole Kristian; Maurstad, Marius Filomeno; Ravinet, Mark; Godiksen, Jane Aanestad & Stige, Leif Christian [Show all 10 contributors for this article] (2024). Delineate the population structure of a keystone marine fish species in the Northern Atlantic region using whole genome sequencing data. Full text in Research Archive
• Hoff, Siv Nam Khang; Maurstad, Marius Filomeno; Alan, Le Moan; Ravinet, Mark; Durant, Joël & Tørresen, Ole K. [Show all 18 contributors for this article] (2023). Identification of multiple chromosomal inversions and fusions in a keystone Arctic species with high gene flow. Full text in Research Archive
• Hoff, Siv Nam Khang; Maurstad, Marius Filomeno; Moan, Alan Le; Ravinet, Mark; Durant, Joël & Tørresen, Ole Kristian [Show all 18 contributors for this article] (2023). Identification of multiple chromosomal inversions and fusions in a keystone Arctic species with high gene flow. Full text in Research Archive
• Tørresen, Ole Kristian & Baalsrud, Helle Tessand (2022). The Norwegian Earth Biogenome Project: the snowy owl genome assembly. Full text in Research Archive
• Tørresen, Ole K.; Baalsrud, Helle Tessand; Sandve, Simen Rød & Jakobsen, Kjetill Sigurd (2022). Bioinfomatic approaches for EBP-Nor. Full text in Research Archive
• Tørresen, Ole K.; Skrede, Inger; Sandve, Simen Rød; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Borge, Ole Johan (2018). Gendykk i norsk natur gir ny kunnskap. Genialt. ISSN 0804-225X. p. 16–18. Full text in Research Archive
• Tørresen, Ole K. (2018). De novo genome assemblies of Atlantic cod. Full text in Research Archive
• Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd (2018). The impact of repetitive DNA on speciation rates in teleost fish. Full text in Research Archive
• Tørresen, Ole K. (2017). Long reads: dream or reality? Full text in Research Archive
• Eide, Marta; Puntervoll, Pål; Lille-Langøy, Roger; Goldstone, Jared V.; Tørresen, Ole Kristian & Nederbragt, Alexander Johan [Show all 11 contributors for this article] (2016). Chemical warfare in the marine environment: genomic survey of the Atlantic cod (Gadus morhua) defensome reveals the absence of an important xenosensor. Full text in Research Archive
• Baalsrud, Helle Tessand; Tørresen, Ole Kristian; Malmstrøm, Martin; Salzburger, Walter; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2015). The hemoglobin repertoire in the order of Gadiformes linked to depth adaptation. Full text in Research Archive
• Tørresen, Ole Kristian; Jentoft, Sissel; Star, Bastiaan; Sandve, Geir Kjetil F.; Skage, Morten & Hansen, Marianne Helén Selander [Show all 9 contributors for this article] (2014). A new, high quality reference genome assembly for Atlantic cod. Full text in Research Archive
• Tørresen, Ole Kristian; Walenz, Brian; Grove, Harald; Lien, Sigbjørn; Knight, James & Star, Bastiaan [Show all 15 contributors for this article] (2014). A new, high quality reference genome assembly for Atlantic cod. Full text in Research Archive
• Matschiner, Michael; Star, Bastiaan; Berg, Paul Ragnar; Tørresen, Ole Kristian; Nederbragt, Alexander Johan & Hansen, Marianne Helén Selander [Show all 11 contributors for this article] (2014). Population differentiation and local adaptation in Atlantic cod. Full text in Research Archive
• Brynildsen, William; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2014). Genomic sequence repeats in fish genomes. Full text in Research Archive
• Nederbragt, Alexander Johan; Walenz, Brian; Tørresen, Ole Kristian; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Miller, Jason Rafe (2014). Towards correction-free assembly of raw PacBio reads. Full text in Research Archive
• Elgvin, Tore Oldeide; Trier, Cassandra Nicole; Tørresen, Ole Kristian; Lien, Sigbjørn; Jensen, Henrik & Sætre, Glenn-Peter (2014). Sparrows, scaffolds and pseudo-chromosomes. Full text in Research Archive
• Tørresen, Ole Kristian (2013). Improving the cod genome assembly: Combining assembly programs and different types of sequencing data. Full text in Research Archive
• Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Miller, Jason Rafe; Walenz, Brian; Jentoft, Sissel & Jakobsen, Kjetill Sigurd (2013). Improving the Atlantic cod genome using long-read PacBio in combination with 454 and Illumina sequencing data. Full text in Research Archive
• Solbakken, Monica Hongrø; Malmstrøm, Martin; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2013). Atlantic cod displays an unusual TLR repertoire – a Gadidae-specific feature? Full text in Research Archive
• Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Skage, Morten; Tooming-Klunderud, Ave; Hansen, Marianne Helén Selander & Jentoft, Sissel [Show all 9 contributors for this article] (2012). The long jump: Long distance mate pairs and long PacBio reads for the Salmon Genome Project. Full text in Research Archive
• Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Lagesen, Karin; Khelik, Ksenia; Rognes, Torbjørn & Jentoft, Sissel [Show all 7 contributors for this article] (2012). Improving the cod genome with the use of multi-platform sequencing data. Full text in Research Archive
• Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Khelik, Ksenia; Lagesen, Karin; Rounge, Trine Ballestad & Star, Bastiaan [Show all 13 contributors for this article] (2012). Challenges and Opportunities for Improving the Atlantic Cod Genome Assembly and Annotation. Full text in Research Archive

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