Ave Tooming-Klunderud

• Dussex, Nicolas; Tørresen, Ole Kristian; van der Valk, Tom; Le Moullec, Mathilde; Veiberg, Vebjørn & Tooming-Klunderud, Ave [Vis alle 17 forfattere av denne artikkelen] (2023). Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer. iScience. ISSN 2589-0042. 26(10). doi: 10.1016/j.isci.2023.107811. Fulltekst i vitenarkiv Vis sammendrag

  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.

• Hepner, Sabrina; Kuleshov, Konstantin; Tooming-Klunderud, Ave; Alig, Nikolas; Gofton, Alexander & Casjens, Sherwood [Vis alle 15 forfattere av denne artikkelen] (2023). A high fidelity approach to assembling the complex Borrelia genome. BMC Genomics. ISSN 1471-2164. 24(1), s. 1–19. doi: 10.1186/s12864-023-09500-4. Fulltekst i vitenarkiv
• Potolitsyna, Evdokiia; Hazell Pickering, Sarah Jai; 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. ISSN 1471-2164. 23(1). doi: 10.1186/s12864-022-08887-w. Fulltekst i vitenarkiv
• Stenmark, Bianca; Harrison, Odile B.; Eriksson, Lorraine; Anton, Brian P.; Fomenkov, Alexey & Roberts, Richard J. [Vis alle 12 forfattere av denne artikkelen] (2020). Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease. Scientific Reports. ISSN 2045-2322. 10(1), s. 1–11. doi: 10.1038/s41598-020-59509-y. Fulltekst i vitenarkiv
• Hoff, Siv Nam Khang; Baalsrud, Helle Tessand; Tooming-Klunderud, Ave; Skage, Morten; Richmond, Todd & Obernosterer, Gregor [Vis alle 10 forfattere av denne artikkelen] (2018). Long‐read sequence capture of the haemoglobin gene clusters across codfish species. Molecular Ecology Resources. ISSN 1755-098X. 19(1), s. 245–259. doi: 10.1111/1755-0998.12955.
• 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), s. 1370–1385. doi: 10.1111/nph.14776.
• Lie, Kai Kristoffer; Tørresen, Ole K.; Solbakken, Monica Hongrø; Rønnestad, Ivar; Tooming-Klunderud, Ave & Nederbragt, Alexander Johan [Vis alle 8 forfattere av denne artikkelen] (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. ISSN 1471-2164. 19(186), s. 1–17. doi: 10.1186/s12864-018-4570-8. Fulltekst i vitenarkiv
• Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Reinar, William Brynildsen; Grove, Harald & Miller, Jason R. [Vis alle 16 forfattere av denne artikkelen] (2017). An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics. ISSN 1471-2164. 18, s. 1–23. doi: 10.1186/s12864-016-3448-x. Fulltekst i vitenarkiv
• Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter & Nome, Torfinn [Vis alle 45 forfattere av denne artikkelen] (2016). The Atlantic salmon genome provides insights into rediploidization. Nature. ISSN 0028-0836. 533(7602), s. 200–205. doi: 10.1038/nature17164. Fulltekst i vitenarkiv
• Frank, Jeremy A.; Pan, Yao; Tooming-Klunderud, Ave; Eijsink, Vincent; McHardy, Alice C & Nederbragt, Alexander Johan [Vis alle 7 forfattere av denne artikkelen] (2016). Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports. ISSN 2045-2322. 6. doi: 10.1038/srep25373. Fulltekst i vitenarkiv
• Stokke, Runar; Dahle, Håkon; Roalkvam, Irene; Wissuwa, Juliane; Daae, Frida Lise & Tooming-Klunderud, Ave [Vis alle 9 forfattere av denne artikkelen] (2015). Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environmental Microbiology. ISSN 1462-2912. 17(10), s. 4063–4077. doi: 10.1111/1462-2920.12970.
• 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. ISSN 1932-6203. 10(5). doi: 10.1371/journal.pone.0127462. Fulltekst i vitenarkiv
• 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. ISSN 1932-6203. 9(8). doi: 10.1371/journal.pone.0106510. Fulltekst i vitenarkiv
• de Been, Mark; Lanza, Val F.; de Toro, Maria; Scharringa, Jelle; Dohmen, Wietske & Du, Yu [Vis alle 16 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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), s. 17–27. doi: 10.1016/j.margen.2013.12.002.
• Sogge, Hanne; Rohrlack, Thomas; Rounge, Trine Ballestad; Sønstebø, Jørn Henrik; Tooming-Klunderud, Ave & Kristensen, Tom [Vis alle 7 forfattere av denne artikkelen] (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), s. 508–515. doi: 10.1128/AEM.02417-12. Fulltekst i vitenarkiv Vis sammendrag

  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.

• Tooming-Klunderud, Ave ; Sogge, Hanne; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Lagesen, Karin & Glöckner, Gernot [Vis alle 9 forfattere av denne artikkelen] (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), s. 6803–6812. doi: 10.1128/AEM.01455-13. Fulltekst i vitenarkiv
• Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik [Vis alle 42 forfattere av denne artikkelen] (2011). The genome sequence of Atlantic cod reveals a unique immune system. Nature. ISSN 0028-0836. 477(7363), s. 207–210. doi: 10.1038/nature10342. Fulltekst i vitenarkiv
• Andersen, Øivind; De Rosa, Maria Cristina; 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. ISSN 1471-2156. 12(51). doi: 10.1186/1471-2156-12-51.
• Gabrielsen, Tove M; Minge, Marianne Aastebøl; Espelund, Mari; Tooming-Klunderud, Ave ; Patil, Viswanath & Nederbragt, Alexander Johan [Vis alle 11 forfattere av denne artikkelen] (2011). Genome Evolution of a Tertiary Dinoflagellate Plastid. PLOS ONE. ISSN 1932-6203. 6(4). doi: 10.1371/journal.pone.0019132.
• Andersen, Øivind; Dahle, Stine Veronica Wiborg; van Nes, Solveig; Bardal, Tora; Tooming-Klunderud, Ave & Kjørsvik, Elin [Vis alle 7 forfattere av denne artikkelen] (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), s. 93–101. doi: 10.1016/j.cbpb.2009.05.009.
• Tooming-Klunderud, Ave ; Mikalsen, Bjørg; Kristensen, Tom & Jakobsen, Kjetill Sigurd (2008). The mosaic structure of the mcyABC operon in Microcystis. Microbiology (Reading). ISSN 1350-0872. 154, s. 1886–1899. doi: 10.1099/mic.0.2007/015875-0.
• Tooming-Klunderud, Ave ; Fewer, DP; Rohrlack, Thomas; Jokela, J; Rouhiainen, L & Sivonen, K [Vis alle 8 forfattere av denne artikkelen] (2008). Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera. BMC Evolutionary Biology. ISSN 1471-2148. 8. doi: 10.1186/1471-2148-8-256.
• Fewer, DP; Tooming-Klunderud, Ave ; Jokela, J; Wahsten, M; Rouhiainen, L & Kristensen, Tom [Vis alle 9 forfattere av denne artikkelen] (2008). Natural occurrence of microcystin synthetase deletion mutants capable of producing microcystins in strains of the genus Anabaena (Cyanobacteria). Microbiology (Reading). ISSN 1350-0872. 154, s. 1007–1014. doi: 10.1099/mic.0.2007/016097-0.
• Østbye, Tone-Kari K; Andersen, Øivind; Frang, Ola T; Tooming-Klunderud, Ave; Jakobsen, Kjetill S. & Yafe, Anat [Vis alle 8 forfattere av denne artikkelen] (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), s. 159–169.
• 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), s. 1382–1393. doi: 10.1099/mic.0.2006/001123-0.
• Østbye, Tone-Kari K; Wetten, Ola F.; Tooming-Klunderud, Ave ; Jakobsen, Kjetill Sigurd; Yafe, Anat & Etzioni, Shulamit [Vis alle 8 forfattere av denne artikkelen] (2007). Myostatin (MSTN) gene duplications in Atlantic salmon (Salmo salar): Evidence for different selective pressure on teleost MSTN-1 and -2. Gene. ISSN 0378-1119. 403, s. 159–169. doi: 10.1016/j.gene.2007.08.008.
• 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, s. 7322–7330. doi: 10.1128/AEM.01475-07.

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• Tørresen, Ole Kristian; Jentoft, Sissel; Star, Bastiaan; Sandve, Geir Kjetil F.; Skage, Morten & Hansen, Marianne Helén Selander [Vis alle 9 forfattere av denne artikkelen] (2014). A new, high quality reference genome assembly for Atlantic cod.
• Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Skage, Morten; Tooming-Klunderud, Ave ; Hansen, Marianne Helén Selander & Jentoft, Sissel [Vis alle 9 forfattere av denne artikkelen] (2012). The long jump: Long distance mate pairs and long PacBio reads for the Salmon Genome Project.
• Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik [Vis alle 18 forfattere av denne artikkelen] (2011). The genome of Atlantic cod reveals a unique immune system.
• Tooming-Klunderud, Ave (2010). From next generation reads to genomes: experiences gained from different genome projects.
• Tooming-Klunderud, Ave (2010). HIgh throughput sequencing at the Norwegian Sequencing Centre: possibilities and procedures.
• Tooming-Klunderud, Ave (2010). 454 sequencing at the Norwegian Sequencing Centre: possibilities, procedures and projects.
• Tooming-Klunderud, Ave (2010). Planktothrix genome project - from 454 reads to interesting results.
• Dahle, Håkon; Roalkvam, Irene; Jørgensen, Steffen Leth; Hoem, Solveig; Mitra, Suparna & Huson, Daniel [Vis alle 10 forfattere av denne artikkelen] (2010). Microbial community structure of biomats and chimney walls of the Loki’s Castle hydrothermal field at 73°N.
• Nederbragt, Alexander Johan & Tooming-Klunderud, Ave (2010). From next generation reads to genomes: experiences gained from different genome projects.
• Grimholt, Unni; Nederbragt, Alexander Johan; Rounge, Trine Ballestad; Malmstrøm, Martin; Star, Bastiaan & Tooming-Klunderud, Ave [Vis alle 12 forfattere av denne artikkelen] (2009). The cod genome project.
• Grimholt, Unni; Malmstrøm, Martin; Nederbragt, Alexander Johan; Rounge, Trine Ballestad; Jentoft, Sissel & Tooming-Klunderud, Ave [Vis alle 10 forfattere av denne artikkelen] (2009). The lack of cod MHC class II.
• Tooming-Klunderud, Ave (2009). Cod genome project.
• Tooming-Klunderud, Ave (2009). Library preparation for pyrosequencing.
• 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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