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Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis

¹ Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan ² CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan ³ National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan ⁴ U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA ⁵ Center for Integrative Genomics, Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA

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.

⁶ These authors contributed equally to this work.

⁷ Corresponding author.
E-mail eiichi{at}ascidian.zool.kyoto-u.ac.jp; fax 81-75-705-1113.

[Supplemental material is available online at www.genome.org.]

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