First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes

Autor: Van, PT, Anselmetti, Y, Bast, J, Dumas, Z, Galtier, N, Jaron, KS, Martens , K, Parker, DJ, Robinson-Rechavi, M, Schwander, T, Simion, P, SCHON, Isa, Andrews, B J

Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference ge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______105::202d7067c8f4971d7235a035b6088189
http://hdl.handle.net/1942/36353

Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova .

Autor: Brandt A; Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany; abrandt3@gwdg.de.; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Tran Van P; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Bluhm C; Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany.; Abteilung Boden und Umwelt, Forstliche Versuchs- und Forschungsanstalt Baden-Wuerttemberg, 79100 Freiburg, Germany., Anselmetti Y; Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France.; CoBIUS Lab, Department of Computer Science, University of Sherbrooke, Sherbrooke, QC J1K2R1, Canada., Dumas Z; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Figuet E; Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France., François CM; Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France.; Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, École Nationale des Travaux Publics de l'État, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France., Galtier N; Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France., Heimburger B; Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany., Jaron KS; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.; Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom., Labédan M; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Maraun M; Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany., Parker DJ; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Robinson-Rechavi M; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Group Evolutionary Bioinformatics, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland., Schaefer I; Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany., Simion P; Group Phylogeny and Molecular Evolution, Institut des Sciences de l'Evolution de Montpellier, 34090 Montpellier, France.; Laboratory of Evolutionary Genetics and Ecology, Unit in Environmental and Evolutionary Biology, Université de Namur, 5000 Namur, Belgium., Scheu S; Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Goettingen, 37073 Goettingen, Germany.; Section Biodiversity and Ecology, Centre of Biodiversity and Sustainable Land Use, 37073 Goettingen, Germany., Schwander T; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Bast J; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Institute for Zoology, University of Cologne, 50674 Cologne, Germany.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2021 Sep 21; Vol. 118 (38).

First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes.

Autor: Tran Van P; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland., Anselmetti Y; ISEM-Institut des Sciences de l'Evolution, Montpellier 34090, France., Bast J; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Dumas Z; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Galtier N; ISEM-Institut des Sciences de l'Evolution, Montpellier 34090, France., Jaron KS; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Martens K; Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium.; Department of Biology, University of Ghent, Ghent 9000, Belgium., Parker DJ; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland., Robinson-Rechavi M; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland., Schwander T; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland., Simion P; ISEM-Institut des Sciences de l'Evolution, Montpellier 34090, France.; Université de Namur, LEGE, URBE, Namur 5000, Belgium., Schön I; Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium.; University of Hasselt, Research Group Zoology, Diepenbeek 3590, Belgium.

Publikováno v: G3 (Bethesda, Md.) [G3 (Bethesda)] 2021 Apr 15; Vol. 11 (4).

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies.

Autor: Waterhouse RM; Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland. robert.waterhouse@unil.ch., Aganezov S; Department of Computer Science, Princeton University, Princeton, NJ, 08450, USA.; Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA., Anselmetti Y; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France., Lee J; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA., Ruzzante L; Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland., Reijnders MJMF; Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland., Feron R; Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland., Bérard S; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France., George P; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA., Hahn MW; Departments of Biology and Computer Science, Indiana University, Bloomington, IN, 47405, USA., Howell PI; Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA., Kamali M; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.; Department of Medical Entomology and Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran., Koren S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA., Lawson D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK., Maslen G; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK., Peery A; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA., Phillippy AM; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA., Sharakhova MV; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.; Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia, 634050., Tannier E; Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, Unité Mixte de Recherche 5558 Centre National de la Recherche Scientifique, 69622, Villeurbanne, France.; Institut national de recherche en informatique et en automatique, Montbonnot, 38334, Grenoble, Rhône-Alpes, France., Unger MF; Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN, 46556, USA., Zhang SV; Departments of Biology and Computer Science, Indiana University, Bloomington, IN, 47405, USA., Alekseyev MA; Department of Mathematics and Computational Biology Institute, George Washington University, Ashburn, VA, 20147, USA., Besansky NJ; Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN, 46556, USA., Chauve C; Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada., Emrich SJ; Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA., Sharakhov IV; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. igor@vt.edu.; Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. igor@vt.edu.; Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia, 634050. igor@vt.edu.

Publikováno v: BMC biology [BMC Biol] 2020 Jan 02; Vol. 18 (1), pp. 1. Date of Electronic Publication: 2020 Jan 02.

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Autor: Anselmetti Y; ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.; Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France., Duchemin W; Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.; INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France., Tannier E; Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.; INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France., Chauve C; Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, V5A1S6, BC, Canada., Bérard S; ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France. Severine.Berard@umontpellier.fr.

Publikováno v: BMC genomics [BMC Genomics] 2018 May 09; Vol. 19 (Suppl 2), pp. 96. Date of Electronic Publication: 2018 May 09.