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

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

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

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

author email corresponding author email

Genome Biology 2007, 8:R41doi:10.1186/gb-2007-8-3-r41


Published:	20 March 2007

Subject areas: Genome studies, Model organisms, Bioinformatics, Evolution

Abstract

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.