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A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

Kerrin S Small1, Michael Brudno2, Matthew M Hill1 and Arend Sidow1*

Author Affiliations

1 Departments of Pathology and of Genetics, Stanford University Medical Center, 300 Pasteur Drive, Stanford, California 94305-5324, USA

2 Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, Toronto, 6 King's College Rd, Ontario, M5S 3G4, Canada

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Genome Biology 2007, 8:R41  doi:10.1186/gb-2007-8-3-r41

Published: 20 March 2007


The sequence of Ciona savignyi was determined using a whole-genome shotgun strategy, but a high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled separately. We designed a multistep strategy to generate a nonredundant reference sequence from the original assembly by reconstructing and aligning the two 'haplomes' (haploid genomes). In the resultant 174 megabase reference sequence, each locus is represented once, misassemblies are corrected, and contiguity and continuity are dramatically improved.