Jeramiah J. Smith, University of KentuckyFollow
Shigehiro Kuraku, RIKEN
Carson Holt, University of Utah
Tatjana Sauka-Spengler, California Institute of Technology
Ning Jiang, Michigan State University
Michael S. Campbell, University of Utah
Mark D. Yandell, University of Utah
Tereza Manousaki, University of Konstanz
Axel Meyer, University of Konstanz
Ona E. Bloom, The Feinstein Institute for Medical Research
Jennifer R. Morgan, Marine Biological Laboratory
Joseph D. Buxbaum, Mount Sinai School of Medicine
Ravi Sachidanandam, Mount Sinai School of Medicine
Carrie Sims, Stowers Institute for Medical Research
Alexander S. Garruss, Stowers Institute for Medical Research
Malcolm Cook, Stowers Institute for Medical Research
Robb Krumlauf, Stowers Institute for Medical Research
Leanne M. Wiedemann, University of Kansas
Stacia A. Sower, University of New Hampshire
Wayne A. Decatur, University of New Hampshire
Jeffrey A. Hall, University of New Hampshire
Chris T. Amemiya, University of Washington
Nil R. Saha, Benaroya Research Institute at Virginia Mason
Katherine M. Buckley, University of Toronto
Jonathan P. Rast, University of Toronto
Sabyasachi Das, Emory University
Masayuki Hirano, Emory University
Nathanael McCurley, Emory University
Peng Guo, Emory University
Nicolas Rohner, Harvard University
Clifford J. Tabin, Harvard University
Paul Piccinelli, Medical Research Council (MRC) National Institute for Medical Research
Greg Elgar, Medical Research Council (MRC) National Institute for Medical Research
Magali Ruffier, Wellcome Trust Sanger Institute
Bronwen L. Aken, Wellcome Trust Sanger Institute
Stephen M.J. Searle, Wellcome Trust Sanger Institute
Matthieu Muffato, European Bioinformatics Institute
Miguel Pignatelli, European Bioinformatics Institute
Javier Herrero, European Bioinformatics Institute
Matthew Jones, California Institute of Technology
C. Titus Brown, Michigan State University
Yu-Wen Chung-Davidson, Michigan State University
Kaben G. Nanlohy, Michigan State University
Scot V. Libants, Michigan State University
Chu-Yin Yeh, Michigan State University
David W. McCauley, University of Oklahoma
James A. Langeland, Kalamazoo College
Zeev Pancer, University of Maryland
Bernd Fritzsch, University of Iowa
Pieter J. de Jong, Children's Hospital Oakland
Baoli Zhu, Children's Hospital Oakland
Lucinda L Fulton, Washington University in St Louis
Brenda Theising, Washington University in St Louis
Paul Flicek, European Bioinformatics Institute
Marianne E. Bronner, California Institute of Technology
Wesley C. Warren, Washington University in St Louis
Sandra W. Clifton, Washington University in St Louis
Richard K. Wilson, Washington University in St Louis
Weiming Li, Michigan State University


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.

Document Type


Publication Date


Notes/Citation Information

Published in Nature Genetics, v. 45, no. 4, p. 415-421.

This work is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License. To view a copy of this license, visit

Supplementary files are listed at the end of this page.

Supplementary PDF file: Supplementary Figures 1–33, Supplementary Tables 2–5, 7, 11–14 and 17–24 and Supplementary Note.

Supplementary Excel file 1: List of reads excluded from the assembly by the Arachne assembler and the reported reason for their exclusion.

Supplementary Excel file 2: A complete list of human/Callorhinchus milii and human/Fugu CNEs aligning to the lamprey genome.

Supplementary Excel file 3: Gene families that show a significant change in the lamprey lineage, within the species tree (lamprey,gnathostomes) or (Ciona,(lamprey,gnathostomes))

Supplementary Excel file 4: A lamprey/chicken comparative map.

Supplementary Excel file 5: A lamprey/human comparative map.

Supplementary Excel file 6: 224 gene families that are found in vertebrates, but not in invertebrate lineages.

Supplementary Excel file 7: Genes in the lamprey genome with immunity-related ontlogies.

Digital Object Identifier (DOI)

ng.2568_S1.pdf (7366 kB)
Supplementary PDF file

ng.2568_S2.xlsx (89109 kB)
Supplementary Excel file 1

ng.2568_S3.xlsx (149 kB)
Supplementary Excel file 2

ng.2568_S4.xlsx (49 kB)
Supplementary Excel file 3

ng.2568_S5.xlsx (2183 kB)
Supplementary Excel file 4

ng.2568_S6.xlsx (2336 kB)
Supplementary Excel file 5

ng.2568_S7.xlsx (60 kB)
Supplementary Excel file 6

ng.2568_S8.xlsx (326 kB)
Supplementary Excel file 7