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.
Document Type
Article
Publication Date
2-24-2013
Digital Object Identifier (DOI)
http://dx.doi.org/10.1038/ng.2568
Repository Citation
Smith, Jeramiah J.; Kuraku, Shigehiro; Holt, Carson; Sauka-Spengler, Tatjana; Jiang, Ning; Campbell, Michael S.; Yandell, Mark D.; Manousaki, Tereza; Meyer, Axel; Bloom, Ona E.; Morgan, Jennifer R.; Buxbaum, Joseph D.; Sachidanandam, Ravi; Sims, Carrie; Garruss, Alexander S.; Cook, Malcolm; Krumlauf, Robb; Wiedemann, Leanne M.; Sower, Stacia A.; Decatur, Wayne A.; Hall, Jeffrey A.; Amemiya, Chris T.; Saha, Nil R.; Buckley, Katherine M.; Rast, Jonathan P.; Das, Sabyasachi; Hirano, Masayuki; McCurley, Nathanael; Guo, Peng; Rohner, Nicolas; Tabin, Clifford J.; Piccinelli, Paul; Elgar, Greg; Ruffier, Magali; Aken, Bronwen L.; Searle, Stephen M.J.; Muffato, Matthieu; Pignatelli, Miguel; Herrero, Javier; Jones, Matthew; Brown, C. Titus; Chung-Davidson, Yu-Wen; Nanlohy, Kaben G.; Libants, Scot V.; Yeh, Chu-Yin; McCauley, David W.; Langeland, James A.; Pancer, Zeev; Fritzsch, Bernd; de Jong, Pieter J.; Zhu, Baoli; Fulton, Lucinda L; Theising, Brenda; Flicek, Paul; Bronner, Marianne E.; Warren, Wesley C.; Clifton, Sandra W.; Wilson, Richard K.; and Li, Weiming, "Sequencing of the Sea Lamprey (Petromyzon marinus) Genome Provides Insights into Vertebrate Evolution" (2013). Biology Faculty Publications. 3.
https://uknowledge.uky.edu/biology_facpub/3
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
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 http://creativecommons.org/licenses/by-nc-sa/3.0/
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.