Jon Bråte

• 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.
• 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. ISSN 1999-4915. 14(12), p. 1–11. doi: 10.3390/v14122734. Full text in Research Archive
• Osnes, Magnus Nygård; Alfsnes, Kristian; Bråte, Jon; Garcia Llorente, Ignacio; 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. ISSN 2057-1577. 7(2), p. 1–7. doi: 10.1093/ve/veab086. Full text in Research Archive
• 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
• 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. ISSN 2045-2322. 11. doi: 10.1038/s41598-021-92092-4. 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
• 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. ISSN 2050-084X. 8, p. 1–27. doi: 10.7554/eLife.49801. 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 2692-8205. doi: 10.1101/563726.
• 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. ISSN 2046-1402. 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.

• 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
• 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. 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. ISSN 2041-1723. 5. doi: 10.1038/ncomms4905. 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] (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. 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.
• 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.
• 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. ISSN 1932-6203. 6(8). doi: 10.1371/journal.pone.0023526. 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.
• 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. ISSN 1471-2180. 10(168). doi: 10.1186/1471-2180-10-168.
• 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.
• 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.
• 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.
• 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.
• 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). ISSN 1759-6653. 1(1), p. 231–238. doi: 10.1093/gbe/evp022.
• 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.
• 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.

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• Ondracka, Andrej; Dudin, Omaya & Bråte, Jon (2023). Time-resolved small RNA transcriptomics of the ichthyosporean Sphaeroforma arctica. F1000 Research. ISSN 2046-1402. doi: 10.12688/f1000research.133935.1. 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.
• Bråte, Jon (2022). Import og evolusjon av SARS-CoV-2 i Norge.
• Bråte, Jon (2019). Dyrenes opprinnelse.
• Bråte, Jon (2019). Evolution and development in single-celled eukaryotes.
• Bråte, Jon (2019). Evolution and Function of the ichthyosporean microRNA system.
• Spilde, Ingrid; Bråte, Jon & Shalchian-Tabrizi, Kamran (2019). Knøttlite mysterium: Hva er egentlig forskjellen på deg og en encellet skapning? [Business/trade/industry journal]. Forskning.no.
• Bråte, Jon & Vogt, Yngve (2017). Leter etter skillet mellom encellete og flercellete dyr. [Business/trade/industry journal]. Apollon.
• Bråte, Jon (2017). Studying protist evolution using single-cell transcriptomics.
• Bråte, Jon (2017). Single-cell transcriptomics of Sphaeroforma arctica.
• Evenstad, Andreas; Lieblein Røsæg, Line; Andresen, Ina Jungersen; Shalchian-Tabrizi, Kamran & Bråte, Jon (2016). Evolution of non-coding RNAs in ctenophores.
• Lieblein Røsæg, Line; Evenstad, Andreas; Andresen, Ina Jungersen; Bråte, Jon & Shalchian-Tabrizi, Kamran (2016). Postembryonic development of Mnemiopsis leidyi inferred from gene expression data.
• Haraldsen, Arthur Alexander Blørstad; Bråte, Jon; Neumann, Ralf Stefan; Fromm, Bastian; Grini, Paul Eivind & Shalchian-Tabrizi, Kamran (2016). Pre-metazoan origin of animal microRNAs.
• Røsjø, Bjarne & Bråte, Jon (2016). På spor av det første flercellede dyret. [Internet]. Titan.uio.no.
• Melteig, Hanna Elina & Bråte, Jon (2016). Omvendt kreftjakt. [Business/trade/industry journal]. www.forskning.no.
• Bråte, Jon (2015). Genomets mørke materie.
• Bråte, Jon (2015). Genomets mørke materie.
• Bråte, Jon (2015). Genomets mørke materie: nye roller til ikke-kodende RNA.
• Bråte, Jon (2014). Single Cell Protistology - Work in Progress.
• Bråte, Jon (2014). Non-coding RNA and the Origin of Animals.
• Bråte, Jon (2014). Genomets mørke materie - nye roller til ikke-kodende RNA.
• Bråte, Jon (2013). Long non-coding RNAs in the sponge Sycon ciliatum. 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 (2013). "Søppel-gen" gjorde folk av oss? Aftenposten (morgenutg. : trykt utg.). ISSN 0804-3116.
• Bråte, Jon (2013). Søppel-DNA: Hva er det og (hvorfor) trenger vi bry oss?
• Bråte, Jon (2013). Betydningen av små RNA fragmenter for evolusjon, økologi og epigenetikk.
• Bråte, Jon (2011). 18S+28S phylogeny divides Radiolaria into Polycystina and Spasmaria and supports the Retaria hypothesis.
• Bråte, Jon (2011). Radiolaria revealed as a reservoir of Marine alveolates.
• Bråte, Jon (2011). Encellede eukaryoter - hvordan studere dem genetisk?
• Lindstrøm, Eli-Anne; Bråte, Jon & Klaveness, Dag (2010). Hydrurus foetidus - a common and important cold-stenotherm (psychrophilic) primary producer.
• Bråte, Jon (2010). Lake Finsevatn sediment diversity investigated by pyrosequencing.
• 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.
• Dolven, Jane Karine Lønne; Bjørklund, Kjell Rasmus; Bråte, Jon; Krabberød, Anders Kristian; Klaveness, Dag & Shalchian-Tabrizi, Kamran (2009). Polycystina. Polycystine radiolarians.
• 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.
• Bråte, Jon (2008). Barriers to Dispersal: Few Marine - Freshwater Colonizations Revealed by Environmental Sequencing.

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