1. Department of Energy Joint Genome Institute, Walnut Creek California 94598, USA
2. Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
3. Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
4. The Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife KY16 8LB, UK
5. Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
6. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
7. Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
8. Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
9. National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
10. Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 645, Barcelona 08028, Spain
11. Department of Biology, Washington University in St Louis, St Louis, Missouri 63130, USA
12. Children's Hospital of Oakland Research Institute, Oakland, California 94609, USA
13. Genetic Information Research Institute, 1925 Landings Drive, Mountain View, California 94043, USA
14. National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
15. RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
16. JGI Stanford Human Genome Center, 975 California Avenue, Palo Alto, California 94304, USA
17. National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
18. Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093-0202, USA
19. Present addresses: Okinawa Institute of Science and Technology (OIST), Uruma, Okinawa 904-2234, Japan (T.K., E.S. and N.S.); Genome Sequencing Center, Department of Genetics, Washington University in St Louis School of Medicine, St Louis, Missouri 63108, USA (A.C.H.); Institute for Evolutionary Discovery, 909 Hiawatha Drive, Mount Pleasant, Michigan 48858, USA (J.J.G-B.).

Correspondence to: Nori Satoh^7,19Daniel S. Rokhsar^1,2 Correspondence and requests for materials should be addressed to D.S.R. (Email: dsrokhsar@yahoo.com) or N.S. (Email: satoh@ascidian.zool.kyoto-u.ac.jp).

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Abstract

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

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