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The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Evelyn E. Schwager, Prashant P. Sharma, Thomas Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G. Extavour, Peter Funch, Jessica Garb, Vanessa L. Gonzalez, Sam Griffiths-Jones, Yi Han, Cheryl Hayashi, Maarten Hilbrant, Daniel S.T. Hughes, Ralf Janssen, Sandra L. Lee, Ignacio Maeso, Shwetha C. Murali, Donna M. Muzny, Rodrigo Nunes da Fonseca, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schönauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, Jack Werren, Carsten Wolff, Kim C. Worley, Gregor Bucher, Richard A. Gibbs, Jonathan Coddington, Hiroki Oda, Mario Stanke, Nadia A. Ayoub, Nikola-Michael Prpic, Jean-François Flot, Nico Posnien, Stephen Richards, View ORCID ProfileAlistair P. McGregor
doi: https://doi.org/10.1101/106385
Evelyn E. Schwager
1Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
2Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street,Lowell, MA 01854
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Prashant P. Sharma
3Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, USA, 53706
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Thomas Clarke
4Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington,Virginia, USA, 24450
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Daniel J. Leite
1Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
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Torsten Wierschin
5Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany
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Matthias Pechmann
6Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, Department for Developmental Biology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
7Current address: University of Cologne, Cologne Biocenter, Institute of Developmental Biology, Zuelpicher Straße 47b, 50674 Cologne, Germany
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Yasuko Akiyama-Oda
8JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
9Osaka Medical College, Takatsuki, Osaka, Japan
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Lauren Esposito
10Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California, 94118, USA
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Jesper Bechsgaard
11Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000 Aarhus C, Denmark
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Trine Bilde
11Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000 Aarhus C, Denmark
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Alexandra D. Buffry
1Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
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Hsu Chao
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Huyen Dinh
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Harsha Vardhan Doddapaneni
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Shannon Dugan
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Cornelius Eibner
13Friedrich-Schiller-University Jena, Department of Genetics, Philosophenweg 12, 07743 Jena, Germany
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Cassandra G. Extavour
14Department of Organismic and Evolutionary Biology, Harvard University. 16 Divinity Avenue, Cambridge MA 02138, USA
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Peter Funch
11Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000 Aarhus C, Denmark
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Jessica Garb
2Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street,Lowell, MA 01854
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Vanessa L. Gonzalez
15Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012 Washington, DC 20013-7012 USA
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Sam Griffiths-Jones
16Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester M13 9PT
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Yi Han
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Cheryl Hayashi
17Department of Biology, University of California, Riverside, Riverside, CA 92521
18Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024 USA
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Maarten Hilbrant
1Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
7Current address: University of Cologne, Cologne Biocenter, Institute of Developmental Biology, Zuelpicher Straße 47b, 50674 Cologne, Germany
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Daniel S.T. Hughes
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Ralf Janssen
19Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236 Uppsala, Sweden
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Sandra L. Lee
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Ignacio Maeso
20Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
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Shwetha C. Murali
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Donna M. Muzny
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Rodrigo Nunes da Fonseca
21Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 27941-222, Brazil
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Jiaxin Qu
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Matthew Ronshaugen
16Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester M13 9PT
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Christoph Schomburg
6Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, Department for Developmental Biology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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Anna Schönauer
1Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
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Angelika Stollewerk
22School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London
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Montserrat Torres-Oliva
6Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, Department for Developmental Biology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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Natascha Turetzek
6Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, Department for Developmental Biology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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Bram Vanthournout
11Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000 Aarhus C, Denmark
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Jack Werren
23Biology Department, University of Rochester, Rochester, NY 14627, USA
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Carsten Wolff
24Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115 Berlin, Germany
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Kim C. Worley
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Gregor Bucher
25Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077 Göttingen
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Richard A. Gibbs
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Jonathan Coddington
16Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester M13 9PT
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Hiroki Oda
8JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
26Department of Biological Sciences, Graduate School of Science, Osaka University
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Mario Stanke
5Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487 Greifswald, Germany
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Nadia A. Ayoub
4Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington,Virginia, USA, 24450
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Nikola-Michael Prpic
6Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, Department for Developmental Biology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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Jean-François Flot
27Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Brussels, Belgium
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Nico Posnien
6Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, Department for Developmental Biology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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Stephen Richards
12Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
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Alistair P. McGregor
1Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
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  • ORCID record for Alistair P. McGregor
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Abstract

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neofunctionalization and subfunctionalization since their duplication, and therefore may have contributed to the diversification of spiders and other pulmonate arachnids.

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The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Evelyn E. Schwager, Prashant P. Sharma, Thomas Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G. Extavour, Peter Funch, Jessica Garb, Vanessa L. Gonzalez, Sam Griffiths-Jones, Yi Han, Cheryl Hayashi, Maarten Hilbrant, Daniel S.T. Hughes, Ralf Janssen, Sandra L. Lee, Ignacio Maeso, Shwetha C. Murali, Donna M. Muzny, Rodrigo Nunes da Fonseca, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schönauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, Jack Werren, Carsten Wolff, Kim C. Worley, Gregor Bucher, Richard A. Gibbs, Jonathan Coddington, Hiroki Oda, Mario Stanke, Nadia A. Ayoub, Nikola-Michael Prpic, Jean-François Flot, Nico Posnien, Stephen Richards, Alistair P. McGregor
bioRxiv 106385; doi: https://doi.org/10.1101/106385
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The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Evelyn E. Schwager, Prashant P. Sharma, Thomas Clarke, Daniel J. Leite, Torsten Wierschin, Matthias Pechmann, Yasuko Akiyama-Oda, Lauren Esposito, Jesper Bechsgaard, Trine Bilde, Alexandra D. Buffry, Hsu Chao, Huyen Dinh, Harsha Vardhan Doddapaneni, Shannon Dugan, Cornelius Eibner, Cassandra G. Extavour, Peter Funch, Jessica Garb, Vanessa L. Gonzalez, Sam Griffiths-Jones, Yi Han, Cheryl Hayashi, Maarten Hilbrant, Daniel S.T. Hughes, Ralf Janssen, Sandra L. Lee, Ignacio Maeso, Shwetha C. Murali, Donna M. Muzny, Rodrigo Nunes da Fonseca, Jiaxin Qu, Matthew Ronshaugen, Christoph Schomburg, Anna Schönauer, Angelika Stollewerk, Montserrat Torres-Oliva, Natascha Turetzek, Bram Vanthournout, Jack Werren, Carsten Wolff, Kim C. Worley, Gregor Bucher, Richard A. Gibbs, Jonathan Coddington, Hiroki Oda, Mario Stanke, Nadia A. Ayoub, Nikola-Michael Prpic, Jean-François Flot, Nico Posnien, Stephen Richards, Alistair P. McGregor
bioRxiv 106385; doi: https://doi.org/10.1101/106385

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