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Genome Biol. 2007;8(3):R41.

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

Author information

  • 1Department of Pathology, Stanford University Medical Center, Stanford, California 94305-5324, USA. kerrin@stanford.edu

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.

PMID:
17374142
[PubMed - indexed for MEDLINE]
PMCID:
PMC1868934
Free PMC Article

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