Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Jeramiah J Smith; Shigehiro Kuraku; Carson Holt; Tatjana Sauka-Spengler; Ning Jiang; Michael S Campbell; Mark D Yandell; Tereza Manousaki; Axel Meyer; Ona E Bloom; Jennifer R Morgan; Joseph D Buxbaum; Ravi Sachidanandam; Carrie Sims; Alexander S Garruss; Malcolm Cook; Robb Krumlauf; Leanne M Wiedemann; Stacia A Sower; Wayne A Decatur; Jeffrey A Hall; Chris T Amemiya; Nil R Saha; Katherine M Buckley; Jonathan P Rast; Sabyasachi Das; Masayuki Hirano; Nathanael McCurley; Peng Guo; Nicolas Rohner; Clifford J Tabin; Paul Piccinelli; Greg Elgar; Magali Ruffier; Bronwen L Aken; Stephen MJ Searle; Matthieu Muffato; Miguel Pignatelli; Javier Herrero; Matthew Jones; C Titus Brown; Yu-Wen Chung-Davidson; Kaben G Nanlohy; Scot V Libants; Chu-Yin Yeh; David W McCauley; James A Langeland; Zeev Pancer; Bernd Fritzsch; Pieter J de Jong; Baoli Zhu; Lucinda L Fulton; Brenda Theising; Paul Flicek; Marianne E Bronner; Wesley C Warren; Sandra W Clifton; Richard K Wilson; Weiming Li

doi:10.1038/ng.2568

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Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

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Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Jeramiah J Smith, Shigehiro Kuraku, Carson Holt, Tatjana Sauka-Spengler, Ning Jiang, Michael S Campbell, Mark D Yandell, Tereza Manousaki, Axel Meyer, Ona E Bloom, …

Nature genetics, Vol.45(4), pp.415-421e2

04/2013

DOI: 10.1038/ng.2568

PMCID: PMC3709584

PMID: 23435085

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Abstract

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ~500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey ( P. marinus ) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.

Details

Title: Subtitle: Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution
Creators: Jeramiah J Smith - Department of Biology, University of Kentucky, Lexington, Kentucky, USA
Shigehiro Kuraku - Genome Resource and Analysis Unit, Center for Developmental Biology, RIKEN, Kobe, Japan
Carson Holt - Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
Tatjana Sauka-Spengler - Division of Biology, California Institute of Technology, Pasadena, California, USA
Ning Jiang - Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
Michael S Campbell - Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
Mark D Yandell - Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
Tereza Manousaki - Department of Biology, University of Konstanz, Konstanz, Germany
Axel Meyer - Department of Biology, University of Konstanz, Konstanz, Germany
Ona E Bloom - The Feinstein Institute for Medical Research, Manhasset, New York, USA
Jennifer R Morgan - Marine Biological Laboratory, Woods Hole, Massachusetts, USA
Joseph D Buxbaum - Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, New York, USA
Ravi Sachidanandam - Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, New York, USA
Carrie Sims - Stowers Institute for Medical Research, Kansas City, Missouri, USA
Alexander S Garruss - Stowers Institute for Medical Research, Kansas City, Missouri, USA
Malcolm Cook - Stowers Institute for Medical Research, Kansas City, Missouri, USA
Robb Krumlauf - Stowers Institute for Medical Research, Kansas City, Missouri, USA
Leanne M Wiedemann - Stowers Institute for Medical Research, Kansas City, Missouri, USA
Stacia A Sower - Center for Molecular and Comparative Endocrinology, University of New Hampshire, Durham, New Hampshire, USA
Wayne A Decatur - Center for Molecular and Comparative Endocrinology, University of New Hampshire, Durham, New Hampshire, USA
Jeffrey A Hall - Center for Molecular and Comparative Endocrinology, University of New Hampshire, Durham, New Hampshire, USA
Chris T Amemiya - Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
Nil R Saha - Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
Katherine M Buckley - Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, Ontario, Canada
Jonathan P Rast - Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, Ontario, Canada
Sabyasachi Das - Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
Masayuki Hirano - Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
Nathanael McCurley - Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
Peng Guo - Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
Nicolas Rohner - Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
Clifford J Tabin - Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
Paul Piccinelli - Medical Research Council (MRC) National Institute for Medical Research, London, UK
Greg Elgar - Medical Research Council (MRC) National Institute for Medical Research, London, UK
Magali Ruffier - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Bronwen L Aken - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Stephen MJ Searle - Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Matthieu Muffato - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
Miguel Pignatelli - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
Javier Herrero - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
Matthew Jones - Division of Biology, California Institute of Technology, Pasadena, California, USA
C Titus Brown - Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA
Yu-Wen Chung-Davidson - Department of Fisheries & Wildlife, Michigan State University, East Lansing, Michigan, USA
Kaben G Nanlohy - Department of Fisheries & Wildlife, Michigan State University, East Lansing, Michigan, USA
Scot V Libants - Department of Fisheries & Wildlife, Michigan State University, East Lansing, Michigan, USA
Chu-Yin Yeh - Department of Fisheries & Wildlife, Michigan State University, East Lansing, Michigan, USA
David W McCauley - Department of Zoology, University of Oklahoma, Norman, Oklahoma, USA
James A Langeland - Department of Biology, Kalamazoo College, Kalamazoo, Michigan, USA
Zeev Pancer - Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
Bernd Fritzsch - Department of Biology, University of Iowa, Iowa City, Iowa, USA
Pieter J de Jong - Children’s Hospital Oakland, Oakland, California, USA
Baoli Zhu - Children’s Hospital Oakland, Oakland, California, USA
Lucinda L Fulton - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
Brenda Theising - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
Paul Flicek - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
Marianne E Bronner - Division of Biology, California Institute of Technology, Pasadena, California, USA
Wesley C Warren - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
Sandra W Clifton - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
Richard K Wilson - The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
Weiming Li - Department of Fisheries & Wildlife, Michigan State University, East Lansing, Michigan, USA
Resource Type: Journal article
Publication Details: Nature genetics, Vol.45(4), pp.415-421e2
DOI: 10.1038/ng.2568
PMID: 23435085
PMCID: PMC3709584
NLM abbreviation: Nat Genet
ISSN: 1061-4036
eISSN: 1546-1718
Grant note: F32 GM087919 || GM / National Institute of General Medical Sciences : NIGMS U54 HG003079 || HG / National Human Genome Research Institute : NHGRI R03 NS078519 || NS / National Institute of Neurological Disorders and Stroke : NINDS R24 RR014085 || RR / National Center for Research Resources : NCRR R01 GM090049 || GM / National Institute of General Medical Sciences : NIGMS R01 DE017911 || DE / National Institute of Dental and Craniofacial Research : NIDCR R37 HD032443 || HD / National Institute of Child Health & Human Development : NICHD R21 GM079492 || GM / National Institute of General Medical Sciences : NIGMS R01 HG004694 || HG / National Human Genome Research Institute : NHGRI R24 GM083982 || GM / National Institute of General Medical Sciences : NIGMS
Language: English
Date published: 04/2013
Academic Unit: Iowa Neuroscience Institute; Biology; Craniofacial Anomalies Research Center
Record Identifier: 9984070351502771

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