Jon Bråte

• Bråte, Jon; Grande, Eugenia Giovanna; Pedersen, Benedikte Nevjen; Frengen, Torstein Gjølgali & Stene-Johansen, Kathrine (2026). Evaluation of a multiplexed tiling PCR scheme for whole-genome amplification of hepatitis B virus using Oxford Nanopore sequencing. Access Microbiology. doi: 10.1099/acmi.0.001232.v1. Full text in Research Archive Show summary

  Here we evaluated the performance of a previously published tiling PCR primer scheme by Ringlander et al. (2022) for whole-genome amplification of Hepatitis B virus (HBV) in combination with Oxford Nanopore sequencing. The primer set originally developed for Ion Torrent sequencing was adapted by removing platform-specific adapters and tested using clinical serum or plasma samples submitted for routine HBV genotyping and resistance testing. Two multiplexing strategies were compared: a single PCR pool containing all primers and a two-pool strategy with non-overlapping amplicons. Sequencing reads were processed using a Nanopore analysis pipeline, and genome coverage and amplicon performance were compared across samples spanning a wide Ct range and representing HBV genotypes A–E. Across all samples, the median genome coverage was approximately 50%, although recovery varied widely, ranging from complete failure to nearly full genomes. Combining all primers into a single PCR reaction, or separating overlapping amplicons into different reactions, had little overall impact on genome recovery, and no consistent differences between the two pooling strategies were observed. In contrast, amplification efficiency differed markedly between individual amplicons. Amplicons 1–5 generally produced higher sequencing depth, whereas amplicons 6–10 frequently showed low coverage and contributed to incomplete genome recovery. Genome coverage was strongly associated with Ct values, with higher coverage observed in samples with lower Ct values, while coverage was broadly similar across genotypes. These results demonstrate that the Ringlander et al. primer scheme can be adapted for multiplex PCR and Nanopore sequencing of HBV, but uneven amplicon performance limits consistent full-genome recovery and highlights the need for further optimization of HBV tiling PCR designs.

• Bråte, Jon; Instefjord, Kamilla Heddeland; Alfsnes, Kristian & Stene-Johansen, Kathrine (2026). HCVTyper: A Nextflow pipeline for hepatitis C virus genome assembly, genotyping and antiviral resistance detection | Microbiology Society. Access Microbiology. doi: 10.1099/acmi.0.001193.v1. Full text in Research Archive Show summary

  High-throughput sequencing is increasingly used for the characterization of hepatitis C virus (HCV), enabling genotyping, detection of mixed infections, and identification of resistance-associated variants (RAVs). However, the bioinformatics analysis of capture-based or metagenomic HCV datasets remains challenging due to high genome diversity, co-infections, and the need for reproducible workflows. We present HCVTyper, a reproducible bioinformatics pipeline for HCV genome analysis implemented in Nextflow. HCVTyper integrates quality control, taxonomic classification, two-step reference-based mapping, consensus generation, de novo assembly, and antiviral resistance annotation. Benchmarking with simulated mixtures and real-world datasets demonstrated robust identification of both major and minor genotypes across a wide abundance range, with user-adjustable thresholds for co-infection detection. Integration with HCV-GLUE enables sensitive detection of RAVs from mapping files, including low-frequency variants. The pipeline is fully containerized using Docker and produces comprehensive reports to facilitate interpretation. HCVTyper is open-source and available at: https://github.com/folkehelseinstituttet/hcvtyper.

• Zhu, Hengyi & Bråte, Jon (2026). Identification and Functional Characterization of microRNAs in Ichthyosporea. F1000 Research. doi: 10.12688/f1000research.162501.1. Full text in Research Archive
• Bråte, Jon; Instefjord, Kamilla Heddeland; Alfsnes, Kristian & Stene-Johansen, Kathrine (2025). HCVTyper: A Nextflow pipeline for hepatitis C virus genome assembly, genotyping and antiviral resistance detection. bioRxiv - the preprint server for biology. doi: 10.1101/2025.10.21.683612. Full text in Research Archive Show summary

  Motivation High-throughput sequencing is increasingly used for the characterization of hepatitis C virus (HCV), enabling genotyping, detection of mixed infections, and identification of resistance-associated variants (RAVs). However, the bioinformatics analysis of capture-based or metagenomic HCV datasets remains challenging due to high genome diversity, co-infections, and the need for reproducible workflows. Results We present HCVTyper , a reproducible bioinformatics pipeline for HCV genome analysis implemented in Nextflow. HCVTyper integrates quality control, taxonomic classification, two-step reference-based mapping, consensus generation, de novo assembly, and antiviral resistance annotation. Benchmarking with simulated mixtures and real-world datasets demonstrated robust identification of both major and minor genotypes across a wide abundance range, with user-adjustable thresholds for co-infection detection. Integration with HCV-GLUE enables sensitive detection of RAVs from mapping files, including low-frequency variants. The pipeline is fully containerized (Docker) and produces comprehensive reports to facilitate interpretation. Availability and implementation HCVTyper is open-source and available at: https://github.com/folkehelseinstituttet/hcvtyper Contact jon.brate@fhi.no

• Llorente, Ignacio Garcia; Bråte, Jon; Fossum, Even; Rohringer, Andreas; Moen, Line Victoria & Hungnes, Olav [Show all 9 contributors for this article] (2024). Recombinant SARS-CoV-2 Delta/Omicron BA.5 emerging in an immunocompromised long-term infected COVID-19 patient. Scientific Reports. 14(1). doi: 10.1038/s41598-024-75241-3. Full text in Research Archive Show summary

  The emergence of the SARS-CoV-2 virus led to a global pandemic, prompting extensive research efforts to understand its molecular biology, transmission dynamics, and pathogenesis. Recombination events have been increasingly recognized as significant contributor to the virus’s diversity and evolution, potentially leading to the emergence of novel strains with altered biological properties. Indeed, recombinant lineages such as the XBB variant and its descendants have subsequently dominated globally. Therefore, continued surveillance and monitoring of viral genome diversity are crucial to identify and understand the emergence and spread of novel strains. Through routine genomic surveillance of SARS-CoV-2 cases in Norway, we discovered a SARS-CoV-2 recombination event in a long-term infected immunocompromised COVID-19 (coronavirus disease) patient. A deeper investigation showed several recombination events between two distinct lineages of the virus, namely AY.98.1 and BA.5, that resulted in a single novel recombinant viral strain with a unique genetic signature. Our data is consistent with the presence of several concomitant recombinants in the patient, suggesting that these events occur frequently in vivo. This study underscores the importance of continued tracking of viral diversity and the potential impact of recombination events on the evolution of the SARS-CoV-2 virus.

• Moen, Line Victoria; Vollan, Hilde Synnøve; Bråte, Jon; Hungnes, Olav & Bragstad, Karoline (2022). Molecular Epidemiology of the Norwegian SARS-CoV-2 Delta Lineage AY.63. Viruses. 14(12), p. 1–11. doi: 10.3390/v14122734. Full text in Research Archive
• Bråte, Jon; Ondracka, Andrej & Dudin, Omaya (2022). Time-resolved small RNA transcriptomics of the ichthyosporean Sphaeroforma arctica. Research Square. ISSN 2693-5015. doi: 10.21203/rs.3.rs-2167455/v1. Full text in Research Archive
• Gulbrandsen, Øyvind Sætren; Andresen, Ina Jungersen; Krabberød, Anders Kristian; Bråte, Jon & Shalchian-Tabrizi, Kamran (2021). Phylogenomic analysis restructures the Ulvophyceae. Journal of Phycology. ISSN 0022-3646. 57(4), p. 1223–1233. doi: 10.1111/jpy.13168. Full text in Research Archive Show summary

  Here, we present new transcriptome sequencing data from seven species of Dasycladales (Ulvophyceae) and a phylogenomic analysis of the Chlorophyta with a particular focus on Ulvophyceae. We have focused on a broad selection of green algal groups and carefully selected genes suitable for reconstructing deep eukaryote evolutionary histories. Increasing the taxon sampling of Dasycladales restructures the Ulvophyceae by identifying Dasycladales as closely related to Scotinosphaerales and Oltmannsiellopsidales. Contrary to previous studies, we do not find support for a close relationship between Dasycladales and a group with Cladophorales and Trentepohliales. Instead, the latter group is sister to the remainder of the Ulvophyceae. Furthermore, our analyses show high and consistent statistical support for a sister relationship between Bryopsidales and Chlorophyceae in trees generated with both homogeneous and heterogeneous (heterotachy) evolutionary models. Our study provides a new framework for interpreting the evolutionary history of Ulvophyceae and the evolution of cellular morphologies.

• Andresen, Ina J.; Orr, Russell John Scott; Shalchian-Tabrizi, Kamran & Bråte, Jon (2021). Compartmentalization of mRNAs in the giant, unicellular green alga Acetabularia acetabulum. Algal Research. ISSN 2211-9264. 59. doi: 10.1016/j.algal.2021.102440. Full text in Research Archive Show summary

  Acetabularia acetabulum is a single-celled green alga which has historically been an important model system in cell biology. Here, we attempt to re-introduce A. acetabulum as a model system through the investigation of the subcellular localization of mRNAs. A. acetabulum is a macroscopic single-celled alga with a highly complex cellular morphology. The cell is gigantic, and the single nucleus, which is located at the basal end, is several centimeters away from the umbrella-shaped tip. To better understand the genetic basis of the morphology of this alga, we aimed to characterize the mRNA composition in four different subcellular regions of adult cells. Analyses of the quantitative gene expression data revealed a high degree of differentially distributed gene products. Gene transcripts involved in photosynthesis were mainly accumulated in the apical cap structure, while the basal end carrying the nucleus was enriched for nuclear processes such as DNA replication and transcription. Cytoskeletal components, intracellular transport and protein translation was present throughout this highly elongated cell. An important observation was that some gene transcripts were distributed throughout the cell while others, often functionally related transcripts, were localized in large pools at distinct subcellular regions. This suggests that post-transcriptional regulation and specific cellular localization of gene products may be important mechanisms behind morphogenesis in this gigantic cell.

• Osnes, Magnus Nygård; Alfsnes, Kristian; Bråte, Jon; Llorente, Ignacio Garcia; Riis, Rasmus Kopperud & Instefjord, Kamilla Heddeland [Show all 16 contributors for this article] (2021). The impact of global lineage dynamics, border restrictions, and emergence of the B.1.1.7 lineage on the SARS-CoV-2 epidemic in Norway. Virus Evolution. 7(2), p. 1–7. doi: 10.1093/ve/veab086. Full text in Research Archive Show summary

  Abstract As the COVID-19 pandemic swept through an immunologically naïve human population, academics and public health professionals scrambled to establish methods and platforms for genomic surveillance and data sharing. This offered a rare opportunity to study the ecology and evolution of SARS-CoV-2 over the course of the ongoing pandemic. Here, we use population genetic and phylogenetic methodology to characterize the population dynamics of SARS-CoV-2 and reconstruct patterns of virus introductions and local transmission in Norway against this backdrop. The analyses demonstrated that the epidemic in Norway was largely import driven and characterized by the repeated introduction, establishment, and suppression of new transmission lineages. This pattern changed with the arrival of the B.1.1.7 lineage, which was able to establish a stable presence concomitant with the imposition of severe border restrictions.

• Andresen, Ina Jungersen; Orr, Russell John Scott; Krabberød, Anders Kristian; Shalchian-Tabrizi, Kamran & Bråte, Jon (2021). Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA. Scientific Reports. 11. doi: 10.1038/s41598-021-92092-4. Full text in Research Archive
• Dudin, Omaya; Ondracka, Andrej; Grau-Bové, Xavier; Haraldsen, Arthur Alexander Blørstad; Toyoda, Atsushi & Suga, Hiroshi [Show all 8 contributors for this article] (2019). A unicellular relative of animals generates an epithelium-like cell layer by actomyosin-dependent cellularization. BioRxiv. ISSN 0362-4331. doi: 10.1101/563726. Full text in Research Archive
• Bråte, Jon; Fuss, Janina; Mehrotra, Shruti; Jakobsen, Kjetill Sigurd & Klaveness, Dag (2019). Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000 Research. 8(401), p. 1–12. doi: 10.12688/f1000research.16734.3. Full text in Research Archive Show summary

  Hydrurus foetidus is a freshwater alga belonging to the phylum Heterokonta. It thrives in cold rivers in polar and high alpine regions. It has several morphological traits reminiscent of single-celled eukaryotes, but can also form macroscopic thalli. Despite its ability to produce polyunsaturated fatty acids, its life under cold conditions and its variable morphology, very little is known about its genome and transcriptome. Here, we present an extensive set of next-generation sequencing data, including genomic short reads from Illumina sequencing and long reads from Nanopore sequencing, as well as full length cDNAs from PacBio IsoSeq sequencing and a small RNA dataset (smaller than 200 bp) sequenced with Illumina. We combined this data with, to our knowledge, the first draft genome assembly of a chrysophyte algae. The assembly consists of 5069 contigs to a total assembly size of 171 Mb and a 77% BUSCO completeness. The new data generated here may contribute to a better understanding of the evolution and ecological roles of chrysophyte algae, as well as to resolve the branching patterns within the Heterokonta.

• Dudin, Omaya; Ondracka, Andrej; Grau-Bové, Xavier; Haraldsen, Arthur Alexander Blørstad; Toyoda, Atsushi & Suga, Hiroshi [Show all 8 contributors for this article] (2019). A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLIFE. 8, p. 1–27. doi: 10.7554/eLife.49801. Full text in Research Archive Show summary

  In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly regulated transcriptional activation of genes involved in cell adhesion. Hereby we demonstrate the presence of a self-organized, clonally-generated, polarized layer of cells in a unicellular relative of animals.

• Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Haraldsen, Arthur Alexander Blørstad; Tarver, James E. & Suga, Hiroshi [Show all 11 contributors for this article] (2018). Unicellular origin of the animal microRNA machinery. Current Biology. ISSN 0960-9822. 28(20), p. 3288–3295.e5. doi: 10.1016/j.cub.2018.08.018. Full text in Research Archive Show summary

  The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major changes in the underlying developmental toolkit and regulatory networks. In fact, most of these systems are ancient, established already in the unicellular ancestors of animals [1, 2, 3, 4, 5]. In contrast, the Microprocessor protein machinery, which is essential for microRNA (miRNA) biogenesis in animals, as well as the miRNA genes themselves produced by this Microprocessor, have not been identified outside of the animal kingdom [6]. Hence, the Microprocessor, with the key proteins Pasha and Drosha, is regarded as an animal innovation [7, 8, 9]. Here, we challenge this evolutionary scenario by investigating unicellular sister lineages of animals through genomic and transcriptomic analyses. We identify in Ichthyosporea both Drosha and Pasha (DGCR8 in vertebrates), indicating that the Microprocessor complex evolved long before the last common ancestor of animals, consistent with a pre-metazoan origin of most of the animal developmental gene elements. Through small RNA sequencing, we also discovered expressed bona fide miRNA genes in several species of the ichthyosporeans harboring the Microprocessor. A deep, pre-metazoan origin of the Microprocessor and miRNAs comply with a view that the origin of multicellular animals was not directly linked to the innovation of these key regulatory components.

• Krabberød, Anders Kristian; Orr, Russell; Bråte, Jon; Kristensen, Tom; Bjørklund, Kjell Rasmus & Shalchian-Tabrizi, Kamran (2017). Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria. Molecular Biology and Evolution (MBE). ISSN 0737-4038. doi: 10.1093/molbev/msx075. Full text in Research Archive Show summary

  The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for the diversity of eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these to the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.

• Bråte, Jon; Adamski, Marcin; Neumann, Ralf Stefan; Shalchian-Tabrizi, Kamran & Adamska, Maja (2015). Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum. Proceedings of the Royal Society of London. Biological Sciences. ISSN 0962-8452. 282(1821), p. 1–9. doi: 10.1098/rspb.2015.1746. Full text in Research Archive Show summary

  Long non-coding RNAs (lncRNAs) play important regulatory roles during animal development, and it has been hypothesized that an RNA-based gene regulation was important for the evolution of developmental complexity in animals. However, most studies of lncRNA gene regulation have been performed using model animal species, and very little is known about this type of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq data derived from a comprehensive set of embryogenesis stages in the calcareous sponge Sycon ciliatum and identified hundreds of developmentally expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization of selected lincRNAs revealed dynamic spatial and temporal expression during embryonic development. More than 600 lincRNAs constitute integral parts of differentially expressed gene modules, which also contain known developmental regulatory genes, e.g. transcription factors and signalling molecules. This study provides insights into the non-coding gene repertoire of one of the earliest evolved animal lineages, and suggests that RNA-based gene regulation was likely present in the last common ancestor of animals.

• Leininger, Sven Dirk; Adamski, Marcin; Bergum, Brith; Guder, Corina; Liu, Jing & Laplante, Mary [Show all 12 contributors for this article] (2014). Developmental gene expression provides clues to relationships between sponge and eumetazoan body plans. Nature Communications. 5. doi: 10.1038/ncomms4905. Full text in Research Archive Show summary

  Elucidation of macroevolutionary transitions between diverse animal body plans remains a major challenge in evolutionary biology. We address the sponge-eumetazoan transition by analyzing expression of a broad range of eumetazoan developmental regulatory genes in Sycon ciliatum (Calcispongiae). Here we show that many members of surprisingly numerous Wnt and Tgfβ gene families are expressed higher or uniquely in the adult apical end and the larval posterior end. Genes involved in formation of the eumetazoan endomesoderm, such as β-catenin, Brachyury and Gata, as well as germline markers Vasa and Pl10, are expressed during formation and maintenance of choanoderm, the feeding epithelium of sponges. Similarity in developmental gene expression between sponges and eumetazoans, especially cnidarians, is consistent with Haeckel’s view that body plans of sponges and cnidarians are homologous. These results provide a framework for further studies aimed at deciphering ancestral developmental regulatory networks and their modifications during animal body plans evolution.

• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom & Bjørklund, Kjell Rasmus [Show all 7 contributors for this article] (2012). Radiolaria Associated with Large Diversity of Marine Alveolates. Protist. ISSN 1434-4610. 163(5), p. 767–777. doi: 10.1016/j.protis.2012.04.004. Full text in Research Archive Show summary

  We have isolated cells of unculturable radiolarians from marine coastal waters. Individual cells were subjected to single cell whole genome amplification (SCWGA) and gene-targeted PCR. Using this approach we recover a surprisingly large diversity of sequences related to the enigmatic marine alveolate groups 1 and 2 (MALV I and MALV II) that most likely represent intracellular symbionts or parasites of the radiolarian cells. 18S rDNA phylogeny of the MALV sequences reveals 4 distinct clades of radiolarian associates here named Radiolarian Associated Sequences (RAS) 1-4. One clade of both phaeodarian and radiolarian associates and one clade of only phaeodarian associates are also identified. The MALV sequences cluster according to host type, i.e. sequences from associates identified in radiolarians, fish, copepods, ciliates or dinoflagellates are not intermixed but separated into distinct clades. This implies several independent colonizations of host lineages and links a large diversity of MALV to radiolarian-associated species. This demonstrates that radiolarians may be an important reservoir for MALV, making them a key group for understanding the impact of intracellular symbionts on the marine ecosystem. This study shows that applying SCWGA on unculturable cells is a promising approach to study the vast diversity and interactions of intracellular eukaryote organisms.

• Zhao, Sen; Burki, Fabien; Bråte, Jon; Keeling, Patrick J; Klaveness, Dag & Shalchian-Tabrizi, Kamran (2012). Collodictyon - An Ancient Lineage in the Tree of Eukaryotes. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 29(6), p. 1557–1568. doi: 10.1093/molbev/mss001. Full text in Research Archive
• Krabberød, Anders Kristian; Bråte, Jon; Dolven, Jane Karine Lønne; Ose, Randi Frida; Klaveness, Dag & Kristensen, Tom [Show all 8 contributors for this article] (2011). Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny. PLOS ONE. 6(8). doi: 10.1371/journal.pone.0023526. Full text in Research Archive Show summary

  Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.

• Shalchian-Tabrizi, Kamran; Røberg, Kjetil; Ree, Dan Kristofer; Klaveness, Dag & Bråte, Jon (2011). Marine-Freshwater Colonizations of Haptophytes Inferred from Phylogeny of Environmental 18S rDNA Sequences. Journal of Eukaryotic Microbiology. ISSN 1066-5234. 58(4), p. 315–318. doi: 10.1111/j.1550-7408.2011.00547.x. Full text in Research Archive
• Klaveness, Dag; Bråte, Jon; Patil, Viswanath; Shalchian-Tabrizi, Kamran; Kluge, Ragnhild & Gislerød, Hans Ragnar [Show all 7 contributors for this article] (2011). The 18S and 28S rDNA indentity and phylogeny of the common lotic chrysophyte Hydrurus foetidus. European journal of phycology. ISSN 0967-0262. 46(3), p. 282–291. doi: 10.1080/09670262.2011.598950. Full text in Research Archive
• Logares, Ramiro; Bråte, Jon; Heinrich, F; Shalchian-Tabrizi, Kamran & Bertilsson, Stefan (2010). Infrequent Transitions between Saline and Fresh Waters in One of the Most Abundant Microbial Lineages (SAR11). Molecular Biology and Evolution (MBE). ISSN 0737-4038. 27(2), p. 347–357. doi: 10.1093/molbev/msp239. Full text in Research Archive
• Bråte, Jon; Klaveness, Dag; Rygh, T; Jakobsen, Kjetill Sigurd & Shalchian-Tabrizi, Kamran (2010). Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations. BMC Microbiology. 10(168). doi: 10.1186/1471-2180-10-168. Full text in Research Archive Show summary

  Background Recent surveys of eukaryote 18S rDNA diversity in marine habitats have uncovered worldwide distribution of the heterotrophic eukaryote phylum Telonemia. Here we investigate the diversity and geographic distribution of Telonemia sequences by in-depth sequencing of several new 18S rDNA clone libraries from both marine and freshwater sites by using a Telonemia-specific PCR strategy. Results In contrast to earlier studies that have employed eukaryote-wide PCR design, we identified a large and unknown diversity of phylotypes and the first rigorous evidence for several freshwater species, altogether comprising 91 unique sequences. Phylogenies of these and publicly available sequences showed 20 statistically supported sub-clades as well as several solitary phylotypes with no clear phylogenetic affiliation. Most of these sub-clades were composed of phylotypes from different geographic regions. Conclusions By using specific PCR primers we reveal a much larger diversity of Telonemia from environmental samples than previously uncovered by eukaryote-wide primers. The new data substantially diminish the geographic structuring of clades identified in earlier studies. Nevertheless, since these clades comprise several distinct phylotypes we cannot exclude endemicity at species level. We identified two freshwater clades and a few solitary phylotypes, implying that Telonemia have colonized freshwater habitats and adapted to the different environmental and ecological conditions at independent occasions.

• Bråte, Jon; Logares, Ramiro; Berney, Cedric; Ree, Dan Kristofer; Klaveness, Dag & Jakobsen, Kjetill Sigurd [Show all 7 contributors for this article] (2010). Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. The ISME Journal. ISSN 1751-7362. 4(9), p. 1144–1153. doi: 10.1038/ismej.2010.39. Full text in Research Archive
• Logares, Ramiro; Bråte, Jon; Bertilsson, Stefan; Clasen, Jessica L; Shalchian-Tabrizi, Kamran & Rengefors, Karin (2009). Infrequent marine-freshwater transitions in the microbial world. Trends in Microbiology. ISSN 0966-842X. 17(9), p. 414–422. doi: 10.1016/j.tim.2009.05.010. Full text in Research Archive
• Burki, Fabien; Inagaki, Yuji; Bråte, Jon; Archibald, John M; Keeling, Patrick J & Cavalier-Smith, Thomas [Show all 14 contributors for this article] (2009). Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates. Genome Biology and Evolution (GBE). 1(1), p. 231–238. doi: 10.1093/gbe/evp022. Full text in Research Archive
• Logares, Ramiro; Bråte, Jon; Friederike, Heinrich; Shalchian-Tabrizi, Kamran & Bertilsson, Stefan (2009). Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Molecular Biology and Evolution (MBE). ISSN 0737-4038. doi: 10.1093/molbev/msp239. Full text in Research Archive
• Vishwanath, Patil; Bråte, Jon; Shalchian-Tabrizi, Kamran & Jakobsen, Kjetill Sigurd (2009). Revisiting the Phylogenetic Position of Synchroma grande. Journal of Eukaryotic Microbiology. ISSN 1066-5234. 56(4), p. 394–396. Full text in Research Archive
• Shalchian-Tabrizi, Kamran; Bråte, Jon; Logares, R; Klaveness, Dag; Berney, Cedrik & Jakobsen, Kjetill Sigurd (2008). Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environmental Microbiology. ISSN 1462-2912. 10(10), p. 2635–2644. doi: 10.1111/j.1462-2920.2008.01685.x. Full text in Research Archive

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• Ondracka, Andrej; Dudin, Omaya & Bråte, Jon (2023). Time-resolved small RNA transcriptomics of the ichthyosporean Sphaeroforma arctica. F1000 Research. doi: 10.12688/f1000research.133935.1. Full text in Research Archive Show summary

  Ichthyosporea, a clade of holozoans, represent a clade closely related to animals, and thus hold a key phylogenetic position for understanding the origin of animals. We have previously discovered that an ichthyosporean, Sphaeroforma arctica, contains microRNAs (miRNAs) as well as the miRNA processing machinery. This was the first discovery of miRNAs among the closest single-celled relatives of animals and raised intriguing questions about the roles of regulatory small RNAs in cell development and differentiation in unicellular eukaryotes. Like many ichthyosporeans, S. arctica also undergoes a transient multicellular developmental life cycle. As miRNAs are, among other roles, key regulators of gene expression during development in animals, we wanted to investigate the dynamics of miRNAs during the developmental cycle in S. arctica. Here we have therefore collected a comprehensive time-resolved small RNA transcriptome linked to specific life stages with a substantially higher sequencing depth than before, which can enable further discovery of functionally relevant small RNAs. The data consists of Illumina-sequenced small RNA libraries from two independent biological replicates of the entire life cycle of S. arctica with high temporal resolution. The dataset is directly linked and comes from the same samples as a previously published mRNA-seq dataset, thus enabling direct cross-functional analyses

• Bråte, Jon (2022). SARS-CoV-2 sequencing at the Norwegian Institute of Public Health. Full text in Research Archive
• Bråte, Jon (2022). Import og evolusjon av SARS-CoV-2 i Norge. Full text in Research Archive
• Spilde, Ingrid; Bråte, Jon & Shalchian-Tabrizi, Kamran (2019). Knøttlite mysterium: Hva er egentlig forskjellen på deg og en encellet skapning? [Journal]. Forskning.no. Full text in Research Archive
• Bråte, Jon (2019). Evolution and Function of the ichthyosporean microRNA system. Full text in Research Archive
• Bråte, Jon (2019). Dyrenes opprinnelse. Full text in Research Archive
• Bråte, Jon (2019). Evolution and development in single-celled eukaryotes. Full text in Research Archive
• Bråte, Jon (2017). Single-cell transcriptomics of Sphaeroforma arctica. Full text in Research Archive
• Bråte, Jon & Vogt, Yngve (2017). Leter etter skillet mellom encellete og flercellete dyr. [Journal]. Apollon. Full text in Research Archive
• Bråte, Jon (2017). Studying protist evolution using single-cell transcriptomics. Full text in Research Archive
• Røsæg, Line Lieblein; Evenstad, Andreas; Andresen, Ina Jungersen; Bråte, Jon & Shalchian-Tabrizi, Kamran (2016). Postembryonic development of Mnemiopsis leidyi inferred from gene expression data. Full text in Research Archive
• Evenstad, Andreas; Røsæg, Line Lieblein; Andresen, Ina Jungersen; Shalchian-Tabrizi, Kamran & Bråte, Jon (2016). Evolution of non-coding RNAs in ctenophores. Full text in Research Archive
• Røsjø, Bjarne & Bråte, Jon (2016). På spor av det første flercellede dyret. [Internet]. Titan.uio.no. Full text in Research Archive
• Melteig, Hanna Elina & Bråte, Jon (2016). Omvendt kreftjakt. [Journal]. www.forskning.no. Full text in Research Archive
• Haraldsen, Arthur Alexander Blørstad; Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Grini, Paul Eivind & Shalchian-Tabrizi, Kamran (2016). Pre-metazoan origin of animal microRNAs. Full text in Research Archive
• Bråte, Jon (2015). Genomets mørke materie. Full text in Research Archive
• Bråte, Jon (2015). Genomets mørke materie. Full text in Research Archive
• Bråte, Jon (2015). Genomets mørke materie: nye roller til ikke-kodende RNA. Full text in Research Archive
• Bråte, Jon (2014). Single Cell Protistology - Work in Progress. Full text in Research Archive
• Bråte, Jon (2014). Non-coding RNA and the Origin of Animals. Full text in Research Archive
• Bråte, Jon (2014). Genomets mørke materie - nye roller til ikke-kodende RNA. Full text in Research Archive
• Bråte, Jon (2013). Betydningen av små RNA fragmenter for evolusjon, økologi og epigenetikk. Full text in Research Archive
• Bråte, Jon (2013). "Søppel-gen" gjorde folk av oss? Full text in Research Archive
• Bråte, Jon (2013). Søppel-DNA: Hva er det og (hvorfor) trenger vi bry oss? Full text in Research Archive
• Bråte, Jon (2013). Long non-coding RNAs in the sponge Sycon ciliatum. Full text in Research Archive Show summary

  We have investigated the repertoire of long non-coding RNA molecules (lncRNAs) in the sponge Sycon ciliatum. Long non-coding RNA molecules have been shown to be highly important for gene regulation in several model organisms. In particular they are involved in epigenetic regulation, cell differentiation and developmental control. lncRNAs have mostly been studied in model organisms, and little is known about the extent of lncRNAs in basal metazoan lineages. As the sponges are among the earliest animal lineages to evolve, it is important to know which gene regulatory mechanisms are present in these species. In my talk I will present preliminary results from an RNA sequencing project of different developmental stages of S. cililatum. We have identified a set of candidate non-protein coding transcripts, and confirmed a tissue specific expression in different developmental stages for a few of these genes by in situ hybridization. This points to a role for these lncRNAs in sponge development.

• Bråte, Jon (2011). Encellede eukaryoter - hvordan studere dem genetisk? Full text in Research Archive
• Bråte, Jon (2011). 18S+28S phylogeny divides Radiolaria into Polycystina and Spasmaria and supports the Retaria hypothesis. Full text in Research Archive
• Bråte, Jon (2011). Radiolaria revealed as a reservoir of Marine alveolates. Full text in Research Archive
• Bråte, Jon (2010). Lake Finsevatn sediment diversity investigated by pyrosequencing. Full text in Research Archive
• Lindstrøm, Eli-Anne; Bråte, Jon & Klaveness, Dag (2010). Hydrurus foetidus - a common and important cold-stenotherm (psychrophilic) primary producer. Full text in Research Archive
• Bråte, Jon; Krabberød, Anders Kristian; Dolven, Jane Karine Lønne; Ose, Randi Frida; Kristensen, Tom & Bjørklund, Kjell Rasmus [Show all 7 contributors for this article] (2010). Diversity of unculturable Radiolaria and their symbionts revealed by 18S rDNA phylogeny. Full text in Research Archive
• Bråte, Jon (2008). Barriers to Dispersal: Few Marine - Freshwater Colonizations Revealed by Environmental Sequencing. Full text in Research Archive
• Patil, Vishwanath; Bråte, Jon; Klaveness, D.; Kluge, Ragnhild; Shalchian-Tabrizi, Kamaran & Gislerød, Hans Ragnar [Show all 7 contributors for this article] (2008). Molecular phylogeny of Hydrurus, a fresh water chrysophyte rich in lipids. Full text in Research Archive

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