Siv Nam Khang Hoff

• 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.

• Maurstad, Marius Filomeno; Hoff, Siv Nam Khang; Cerca, José; Ravinet, Mark; Bradbury, Ian & Jakobsen, Kjetill Sigurd [Show all 8 contributors for this article] (2025). Reference genome bias in light of species-specific chromosomal reorganization and translocations. Genome Biology. ISSN 1465-6906. 26(1), p. 1–26. doi: 10.1186/s13059-025-03761-w. Full text in Research Archive Show summary

  Abstract Background Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements—such as chromosomal inversions—in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. Results Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod ( Arctogadus glacialis ), polar cod ( Boreogadus saida ), and Atlantic cod ( Gadus morhua ) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15–20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (D XY ). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. Conclusions Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

• 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.

• Helmerson, Cecilia; Durant, Joël; Hoff, Siv Nam Khang; Brieuc, Marine Servane Ono; Berg, Paul Ragnar & Jorde, Per Erik [Show all 14 contributors for this article] (2025). A century of anthropogenic perturbations impact genomic signatures of the iconic migratory Atlantic cod. Science Advances. 11(31). doi: 10.1126/sciadv.adp3342. Full text in Research Archive Show summary

  Anthropogenic stressors have led to marked ecosystem perturbations, including population declines and shifts in habitat range for key marine fish species. Understanding how these changes affect genome-wide characteristics, causing long-term evolutionary responses, is still in its infancy. Genome-wide retrospective assessment of the iconic migratory Atlantic cod ( Gadus morhua ) from the Barents Sea, unraveled varying degree of admixture with the nonmigratory coastal ecotype throughout the 20th century, and intriguingly more intensified during recent decades. These genomic changes were supported by an increased number of individuals displaying the heterozygous state of the chromosomal inversion coupled to migratory behavior in Atlantic cod. Ecological models and genome-wide scans identified that some of the observed frequency shifts, coupled to neural development, metabolic, and growth regulation, covaried with intensified fisheries, reduced generation time, and ocean warming. Our results demonstrate how anthropogenic perturbations impact the dynamics between two well-known ecotypes of Atlantic cod and thus, their genomic signatures, with potential implications for future management programs.

• 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
• 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.

• Pinninti, Likith Reddy; Maurstad, Marius Filomeno; Hoff, Siv Nam Khang; Kristensen, Torstein; Noble, Leslie Robert & Jentoft, Sissel [Show all 7 contributors for this article] (2023). The complete mitochondrial genome of the Atlantic spiny lumpsucker Eumicrotremus spinosus (Fabricius, 1776). Mitochondrial DNA Part B: Resources. 8(3), p. 364–367. doi: 10.1080/23802359.2023.2184649. Full text in Research Archive Show summary

  The complete mitogenome of the Atlantic spiny lumpsucker (Eumicrotremus spinosus) was generated using the PacBio Sequel II HiFi sequencing platform. The mitogenome assembly has a length of 19,281 bp and contains 13 protein-coding sequences, 22 tRNA genes, 2 rRNA genes, one control region containing the D-loop (2383 bp) and a duplicate control region (1133 bp) Phylogenetic analysis using maximum likelihood revealed that E. spinosus is closely related to the Siberian lumpsucker (E. asperrimus). The mitogenome of the spiny lumpsucker will be useful in population genomics and systematic studies of Cyclopteridae, Liparidae, and Cottidae.

• Nilsson, Pernille; Ravinet, Mark; Cui, Yujun; Berg, Paul Ragnar; Zhang, Yujiang & Guo, Rong [Show all 17 contributors for this article] (2022). Polygenic plague resistance in the great gerbil uncovered by population sequencing. PNAS Nexus. 1(5). doi: 10.1093/pnasnexus/pgac211. Full text in Research Archive
• 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
• 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

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• 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
• Hoff, Siv Nam Khang (2016). Comparative genomics by targeted capture and long read sequencing reveal dynamic evolution of hemoglobin gene clusters in codfishes. Full text in Research Archive
• Frigstad, Helene; Ramon, Paula; Borgersen, Gunhild; Engesmo, Anette; Staalstrøm, Andre & Naustvoll, Lars Johan [Show all 22 contributors for this article] (2024). Tilstandsrapport for Oslofjorden. Norsk institutt for vannforskning (NIVA). ISSN 9788257777739. Full text in Research Archive Show summary

  I 2021 la regjeringen frem en helhetlig tiltaksplan som viser regjeringens viktigste prioriteringer for å gjøre Oslofjorden ren, rik og tilgjengelig for alle fram mot 2026. Tilstandsrapport for Oslofjorden, ledet av NIVA i samarbeid med HI, NINA, NMBU og UiO, gir en oversikt over miljøtilstanden i Oslofjorden de siste 5-10 årene og utviklingen de siste 10-50 årene. Oslofjorden har opplevd negativ utvikling på grunn av blant annet forurensing, overfiske og bygging i strandnære områder. Klimaendringer forventes å forverre situasjonen ytterligere. Økologisk tilstand viser forbedring i Indre Oslofjord, men forverring i Ytre Oslofjord og Skagerrak. For miljøgifter er det ofte overskridelser av grenseverdier for kjemisk tilstand. Blåskjell, dyreplankton, sjøpattedyr, fisk og sjøfugler er viktige indikatorer på fjordens helse, men det er registret nedgang i mange arter, spesielt for torskebestanden. Utbredelse av stortareskog, sukkertareskog og ålegressenger er redusert, og det er økt forekomst av lurv. Flere arter og naturtyper er regnet som truet og rødlistet. Det er registrert flere fremmede arter, som utgjør en økologisk risiko i Oslofjorden.

• Husson, Berengere; Eriksen, Elena; Jentoft, Sissel; Boge, Erling; Borgå, Katrine & Chierici, Melissa [Show all 36 contributors for this article] (2023). Polar cod connectivity cruise 2022 Cruise Report. UiT Norges arktiske universitet. doi: 10.7557/nlrs.6944. Full text in Research Archive
• Reigstad, Marit; Gabrielsen, Tove M.; Amargant-Arumi, Marti; Amundsen, Rita; Bluhm, Bodil & Bodur, Yasemin V. [Show all 37 contributors for this article] (2022). Seasonal Cruise Q3: Cruise Report. Septentrio Academic Publishing. Full text in Research Archive Show summary

  The Nansen Legacy Q3 cruise, 5-27 August 2019, initiated the seasonal investigations of the Nansen Legacy transect. The transect represent an environmental gradient going through the northern Barents Sea, and included 7 process stations (P1-P7) lasting 6-53 hrs. CTD stations were taken to increase the hydrographic resolution on the transect. The program included measurements and sampling from the atmosphere, sea ice, ocean and sea floor. Data collected ranged from physical observations, chemical, biological and geological data collection, and the aim was to link observations and measurements to improve our understanding of the systems involving both climate, human impacts and the ecosystems. Deployment of moorings and gliders extended the observational capacity in time and space, outside the cruise period.

• Ingvaldsen, Randi Brunvær; Bluhm, Bodil; Aberle-Malzahn, Nicole; Amundsen, Rita; Ardelan, Murat Van & Bagøien, Espen [Show all 33 contributors for this article] (2020). Joint Cruise 1-2 2018: Cruise Report. Septentrio Academic Publishing. Full text in Research Archive

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