Publications
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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.
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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.
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Koch, Thomas Lund; Ferrari, Giada; Sumanam, Sunita B; Salcedo, Paula Flórez; Watkins, Maren & Chase, Kevin
[Show all 13 contributors for this article]
(2026).
From neuropeptides to toxins: illuminating the origins of venom complexity in cone snails.
Molecular Biology and Evolution (MBE).
ISSN 0737-4038.
43,
p. 1–20.
doi:
10.1093/molbev/msag206.
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New genes and gene functions are key drivers of evolutionary innovation. Venomous animals, such as cone snails, provide striking examples of gene innovation, yet the mechanisms by which toxins arise remain poorly understood. Using the Conus textile genome, we uncover how neuropeptide genes were recruited into the venom and neofunctionalized as doppelgänger toxins. We identify over 20 independent recruitment events that evolved dynamically across the Conus lineage. Rather than arising from ohnologs of a whole-genome duplication event ∼200 mya, these toxins evolved through diverse mechanisms, including exon shuffling, alternative splicing, and ectopic recombination, often facilitated by lineage-specific transposable elements. Our findings reveal a dynamic interplay between genome architecture and molecular innovation, offering broad insight into the evolution of complex gene repertoires in venoms and beyond.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Hepner, Sabrina; Kuleshov, Konstantin; Tooming-Klunderud, Ave; Alig, Nikolas; Gofton, Alexander & Casjens, Sherwood
[Show all 15 contributors for this article]
(2023).
A high fidelity approach to assembling the complex Borrelia genome.
BMC Genomics.
24(1),
p. 1–19.
doi:
10.1186/s12864-023-09500-4.
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Background Bacteria of the Borrelia burgdorferi sensu lato (s.l.) complex can cause Lyme borreliosis. Different B. burgdorferi s.l. genospecies vary in their host and vector associations and human pathogenicity but the genetic basis for these adaptations is unresolved and requires completed and reliable genomes for comparative analyses. The de novo assembly of a complete Borrelia genome is challenging due to the high levels of complexity, represented by a high number of circular and linear plasmids that are dynamic, showing mosaic structure and sequence homology. Previous work demonstrated that even advanced approaches, such as a combination of short-read and long-read data, might lead to incomplete plasmid reconstruction. Here, using recently developed high-fidelity (HiFi) PacBio sequencing, we explored strategies to obtain gap-free, complete and high quality Borrelia genome assemblies. Optimizing genome assembly, quality control and refinement steps, we critically appraised existing techniques to create a workflow that lead to improved genome reconstruction. Results Despite the latest available technologies, stand-alone sequencing and assembly methods are insufficient for the generation of complete and high quality Borrelia genome assemblies. We developed a workflow pipeline for the de novo genome assembly for Borrelia using several types of sequence data and incorporating multiple assemblers to recover the complete genome including both circular and linear plasmid sequences. Conclusion Our study demonstrates that, with HiFi data and an ensemble reconstruction pipeline with refinement steps, chromosomal and plasmid sequences can be fully resolved, even for complex genomes such as Borrelia. The presented pipeline may be of interest for the assembly of further complex microbial genomes.
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Potolitsyna, Evdokiia; Pickering, Sarah Jai Hazell; Tooming-Klunderud, Ave; Collas, Philippe & Briand, Nolwenn
(2022).
De novo annotation of lncRNA HOTAIR transcripts by long-read RNA capture-seq reveals a differentiation-driven isoform switch.
BMC Genomics.
23(1).
doi:
10.1186/s12864-022-08887-w.
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Background LncRNAs are tissue-specific and emerge as important regulators of various biological processes and as disease biomarkers. HOTAIR is a well-established pro-oncogenic lncRNA which has been attributed a variety of functions in cancer and native contexts. However, a lack of an exhaustive, cell type-specific annotation questions whether HOTAIR functions are supported by the expression of multiple isoforms. Results Using a capture long-read sequencing approach, we characterize HOTAIR isoforms expressed in human primary adipose stem cells. We find HOTAIR isoforms population displays varied splicing patterns, frequently leading to the exclusion or truncation of canonical LSD1 and PRC2 binding domains. We identify a highly cell type-specific HOTAIR isoform pool regulated by distinct promoter usage, and uncover a shift in the HOTAIR TSS usage that modulates the balance of HOTAIR isoforms at differentiation onset. Conclusion Our results highlight the complexity and cell type-specificity of HOTAIR isoforms and open perspectives on functional implications of these variants and their balance to key cellular processes.
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Stenmark, Bianca; Harrison, Odile B.; Eriksson, Lorraine; Anton, Brian P.; Fomenkov, Alexey & Roberts, Richard J.
[Show all 12 contributors for this article]
(2020).
Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.
Scientific Reports.
10(1),
p. 1–11.
doi:
10.1038/s41598-020-59509-y.
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Abstract Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif C A CNNNNN T AC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.
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Tedersoo, Leho; Tooming-Klunderud, Ave & Anslan, Sten
(2018).
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives.
New Phytologist.
ISSN 0028-646X.
217(3),
p. 1370–1385.
doi:
10.1111/nph.14776.
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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.
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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.
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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.
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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.
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Frank, Jeremy A.; Pan, Yao; Tooming-Klunderud, Ave; Eijsink, Vincent; McHardy, Alice C & Nederbragt, Alexander Johan
[Show all 7 contributors for this article]
(2016).
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.
Scientific Reports.
6.
doi:
10.1038/srep25373.
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DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.
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Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter & Nome, Torfinn
[Show all 45 contributors for this article]
(2016).
The Atlantic salmon genome provides
insights into rediploidization.
Nature.
ISSN 0028-0836.
533(7602),
p. 200–205.
doi:
10.1038/nature17164.
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The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.
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Baldo, Laura; Riera, Joan Lluis; Tooming-Klunderud, Ave; Alba, M. Mar & Salzburger, Walter
(2015).
Gut microbiota dynamics during dietary shift in eastern African cichlid fishes.
PLOS ONE.
10(5).
doi:
10.1371/journal.pone.0127462.
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The gut microbiota structure reflects both a host phylogenetic history and a signature of adaptation to the host ecological, mainly trophic niches. African cichlid fishes, with their array of closely related species that underwent a rapid dietary niche radiation, offer a particularly interesting system to explore the relative contribution of these two factors in nature. Here we surveyed the host intra- and interspecific natural variation of the gut microbiota of five cichlid species from the monophyletic tribe Perissodini of lake Tanganyika, whose members transitioned from being zooplanktivorous to feeding primarily on fish scales. The outgroup riverine species Astatotilapia burtoni, largely omnivorous, was also included in the study. Fusobacteria, Firmicutes and Proteobacteria represented the dominant components in the gut microbiota of all 30 specimens analysed according to two distinct 16S rRNA markers. All members of the Perissodini tribe showed a homogenous pattern of microbial alpha and beta diversities, with no significant qualitative differences, despite changes in diet. The recent diet shift between zooplantkon- and scale-eaters simply reflects on a significant enrichment of Clostridium taxa in scale-eaters where they might be involved in the scale metabolism. Comparison with the omnivorous species A. burtoni suggests that, with increased host phylogenetic distance and/or increasing herbivory, the gut microbiota begins differentiating also at qualitative level. The cichlids show presence of a large conserved core of taxa and a small set of core OTUs (average 13–15%), remarkably stable also in captivity, and putatively favoured by both restricted microbial transmission among related hosts (putatively enhanced by mouthbrooding behavior) and common host constraints. This study sets the basis for a future large-scale investigation of the gut microbiota of cichlids and its adaptation in the process of the host adaptive radiation.
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Been, Mark de; Lanza, Val F.; Toro, Maria de; Scharringa, Jelle; Dohmen, Wietske & Du, Yu
[Show all 16 contributors for this article]
(2014).
Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages.
PLoS Genetics.
ISSN 1553-7390.
10(12).
doi:
10.1371/journal.pgen.1004776.
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Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.
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Brembu, Tore; Winge, Per; Tooming-Klunderud, Ave; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd & Bones, Atle M.
(2014).
The chloroplast genome of the diatom Seminavis robusta: New features introduced through multiple mechanisms of horizontal gene transfer.
Marine Genomics.
ISSN 1874-7787.
16(1),
p. 17–27.
doi:
10.1016/j.margen.2013.12.002.
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Xiao, Xi; Sogge, Hanne; Lagesen, Karin; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd & Rohrlack, Thomas
(2014).
Use of high throughput sequencing and light microscopy show contrasting results in a study of phytoplankton occurrence in a freshwater environment.
PLOS ONE.
9(8).
doi:
10.1371/journal.pone.0106510.
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Assessing phytoplankton diversity is of primary importance for both basic and applied ecological studies. Following the advances in molecular methods, phytoplankton studies are switching from using classical microscopy to high throughput sequencing approaches. However, methodological comparisons of these approaches have rarely been reported. In this study, we compared the two methods, using a unique dataset of multiple water samples taken from a natural freshwater environment. Environmental DNA was extracted from 300 water samples collected weekly during 20 years, followed by high throughput sequencing of amplicons from the 16S and 18S rRNA hypervariable regions. For each water sample, phytoplankton diversity was also estimated using light microscopy. Our study indicates that species compositions detected by light microscopy and 454 high throughput sequencing do not always match. High throughput sequencing detected more rare species and picoplankton than light microscopy, and thus gave a better assessment of phytoplankton diversity. However, when compared to light microscopy, high throughput sequencing of 16S and 18S rRNA amplicons did not adequately identify phytoplankton at the species level. In summary, our study recommends a combined strategy using both morphological and molecular techniques.
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Tooming-Klunderud, Ave; Sogge, Hanne; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Lagesen, Karin & Glöckner, Gernot
[Show all 9 contributors for this article]
(2013).
From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains.
Applied and Environmental Microbiology.
ISSN 0099-2240.
79(21),
p. 6803–6812.
doi:
10.1128/AEM.01455-13.
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Horizontal gene transfer is common in cyanobacteria, and transfer of large gene clusters may lead to acquisition of new functions and conceivably niche adaption. In the present study, we demonstrate that horizontal gene transfer between closely related Planktothrix strains can explain the production of the same oligopeptide isoforms by strains of different colors. Comparison of the genomes of eight Planktothrix strains revealed that strains producing the same oligopeptide isoforms are closely related, regardless of color. We have investigated genes involved in the synthesis of the photosynthetic pigments phycocyanin and phycoerythrin, which are responsible for green and red appearance, respectively. Sequence comparisons suggest the transfer of a functional phycoerythrin gene cluster generating a red phenotype in a strain that is otherwise more closely related to green strains. Our data show that the insertion of a DNA fragment containing the 19.7-kb phycoerythrin gene cluster has been facilitated by homologous recombination, also replacing a region of the phycocyanin operon. These findings demonstrate that large DNA fragments spanning entire functional gene clusters can be effectively transferred between closely related cyanobacterial strains and result in a changed phenotype. Further, the results shed new light on the discussion of the role of horizontal gene transfer in the sporadic distribution of large gene clusters in cyanobacteria, as well as the appearance of red and green strains.
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Sogge, Hanne; Rohrlack, Thomas; Rounge, Trine Ballestad; Sønstebø, Jørn Henrik; Tooming-Klunderud, Ave & Kristensen, Tom
[Show all 7 contributors for this article]
(2013).
Gene flow, recombination, and selection in cyanobacteria: population structure of geographically related Planktothrix Freshwater Strains.
Applied and Environmental Microbiology.
ISSN 0099-2240.
79(2),
p. 508–515.
doi:
10.1128/AEM.02417-12.
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Several Planktothrix strains, each producing a distinct oligopeptide profile, have been shown to coexist within Lake Steinsfjorden (Norway). Using nonribosomal peptide synthetase (NRPS) genes as markers, it has been shown that the Planktothrix community comprises distinct genetic variants displaying differences in bloom dynamics, suggesting a Planktothrix subpopulation structure. Here, we investigate the Planktothrix variants inhabiting four lakes in southeast of Norway utilizing both NRPS and non-NRPS genes. Phylogenetic analyses showed similar topologies for both NRPS and non-NRPS genes, and the lakes appear to have similar structuring of Planktothrix genetic variants. The structure of distinct variants was also supported by very low genetic diversity within variants compared to the between-variant diversity. Incongruent topologies and split decomposition revealed recombination events between Planktothrix variants. In several strains the gene variants seem to be a result of recombination. Both NRPS and non-NRPS genes are dominated by purifying selection; however, sites subjected to positive selection were also detected. The presence of similar and well-separated Planktothrix variants with low internal genetic diversity indicates gene flow within Planktothrix populations. Further, the low genetic diversity found between lakes (similar range as within lakes) indicates gene flow also between Planktothrix populations and suggests recent, or recurrent, dispersals. Our data also indicate that recombination has resulted in new genetic variants. Stability within variants and the development of new variants are likely to be influenced by selection patterns and within-variant homologous recombination.
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Andersen, Øivind; Rosa, Maria Cristina De; Pirolli, Davide; Tooming-Klunderud, Ave; Petersen, Petra E & André, Carl
(2011).
Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua) - Conserved synteny between fish monolobal and tetrapod bilobal transferrin loci.
BMC Genetics.
12(51).
doi:
10.1186/1471-2156-12-51.
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Background The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. Results The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp). Whereas Tf1 and Tf2 were differentially expressed in liver and brain, the Omp transcript was restricted to the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, that might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. Conclusions The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive selection and local adaptation in trans-Atlantic cod populations.
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Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik
[Show all 42 contributors for this article]
(2011).
The genome sequence of Atlantic cod reveals a unique immune system.
Nature.
ISSN 0028-0836.
477(7363),
p. 207–210.
doi:
10.1038/nature10342.
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Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions5. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
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Andersen, Øivind; Dahle, Stine Veronica Wiborg; Nes, Solveig van; Bardal, Tora; Tooming-Klunderud, Ave & Kjørsvik, Elin
[Show all 7 contributors for this article]
(2009).
Differential spatio-temporal expression and functional diversification of the myogenic regulatory factors MyoD1 and MyoD2 in Atlantic halibut (Hippoglossus hippoglossus).
Comparative Biochemistry and Physiology - Part B: Biochemistry & Molecular Biology.
ISSN 1096-4959.
154(1),
p. 93–101.
doi:
10.1016/j.cbpb.2009.05.009.
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Rounge, Trine Ballestad; Rohrlack, Thomas; Tooming-Klunderud, Ave; Kristensen, Tom & Jakobsen, Kjetill Sigurd
(2007).
Comparison of cyanopeptolin genes in Planktothrix, Microcystis, and Anabaena strains: Evidence for independent evolution within each genus.
Applied and Environmental Microbiology.
ISSN 0099-2240.
73,
p. 7322–7330.
doi:
10.1128/AEM.01475-07.
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Østbye, Tone-Kari K; Andersen, Øivind; Frang, Ola T; Tooming-Klunderud, Ave; Jakobsen, Kjetill S. & Yafe, Anat
[Show all 8 contributors for this article]
(2007).
Molecular cloning of the Atlantic salmon activin receptor IIB cDNA - Localization of the receptor and myostatin in vivo and in vitro in muscle cells.
Gene.
ISSN 0378-1119.
403(01.feb),
p. 159–169.
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Tooming-Klunderud, Ave; Rohrlack, Thomas; Shalchian-Tabrizi, Kamran; Kristensen, Tom & Jakobsen, Kjetill Sigurd
(2007).
Structural analysis of a non-ribosomal halogenated cyclic peptide and its putative operon from Microcystis: implications for evolution of cyanopeptolins.
Microbiology (Reading).
ISSN 1350-0872.
153(5),
p. 1382–1393.
doi:
10.1099/mic.0.2006/001123-0.
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Nederbragt, Alexander Johan & Tooming-Klunderud, Ave
(2010).
From next generation reads to genomes: experiences gained from different genome projects.
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Tooming-Klunderud, Ave
(2010).
From next generation reads to genomes: experiences gained from different genome projects.
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Tooming-Klunderud, Ave
(2010).
HIgh throughput sequencing at the Norwegian Sequencing Centre: possibilities and procedures.
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Tooming-Klunderud, Ave
(2010).
454 sequencing at the Norwegian Sequencing Centre: possibilities, procedures and projects.
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Tooming-Klunderud, Ave; Nederbragt, Alexander Johan; Skage, Morten & Jakobsen, Kjetill Sigurd
(2009).
The Ultra-high Throughput Sequencing Platform at the University of Oslo.
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Published
Nov. 3, 2010 3:34 PM
- Last modified
Feb. 3, 2011 12:18 PM
