Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis (original) (raw)

  1. Eiichi Shoguchi1,2,6,7,
  2. Takeshi Kawashima1,6,
  3. Yutaka Satou1,6,
  4. Makoto Hamaguchi1,
  5. Tadasu Sin-I3,
  6. Yuji Kohara3,
  7. Nik Putnam4,
  8. Daniel S. Rokhsar4,5, and
  9. Nori Satoh1,2
  10. 1 Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
  11. 2 CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
  12. 3 National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
  13. 4 U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
  14. 5 Center for Integrative Genomics, Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA

Abstract

The draft genome (∼160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromosomes, important biological questions including regulation of gene expression at the genome-wide level cannot yet be addressed. Here, we report the molecular cytogenetic characterization of all 14 pairs of C. intestinalis chromosomes, as well as initial large-scale mapping of genomic sequences onto chromosomes by fluorescent in situ hybridization (FISH). Two-color FISH using 170 bacterial artificial chromosome (BAC) clones and construction of joined scaffolds using paired BAC end sequences allowed for mapping of up to 65% of the deduced 117-Mb nonrepetitive sequence onto chromosomes. This map lays the foundation for future studies of the protochordate C. intestinalis genome at the chromosomal level.

Footnotes