Biology subjects

Torresen, O. K.

Publications and source records attributed to Torresen, O. K..

At least 19 recordsLinked to original sources

bioRxiv2026

A chromosome-level reference genome of the largest cervid species - the European moose (Alces alces; Linnaeus, 1758)

We describe a chromosome-level, haplotype-resolved genome assembly from a male European moose (Alces alces alces). The assembly comprises two pseudo-haplotypes of 3,148 Mb and 3,112 Mb, with sex chromosomes in haplotype one, and 33 autosomes in each haplotype (68 in total). Assembly completeness is high (BUSCO 98.3% and 95.7%), with 21,496 and 20,498 annotated protein-coding genes for haplotypes one and two, respectively. This genome assembly is the most complete so far generated for European moose.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798)

We present a chromosome-level genome assembly of a female great grey owl (Strix nebulosa lapponica). The assembly comprises two pseudo-haplotypes of 1554 Mb and 1242 Mb, with 83.2% and 91.4% scaffolded into 40 autosomal chromosomes, in addition to the W and Z sex chromosomes both placed in hap1. Assembly completeness is high (BUSCO 99.2% and 94.8%), with 18,493 and 17,279 annotated protein-coding genes for hap1 and hap2, respectively. This genome establishes a reference for investigating genetic variation and chromosome evolution in great grey owls. Compared with the previous S. nebulosa assembly, this assembly includes both sex chromosomes, separates regions that were previously collapsed, and resolves 82 chromosomes total. While larger chromosomes show broadly conserved synteny across owl assemblies, the recovery of additional conserved microchromosome-associated genes suggests that ONT reads improved resolution of the smallest chromosomes relative to HiFi-based assemblies.

genomics↗

bioRxiv2026

A chromosome-level genome assembly of a "living fossil", the tadpole shrimp Lepidurus arcticus (Pallas, 1793)

We present the first chromosome-level reference genome for Lepidurus arcticus (Pallas, 1793), a freshwater crustacean with circumpolar distribution. L. arcticus belongs to the small order of freshwater Notostracan crustaceans that are representatives of the ancient group Branchiopoda. This group has a remarkable morphological stability and is frequently labelled "living fossils". Its ancient origin, streamlined genome (estimated to 0.11 Gb) and reproductive flexibility makes this a very interesting candidate for genomic studies. The haplotype-resolved assemblies are composed of two pseudo-haplotypes spanning 81.2 megabases (Mb) and 81.8 Mb, respectively, and each scaffolded into 6 chromosomes. Both haplotypes (hap) show high completeness and identical BUSCO scores of 98.3 for hap1 and hap2. The scaffold N50 length is 13.4 Mb for hap1 and 13.9 Mb for hap2, and k-mer completeness estimated from PacBio HiFi reads was 95.79% and 96.18%, respectively. The haplotypes display very low estimated genome-wide heterozygosity of 0.133%. The assembly contains 10901 (hap1) and 10910 (hap2) protein-coding genes. Repetitive elements comprised approximately 24-25% of each haplotype, with long terminal repeat retrotransposons representing the most abundant transposable element class at approximately 8-9%. Comparison with the near chromosome-level genome of Lepidurus packardi revealed substantial intrachromosomal rearrangements, despite similar chromosome numbers and chromosome sizes. Differences in transposable element content between L. arcticus and L. packardi were primarily driven by retrotransposons, particularly LTR and LINE elements. This reference genome provides a valuable resource for future population genomic studies and for investigating evolutionary stasis at the genome level.

genomics↗

bioRxiv2026

Range-wide phylogeography, population genomics, and demography of three widespread Ara macaws (Psittacidae)

Macaws of the genus Ara comprise eight extant species distributed throughout the Neotropics. Among them, four have broad geographic ranges, yet little is known about the evolutionary history and demographic processes that shaped their genomic variation and present-day distributions. This is particularly relevant because, although these wide-ranging macaws are classified as Least Concern by the IUCN, many of their populations are declining due to habitat fragmentation, illegal trade, and climate change. Here, we used nuclear and mitochondrial genomic data to characterize the evolutionary relationships, population structure, genetic diversity, and demographic histories of three widely distributed species (A. ararauna, A. chloropterus, and A. severus) across their geographic distributions. We identified two main populations within Ara severus, and this species showed the highest heterozygosity levels among the three species. In A. ararauna and A. chloropterus, we observed four main genetic clusters corresponding to two populations in the Amazon rainforest biome and and two populations in the Cerrado savanna biome. Cerrado populations in both species exhibited markedly reduced heterozygosity and elevated inbreeding relative to Amazonian populations, consistent with smaller effective population sizes and increased isolation. Genome-wide scans suggested that genetic drift and divergent demographic histories played a predominant role in driving the strong differentiation between Amazon and Cerrado in these two species. Nevertheless, we detected two candidate genes, NALCN and RBBP6, with convergent selection signals across A. ararauna and A. chloropterus, suggesting possible local adaptation to the Cerrado biome.

evolutionary biology↗

bioRxiv2026

A mosaic of genomic architectures underpins parasitism loss in a jawless vertebrate

Lampreys are the only ancestrally parasitic vertebrate lineage, yet parasitism has been repeatedly lost alongside a suite of life-history changes, such as loss of migration and juvenile feeding and accelerated maturation. Combining whole-genome resequencing, haplotype-resolved assemblies, hybrid-zone genotyping, multi-tissue transcriptomics, and sperm phenotyping, we map this life-history syndrome in European Lampetra to six chromosomes spanning a mosaic of genomic architectures: a [~]20 Mb low-recombination region on chromosome 1 lacking chromosomal rearrangements within Lampetra but involving inter-specific rearrangements across deep lamprey lineages; a translocated inversion with ecotype-dependent sperm-velocity effects; and ecotype-divergent deletions overlapping genes crucial for nervous system (CNTNAP2) and reproductive development (FSHR). However, this genomic basis is not shared with a convergent sister lineage, pointing to independent routes to a recurring life-history transition in lampreys.

evolutionary biology↗

bioRxiv2025

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758)

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 little 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 8 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 (LTR) 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.

genomics↗

bioRxiv2025

The genome of the Glacier lanternfish shows loss of MHC I and II function and provides insight into evolution of lanternfish immune systems

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.

genomics↗

bioRxiv2025

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids

Arctic and alpine insects face extreme environmental stressors, yet the genomic basis of their adaptation remains poorly understood. Here, we present the first haplotype-resolved, chromosome-level genomes for four species of Diamesa (Diptera: Chironomidae), a genus of cold-adapted midges inhabiting glacial and high-altitude freshwater ecosystems. Using PacBio HiFi sequencing and Hi-C scaffolding, we assembled high-quality genomes with chromosome-level resolution and high k-mer completeness. Phylogenomic analyses support Diamesinae as sister to other Chironomidae except Podonominae, and genomic comparisons provide evidence for introgression between the evolutionary distinct D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species revealed significant gene family contractions in Diamesa associated with oxygen transport and metabolism, suggesting adaptations to high-altitude, low-oxygen environments. Conversely, expansions were detected in histone-related and Toll-like receptor gene families, likely enhancing chromatin remodeling and immune regulation under cold stress. A single gene family encoding glucose dehydrogenase was significantly expanded across all cold-adapted species studied, implicating its role in cryoprotectant synthesis and oxidative stress mitigation. Notably, Diamesa species exhibit the largest gene family contraction at any node, with minimal overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation. Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These genome assemblies represent a valuable resource for investigating adaptation, speciation, and conservation in cold-specialist insects. Future work integrating gene expression and population genomics will further illuminate the evolutionary resilience of Diamesa in a warming world.

genomics↗

bioRxiv2025

Chromosome-level assembly of the octoploid cloudberry(Rubus chamaemorus)

We describe a chromosome-level genome assembly from an individual male plant of the cloudberry (Rubus chamaemorus). The haplotype-resolved assemblies contain one pseudo-haplotype spanning 1198 megabases and one pseudo-haplotype spanning 1161 megabases. Most of these two assemblies, 93.57% and 96.55% respectively, are each scaffolded into 28 pseudo-chromosomes. Both assemblies show high completeness, with the same BUSCO completeness score of 99.2%. Most BUSCO genes are duplicated in both pseudo-haplotypes, in line with the polyploid nature of the cloudberry genome. The assemblies contain 74,132 and 70,692 predicted protein-coding genes, respectively. Analysis of repetitive sequences classified [~]60% of each haplotype as repeats. Comparative synteny with red raspberry (Rubus idaeus) reveals a 4:1 chromosome correspondence, supporting an octoploid origin. Ks distributions and k-mer clustering indicate a fairly recent polyploidization involving one divergent ({beta}) and three closely related () subgenomes. Low coverage targeted sequencing data mapped to our assembly link the {beta}-subgenome to a relative of R. pedatus or R. lasiococcus, while the -subgenomes might derive from a putative auto-allohexaploid within the main Rubus clade. In conclusion, these results indicate that the cloudberry genome arose through multiple hybridization events, including recurrent allopolyploidy and possibly autopolyploidy. Significance statementCloudberry cultivation has lagged due to unclear origin and genome structure. We present a haplotype-resolved, chromosome-scale assembly that resolves four homologs per ancestral chromosome into 28 pseudo-chromosomes per haplotype and shows a 4:1 correspondence with red raspberry (Rubus idaeus). Genomic analyses indicate a recent polyploidization in which three closely related subgenomes likely derive from a putative hexaploid within the main Rubus clade, associated with R. arcticus (Arctic raspberry), whereas the fourth, more divergent subgenome is linked to relatives of R. pedatus (strawberryleaf raspberry) and R. lasiococcus (dwarf bramble). These results clarify cloudberrys formation and provide a foundation for trait discovery and accelerated breeding.

genomics↗

bioRxiv2025

Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus)

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 megabases and hap 2 spanning 2,633 megabases. Contig N50 and scaffold N50 lengths are in the range of 31-41 Mb and 66-69 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) and a comparison with previously published genome assemblies of reindeer.

genomics↗

bioRxiv2025

Chromosomal inversions mediated by tandem insertions of transposable elements

Chromosomal inversions play a crucial role in evolution by influencing phenotypes through the linkage of co-adapted alleles. While inversions have been found across a large number of taxa, mapping and characterizing inversion breakpoint regions remains challenging, often due to the presence of complex tandem repeats and transposable elements (TEs). Here, we identify and quantify TEs 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 TE orders and superfamilies with terminal inverted repeats (TIRs) within the inversion breakpoints of chromosomes 1, 7 and 12. Notably, we discovered a tandem accumulation of miniature inverted-repeat transposable elements (MITEs) 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 TEs in breakpoint regions suggests that they have driven the appearance of inversions through ectopic recombination, further supporting the potential of TEs in facilitating chromosomal reorganizations with large evolutionary implications.

evolutionary biology↗

bioRxiv2024

Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri)

We present haplotype-resolved whole-genome assemblies from one individual European river lamprey (Lampetra fluviatilis) and one individual brook lamprey (Lampetra planeri), usually regarded as sister species. The genome assembly of L. fluviatilis consists of pseudo-haplotype one, spanning 1073 Mb and pseudo-haplotype two, spanning 963 Mb. Likewise for the L. planeri specimen, the genome assembly spans 1049 Mb and 960 Mb for pseudo-haplotypes one and two, respectively. Both the L. fluviatilis pseudo-haplotypes have been scaffolded into 82 pseudo-chromosomes, with the same number for the L. planeri pseudo-haplotypes. All four pseudo-haplotype assemblies were annotated, identifying 21,479 and 16,973 genes in pseudo-haplotypes one and two for L. fluviatilis, and 24,961 and 21,668 genes in pseudo-haplotypes one and two for L. planeri. A comparison of the genomes of L. fluviatilis and L. planeri, alongside a separate chromosome level assembly of L. fluviatilis from the UK, indicates that they form a species complex, potentially representing distinct ecotypes. This is further supported by phylogenetic analyses of the three reference Lampetra genomes in addition to sea lamprey (Petromyzon marinus).

genomics↗

bioRxiv2024

Evolutionary new centromeres in the snowy owl genome putatively seeded from a transposable element

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 centromeric satellite DNA, which appears to have originated from an endogenous retrovirus (ERV1). Using gene collinearity analyses we show that the position of these evolutionary new centromeres (ECNs) 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 transposable element-driven evolution of lineage-specific centromeres, which could have played a role in reproductive isolation and speciation of the snowy owl.

genomics↗

bioRxiv2024

Population divergence manifested by genomic rearrangements in a keystone Arctic species with high gene flow

Genomic rearrangements have in recent years gained attention due to their evolutionary role in processes related to adaptation to local environmental conditions as well as diversification and speciation. In this study, we report on genomic rearrangements in the cold-water adapted polar cod (Boreogadus saida), a keystone Arctic fish species. By taking advantage of a new chromosome-level genome assembly in combination with whole-genome population sequencing data from specimens across the northern Barents Sea and adjacent regions, we identified a substantial number of larger chromosomal inversions (n=20) and characterized the previously identified chromosomal fusions (n=5). These genomic features -- encompassing over 20% of the genome -- exhibited genetic divergence, strong internal linkage disequilibrium, and signals of selection. Two of the identified inversions were associated with the two previously described hemoglobin clusters, while a third chromosomal region was found to differentiate between males and females. Moreover, clustering analyses on genotype frequencies of inversions revealed sub- structuring according to five geographic sub-groups suggesting sub-populations and/or the existence of cryptic ecotypes. These results provide novel insights into the impact of genomic rearrangements in population divergence and thus, potentially local adaptation, especially in species with high gene flow.

genomics↗

bioRxiv2024

Chromosomal fusions and large-scale inversions are key features for adaptation in Arctic codfish species

The evolutionary impact of structural variants, such as chromosomal inversions, is well documented, especially for their role in local adaptation in high gene flow systems. However, the role of other genomic rearrangements like chromosomal fusions, fissions, and translocations is still relatively unexplored. Here we present six chromosome-level Gadid reference genomes for the non-migratory Atlantic cod (Gadus morhua) i.e., Norwegian coastal cod (NCC), Atlantic haddock (Melanogrammus aeglefinus), burbot (Lota lota), European hake (Merluccius merluccius) as well as two keystone Arctic codfishes: the polar cod (Boreogadus saida) and Arctic cod (Arctogadus glacialis). Within a comparative genomics framework, we uncovered several lineage-specific chromosomal fusions, resulting in a reduced number of chromosomes compared to the ancestral state in the two cold-water adapted codfishes. The identified fusions were not homologous, i.e., indicating that they originate from independent evolutionary events. Additionally, a high number of partly overlapping chromosomal inversions between the two species were detected. Using a smaller population dataset, we uncovered a high degree of conservation for some of the overlapping inversions (including some breakpoint regions), suggesting that these regions are under selection, and potentially of evolutionary importance. With the use of chromosome-level genome assemblies, we demonstrate how large genomic reorganizations are likely to play important roles in speciation processes and thus, in particular to adaptation to freezing environmental conditions. Moreover, we observe that such massive rearrangement events can take place across relatively short evolutionary time scales.

genomics↗

bioRxiv2023

Genomic repeat landscape evolution across the teleost fish lineages

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity have 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 found that TE content, the degree of parental care and short tandem repeat (STR) content contributed to genome size variability. In contrast to TEs, STR content showed a negative relationship with genome size. STR content did not correlate with TE content, which implies independent evolutionary paths. Last, marine and freshwater fish have large differences in STR content. The most extreme propagation was found 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.

evolutionary biology↗

bioRxiv2022

Genomic consequences of range expansion and colonisation in the reed warbler (Acrocephalus scirpaceus)

Range expansion is a common natural phenomenon, which may be intensified by human-induced drivers such as climate change and alterations of habitat. The genetic consequences of range expansion are potentially major, and it is important to study known cases of range expansion to understand how human activities affect contemporary evolution, and to learn more about the genetic adaptive potential of species. The reed warbler (Acrocephalus scirpaceus) is a long-distance migratory bird breeding in Eurasia and wintering south of Sahara. It is currently expanding its range northwards, likely as a consequence of climate change. Interestingly, however, reed warblers have also recently colonised new territory southwards, following habitat restoration at the southern range margin. In this study, we investigate the genetic consequences of these two-directional range expansions with RAD-seq, looking at 10 populations from north to south in Europe. We investigate population structure and genome diversity, and assess the role of selection in divergence between populations across the species range. We do not find evidence of strong genetic structure in the reed warbler populations, and the youngest edge populations do not exhibit any substantial loss in genetic diversity, suggesting ongoing gene flow. On a smaller scale, the edge populations are the most genetically distinct, and we identify environmental disparity, especially in precipitation variability, as the main barrier of gene flow, to a greater extent than geographic distance. We find no evidence that the loci involved in population divergence and adaptation in the core populations are the same that are involved in adaptation at the range edges. Using three genome scan methods to identify selection, we found 49 SNPs putatively under selection, of which 33 were located in introns of 28 unique genes. Most of these are correlated with differences in climatic variables of temperature and precipitation. Some genome scan outliers show signs of being part of nascent selective sweeps, especially one which is distinct for the northern range edge. Our results suggest that in the reed warbler, contemporary range expansion has had little effect on molecular diversity and has been rapidly followed by local adaptation to climatic conditions, which could further corroborate the rapid pace at which colonisation of novel environments has occurred both northwards and southwards.

evolutionary biology↗

bioRxiv2021

A Chromosome-level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)

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 behaviour 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, 10X 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 genes in the assembly 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, of which 97.5% were complete BUSCO orthologs. 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. Significance statementThe reed warbler (Acrocephalus scirpaceus) has been lacking a genomic resource, despite having been broadly researched in studies of coevolution, ecology and adaptations to climate change. Here, we generated a chromosome-length genome assembly of the reed warbler, and found evidence of macrochromosomal fusions in its genome, which are likely of recent origin. This genome will provide the opportunity for a deeper understanding of the evolution of genomes in birds, as well as the evolutionary path and possible future of the reed warbler.

genomics↗