The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

  1. Matthew M. Hill1,2,
  2. Karl W. Broman3,
  3. Elia Stupka4,
  4. William C. Smith5,
  5. Di Jiang6, and
  6. Arend Sidow1,2,7
  1. 1 Department of Pathology, SUMC, Stanford, California 94305-5324, USA;
  2. 2 Department of Genetics, SUMC, Stanford, California 94305-5120, USA;
  3. 3 Department of Biostatistics and Biomedical Informatics, University of Wisconsin, Madison, Madison, Wisconsin 53792, USA;
  4. 4 CBM S.c.r.l., Area Science Park, Trieste, 34012, Italy;
  5. 5 Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106, USA;
  6. 6 Sars International Centre for Marine Molecular Biology, N-5008 Bergen, Norway

Abstract

The urochordate Ciona savignyi is an emerging model organism for the study of chordate evolution, development, and gene regulation. The extreme level of polymorphism in its population has inspired novel approaches in genome assembly, which we here continue to develop. Specifically, we present the reconstruction of all of C. savignyi’s chromosomes via the development of a comprehensive genetic map, without a physical map intermediate. The resulting genetic map is complete, having one linkage group for each one of the 14 chromosomes. Eighty-three percent of the reference genome sequence is covered. The chromosomal reconstruction allowed us to investigate the evolution of genome structure in highly polymorphic species, by comparing the genome of C. savignyi to its divergent sister species, Ciona intestinalis. Both genomes have been extensively reshaped by intrachromosomal rearrangements. Interchromosomal changes have been extremely rare. This is in striking contrast to what has been observed in vertebrates, where interchromosomal events are commonplace. These results, when considered in light of the neutral theory, suggest fundamentally different modes of evolution of animal species with large versus small population sizes.

Footnotes

  • ↵7 Corresponding author.

    ↵7 E-mail arend{at}stanford.edu; fax (650) 725-4905.

  • [Supplemental material is available online at www.genome.org and at mendel.stanford.edu/sidowlab/ciona.html.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.078576.108.

    • Received March 18, 2008.
    • Accepted May 20, 2008.
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  1. Published in Advance June 2, 2008, doi: 10.1101/gr.078576.108 Genome Res. 18: 1369-1379 Copyright © 2008, Cold Spring Harbor Laboratory Press

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