Russell Orr

• Nilsson, Pernille; Solbakken, Monica Hongrø; Schmid, Boris Valentijn; Orr, Russell; Lv, Ruichen; Cui, Yujun; Song, Yajun; Zhang, Yujiang; Baalsrud, Helle Tessand; Tørresen, Ole K.; Stenseth, Nils Christian; Yang, Ruifu; Jakobsen, Kjetill Sigurd; Easterday, William Ryan & Jentoft, Sissel (2020). The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biology and Evolution.  ISSN 1759-6653. . doi: https://doi.org/10.1093/gbe/evaa008 Full text in Research Archive.
• Orr, Russell; Haugen, Marianne Nilsen; Berning, Björn; Bock, Phil; Cumming, Robyn L.; Florence, Wayne; Hirose, Masato; Di Martino, Emanuela; Ramsfjell, Mali Hamre; Sannum, Maja Margret; Smith, Abigail M.; Vieira, Leandro; Waeschenbach, Andrea & Liow, Lee Hsiang (2019). A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae. BMC Evolutionary Biology.  ISSN 1471-2148.  19(235) . doi: 10.1186/s12862-019-1563-4 Full text in Research Archive.
• Orr, Russell; Waeschenbach, Andrea; Enevoldsen, Emily; Boeve, Jeroen Pieter; Haugen, Marianne Nilsen; Voje, Kjetil L.; Porter, Joanne; Zagorsek, Kamil; Smith, Abigail M.; Gordon, Dennis & Liow, Lee Hsiang (2018). Bryozoan genera Fenestrulina and Microporella no longer confamilial; multi-gene phylogeny supports separation. Zoological Journal of the Linnean Society.  ISSN 0024-4082.  s 1- 10 . doi: 10.1093/zoolinnean/zly055 Full text in Research Archive.
• Orr, Russell; Zhao, Sen; Klaveness, Dag; Yabuki, Akinori; Ikeda, Keiji; Makoto, Watanabe M. & Shalchian-Tabrizi, Kamran (2018). Enigmatic diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution. BMC Evolutionary Biology.  ISSN 1471-2148.  18(115), s 1- 13 . doi: 10.1186/s12862-018-1224-z 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.  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.

• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Draft genome sequences of two unclassified bacteria, Hydrogenophaga sp. strains IBVHS1 and IBVHS2, isolated from environmental samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(34) . doi: 10.1128/genomeA.00884-17
• Orr, Russell; Shalchian-Tabrizi, Kamran; Van de Peer, Yves & Rombauts, S (2017). Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(34) . doi: 10.1128/genomeA.00894-17
• Orr, Russell; Shalchian-Tabrizi, Kamran; Van de Peer, Yves & Rombauts, S (2017). Draft genome Sequences of two Unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287. . doi: 10.1128/genomeA.00787-17
• Murray, Shauna A.; Diwan, Rutuja; Orr, Russell; Kohli, Gurjeet S. & John, Uwe (2015). Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates. Molecular Phylogenetics and Evolution.  ISSN 1055-7903.  92, s 165- 180 . doi: 10.1016/j.ympev.2015.06.017
• Stø, Ida Myhrer; Orr, Russell; Fooyontphanich, Kim; Jin, Xu; Knutsen, Jonfinn Mordekai Blix; Fischer, Urs; Tranbarger, Timothy J.; Nordal, Inger & Aalen, Reidunn B. (2015). Conservation of the abscission signaling peptide IDA during Angiosperm evolution: Withstanding genome duplications and gain and loss of the receptors HAE/HSL2. Frontiers in Plant Science.  ISSN 1664-462X.  6(OCTOBER) . doi: 10.3389/fpls.2015.00931
• Murray, Shauna A.; Hoppenrath, Mona; Orr, Russell; Bolch, Christopher; John, Uwe; Diwan, Rutuja; Yauwenas, Rouna; Harwood, Tim; de Salas, Miguel; Neilan, Brett A. & Hallegraeff, Gustaaf (2014). Alexandrium diversaporum sp. nov., a new non-saxitoxin producing species: Phylogeny, morphology and sxtA genes. Harmful Algae.  ISSN 1568-9883.  31, s 54- 65 . doi: 10.1016/j.hal.2013.09.005
• Stensrud, Øyvind; Orr, Russell; Reier-Røberg, Kjetil; Schumacher, Trond & Høiland, Klaus (2014). Phylogenetic relationships in Cortinarius with focus on North European species. Karstenia.  ISSN 0453-3402.  54(2), s 57- 71 . doi: 10.29203/ka.2014.464 Show summary

  Cortinarius is an ectomycorrhizal Agaricales genus with high diversity of which rDNA sequences of 86 species together with four outgroup taxa were investigated phylogenetically by aid of Maximum Likelihood and Bayesian analyses. The Cortinarius data set represents 81 taxa from the Northern Hemisphere showing the main variation spectrum among the species. In addition, five species from the Southern Hemisphere are included. The phylogenetic tree of Cortinarius gives statistical support to twelve monophyletic groups in the upper level. They are discussed in context of morphology, chemistry (secondary compounds), and ecology. The phylogenetic tree lacks, however, satisfactory support for its backbone. Several species could not be included in any group, especially those forming the basal framework of the tree. Of special interest is a “superclade” comprising eight of our monophyletic clades and two singletons. Here we find the majority of species with soluble pigments of octaketide origin, all species with compounds of nonaketide origin, the majority of species with hygrophaneous pileus, few species with viscid pileus, and no species with bulbous stipe base. Moreover, all species except one have duplex pileus cuticle. The morphological traits are not indicative for any clade, although some are more frequent in some clades than others. During the evolution they have been gained and lost several times. The chemical characteristics are – to a certain degree – more indicative for the clades. The evolution and ecological role of these compounds are discussed. Concerning the North European species, there are ecological differences between the clades, especially between clades specializing to rich or calcareous forests and clades specializing to poor forests or arctic-alpine environments.

• Orr, Russell; Stüken, Anke; Murray, Shauna A. & Jakobsen, Kjetill Sigurd (2013). Evolution and Distribution of Saxitoxin Biosynthesis in Dinoflagellates. Marine Drugs.  ISSN 1660-3397.  11(8), s 2814- 2828 . doi: 10.3390/md11082814
• Orr, Russell; Stüken, Anke; Murray, Shauna A. & Jakobsen, Kjetill Sigurd (2013). Evolutionary Acquisition and Loss of Saxitoxin Biosynthesis in Dinoflagellates: the Second "Core" Gene, sxtG. Applied and Environmental Microbiology.  ISSN 0099-2240.  79(7), s 2128- 2136 . doi: 10.1128/AEM.03279-12 Full text in Research Archive.
• Dittami, Simon; Riisberg, Ingvild; John, Uwe; Orr, Russell; Jakobsen, Kjetill Sigurd & Edvardsen, Bente (2012). Analysis of Expressed Sequence Tags from the Marine Microalga Pseudochattonella farcimen (Dictyochophyceae). Protist.  ISSN 1434-4610.  163(1), s 143- 161 . doi: 10.1016/j.protis.2011.07.004
• Murray, Shauna A.; Wiese, Maria; Neilan, Brett A.; Orr, Russell; de Salas, Miguel; Brett, Steve & Hallegraeff, Gustaaf (2012). A reinvestigation of saxitoxin production and sxtA in the 'non-toxic' Alexandrium tamarense Group V clade. Harmful Algae.  ISSN 1568-9883.  18, s 96- 104 . doi: 10.1016/j.hal.2012.05.001
• Orr, Russell; Murray, Shauna A.; Stüken, Anke; Rhodes, Lesley & Jakobsen, Kjetill Sigurd (2012). When Naked Became Armored: An Eight-Gene Phylogeny Reveals Monophyletic Origin of Theca in Dinoflagellates. PLOS ONE.  ISSN 1932-6203.  7(11) . doi: 10.1371/journal.pone.0050004 Full text in Research Archive.
• Orr, Russell; Stüken, Anke; Rundberget, Thomas; Eikrem, Wenche & Jakobsen, Kjetill Sigurd (2011). Improved phylogenetic resolution of toxic and non-toxic Alexandrium strains using a concatenated rDNA approach. Harmful Algae.  ISSN 1568-9883.  10(6), s 676- 688 . doi: 10.1016/j.hal.2011.05.003
• Stüken, Anke Corinna; Orr, Russell; Kellmann, Ralf; Murray, Shauna A.; Neilan, Brett A. & Jakobsen, Kjetill Sigurd (2011). Discovery of Nuclear-Encoded Genes for the Neurotoxin Saxitoxin in Dinoflagellates. PLOS ONE.  ISSN 1932-6203.  6(5) . doi: 10.1371/journal.pone.0020096
• Kellmann, Ralf; Stüken, Anke; Orr, Russell J. S.; Svendsen, Helene M. & Jakobsen, Kjetill S. (2010). Biosynthesis and Molecular Genetics of Polyketides in Marine Dinoflagellates. Marine Drugs.  ISSN 1660-3397.  8(4), s 1011- 1048 . doi: 10.3390/md8041011
• Riisberg, Ingvild; Orr, Russell; Kluge, Ragnhild; Shalchian-Tabrizi, Kamran; Bowers, HA; Vishwanath, Patil; Edvardsen, Bente & Jakobsen, Kjetill Sigurd (2009). Seven Gene Phylogeny of Heterokonts. Protist.  ISSN 1434-4610.  160(2), s 191- 204 . doi: 10.1016/j.protis.2008.11.004
• Kumar, Surendra; Skjæveland, Åsmund; Orr, Russell; Enger, Pål; Ruden, Torgeir Andersen; Mevik, Bjørn-Helge; Burki, Fabien; Botnen, Andreas Valeur & Shalchian-Tabrizi, Kamran (2009). AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics.  ISSN 1471-2105.  10 . doi: 10.1186/1471-2105-10-357 Full text in Research Archive. Show summary

  Background: Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. Results: Here we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal (www.bioportal.uio.no), University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. Conclusions: The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

• Minge, Marianne Aastebøl; Silberman, Jeffrey; Orr, Russell; Cavalier-Smith, Thomas; Shalchian-Tabrizi, Kamran; Burki, Fabien; Skjæveland, Åsmund & Jakobsen, Kjetill Sigurd (2009). Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proceedings of the Royal Society of London. Biological Sciences.  ISSN 0962-8452.  276(1657), s 597- 604 . doi: 10.1098/rspb.2008.1358
• Shalchian-Tabrizi, Kamran; Minge, Marianne Aastebøl; Espelund, Mari; Orr, Russell; Ruden, Torgeir Andersen; Jakobsen, Kjetill Sigurd & Cavalier-Smith, Thomas (2008). Multigene Phylogeny of Choanozoa and the Origin of Animals. PLOS ONE.  ISSN 1932-6203.  3(5)

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• Orr, Russell (2017). In Silico Prediction of Ligand-Binding Sites of Plant Receptor Kinases Using Conservation Mapping. Plant Receptor Kinases: Methods and Protocols. Humana Press.  ISBN 978-1-4939-7063-6.  196 s.

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• Orr, Russell (2017). Deep Genome Initiative.
• Orr, Russell (2017). Genome Dynamics in early eukaryote evolution an update!.
• Orr, Russell (2017). Genome dynamics in early eukaryote evolution, progress rapport!.
• Orr, Russell; Rombauts, S; Van De Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Erratum to "Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples" [Genome Announc., 2017, 5 (34):e00894-17.] Doi: 10.1128/genomeA.00894-17.. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(41) . doi: 10.1128/genomeA.01175-17
• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Draft genome sequences of two unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, isolated from environmental samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(33), s 1- 3 . doi: 10.1128/genomeA.00787-17
• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Draft genome sequences of two unclassified bacteria, Sphingomonas sp. strains IBVSS1 and IBVSS2, isolated from environmental samples. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5:e00894-17(34), s 1- 3 . doi: 10.1128/genomeA.00894-17
• Orr, Russell; Rombauts, Stephane; Van de Peer, Yves & Shalchian-Tabrizi, Kamran (2017). Erratum: "Draft genome sequences of two unclassified Chitinophagaceae bacteria, IBVUCB1 and IBVUCB2, isolated from environmental samples" [Genome Announc, 5, 33, (2017), (e00787-17)] DOI:10.1128/genomeA.00787-17. Microbiology Resource Announcements (MRA).  ISSN 2169-8287.  5(41:e01152-17), s 1- 1 . doi: 10.1128/genomeA.01152-17
• Enevoldsen, Emily; Boeve, Jeroen; Orr, Russell; Waeschenbach, Andrea & Liow, Lee Hsiang (2016). Advancing bryozoan phylogenetics: mitochondrial and nuclear genes.
• Orr, Russell (2016). Genome dynamics in early eukaryotic evolution. Importance of enigmatic lineages.
• Orr, Russell (2016). Genome dynamics in early eukaryotic evolution. Importance of enigmatic lineages.
• Orr, Russell (2016). PacBio sequencing reveals the diversity and ecology of a deeply diverging eukaryote lineage..
• Orr, Russell; Zhao, Sen; Yabuki, Akinori & Shalchian-Tabrizi, Kamran (2016). PacBio sequencing reveals the diversity and ecology of a deeply diverging eukaryote lineage.
• Orr, Russell (2015). Genome dynamics in early eukaryotic evolution. Importance of enigmatic lineages.
• Orr, Russell (2015). Genome dynamics in early eukaryotic evolution. Importance of enigmatic lineages.
• Enevoldsen, Emily; Liow, Lee Hsiang; Voje, Kjetil L.; Orr, Russell; Shalchian-Tabrizi, Kamran & Krabberød, Anders Kristian (2014). Macroevolution through molecular and morphological lenses: a history of microporellids.
• Orr, Russell (2014). Genome dynamics in early eukaryotic evolution: importance of enigmatic lineages.
• Orr, Russell (2014). Genome dynamics in early eukaryotic evolution: importance of enigmatic lineages.
• Orr, Russell (2014). Genome dynamics in early eukaryotic evolution: importance of enigmatic lineages. Show summary

  The origin of the eukaryotic cell from its bacterial ancestor is probably the most complex transition in evolution. Understanding the mechanisms of, and reasons for this major evolutionary transition is of fundamental importance for both cellular and evolutionary biology. To reconstruct the origin and evolution of the eukaryote cell one needs to study the changes that have occurred to an organisms hereditary information (genome) over time; from the most primitive to the most modern organisms. Recent improvements to the eukaryote tree of life have divided organisms it into a small number of so-called supergroups. These supergroups encompass the majority of living eukaryotes but there are still some enigmatic species that place external to these known groupings. Some of these species represent our earliest ancestors, and as such, are of major importance to understanding how the eukaryotic cell has evolved over time. Projects that map eukaryotic genomes are yet to study a species outside the known supergroups. Though, such a genome will give insight and resolution into how eukaryotes have evolved from a bacterial ancestor toward advanced eukaryotes. The overall objective of this project is therefore to explore the dynamics of genome changes that have occurred during evolution. This will be investigated by mapping the genomes from numerous enigmatic species that fall outside of the known supergroups. This information will then be compared with that of other eukaryotic organisms that place within the know groupings. The project builds on recent developments in techniques used for the extraction of genome information and comparison thereof, to focus on fundamental questions about the origin and evolution of eukaryotes. The project can therefore have significant bearing on central evolutionary issues and further our understanding of the developments that have occurred during eukaryotic evolution. The project will increase general understanding of processes that have form

• Stüken, Anke; Figueroa, Rosa; Orr, Russell & Jakobsen, Kjetill Sigurd (2012). Is sxt gene copy number related to saxitoxin synthesis?.
• Stüken, Anke; Orr, Russell; Kellmann, Ralf; Murray, Shauna A.; Neilan, Brett A. & Jakobsen, Kjetill Sigurd (2011). Discovery of nucelar-encoded genes for the neurotoxin saxitoxin in dinoflagellates.
• Stüken, Anke; Orr, Russell; Kellmann, Ralf; Murray, Shauna A.; Neilan, Brett A. & Jakobsen, Kjetill Sigurd (2011). Discovery of nucelar-encoded genes for the neurotoxin saxitoxin in dinoflagellates.
• Dittami, Simon; Riisberg, Ingvild; John, Uwe; Orr, Russell; Shalchian-Tabrizi, Kamran; Jakobsen, Kjetill Sigurd & Edvardsen, Bente (2010). Analysis of expressed sequence tags from the ichtyotoxic dictyochophyte Pseudochattonella farcimen. Show summary

  Pseudochattonella farcimen (Eikrem, Edvardsen, et Throndsen) is an ichthyotoxic alga within the Dictyochophyceae (Heterokonta), which has been shown to form blooms in Scandinavian waters every year since 1998. To improve our understanding of the biology of this alga and to facilitate future genomic studies, we report the sequencing and analysis of >10,000 expressed sequence tags (ESTs) corresponding to 8149 unique sequences from this species. A direct comparison with EST libraries from other heterokonts revealed several functional categories to be significantly overrepresented among the P. facimen ESTs, such as genes involved in cell communication, transporters, or genes targeted to cell organelles. Interestingly, P. farcimen ESTs also code for a high proportion (1.4%) of proteins related to fatty acid metabolism, including eight fatty acid desaturases and two phospholipase A2 genes. Three of the desaturases belong to a family of delta-4 desaturases, known so far only from haptophytes, where they catalyze the conversion of n3-docosapentaenoic (n3-DPA) acid to docosahexaenoic acid (DHA). These findings may partially explain the unusual fatty acid profiles observed in P. farcimen and are discussed both from an evolutionary point of view and in relation the ichthyotoxic effects of this alga.

• Orr, Russell; Stüken, Anke; Rundberget, Thomas; Eikrem, Wenche & Jakobsen, Kjetill Sigurd (2010). Improved phylogenetic resolution of toxic and non-toxic Alexandrium strains using a concatenated rDNA approach.
• Orr, Russell; Stüken, Anke; Rundberget, Thomas; Eikrem, Wenche & Jakobsen, Kjetill Sigurd (2010). Improved phylogenetic resolution of toxic and non-toxic Alexandrium strains using a concatenated rDNA approach.
• Stüken, Anke; Orr, Russell; Kellmann, Ralf; Murray, Shauna A.; Mihali, Troco Kaan; Neilan, Brett A. & Jakobsen, Kjetill Sigurd (2010). Saxitoxin gene identified in dinoflagellates.
• Minge, Marianne Aastebøl; Silberman, Jeffrey; Orr, Russell; Cavalier-Smith, Thomas; Shalchian-Tabrizi, Kamran; Burki, Fabien; Skjæveland, Åsmund & Jakobsen, Kjetill Sigurd (2008). Breviata anathema - an unusual Amoebozoa.
• Orr, Russell; Espelund, Mari; Kellmann, Ralf & Jakobsen, Kjetill Sigurd (2008). Evolution witihin the genus Alexandrium focusing on toxicity.
• Shalchian-Tabrizi, Kamran; Minge, Marianne Aastebøl; Espelund, Mari; Orr, Russell; Ruden, Torgeir A.; Jakobsen, Kjetill Sigurd & Cavalier-Smith, Thomas (2008). The Choanozoan Ministeria vibrans: Multigene Phylogeny and the Origin of Animals. Show summary

  Ministeria vibrans is a unicellular protozoan belonging to the phylum Choanozoa, the evolutionary closest related group to the animals. Ministeria is a minute bacteria-eating cell possessing slender radiating tentacles, that has recently been shown to be the most close relative to Capsaspora, another protozoan with thread-like (filose) tentacles. Forming the novel clade Filasterea, Ministeria/Capsaspora was shown to be sister to animals and choanoflagellates. Presumably, their last common ancestor evolved filose tentacles well before they were aggregated as a periciliary collar in the choanoflagellates. Several successive evolutionary innovations occurred among the unicellular closest relatives of the animals prior to the origin of multicellularity. We have analysed an EST library from this early branching choanozoan organism and have found many domains of key significance for animal cell biology. New domain combinations as well as domain duplications must have taken place along the path to multicellularity.

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