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A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
Kerrin S Small1, Michael Brudno, Matthew M Hill
1Department of Pathology, Stanford University Medical Center, Stanford, California 94305-5324, USA. kerrin@stanford.edu
Genome Biology
|March 22, 2007
Summary
Researchers improved the Ciona savignyi genome assembly by separating and realigning its two haploid genomes. This created a more contiguous and accurate reference sequence for this important marine invertebrate model.
Area of Science:
- Genomics
- Marine Biology
- Bioinformatics
Background:
- The initial sequencing of the Ciona savignyi genome using a whole-genome shotgun strategy resulted in a highly fragmented assembly.
- Significant genetic polymorphism within Ciona savignyi led to the separate assembly of allelic sequences from the same genomic regions, hindering downstream analyses.
Purpose of the Study:
- To develop a robust, nonredundant reference genome sequence for Ciona savignyi.
- To overcome challenges posed by high polymorphism and allelic separation in the original genome assembly.
- To improve the contiguity and continuity of the Ciona savignyi reference genome.
Main Methods:
- A multistep strategy was employed to reconstruct and align the two distinct haploid genomes (haplomes) present in the original assembly.
- Bioinformatic approaches were used to identify and separate allelic sequences.
- The reconstructed haplomes were aligned to generate a unified, nonredundant reference sequence.
Main Results:
- A 174 megabase nonredundant reference sequence for Ciona savignyi was successfully generated.
- Each genetic locus is represented only once in the new reference sequence.
- Significant improvements in contiguity and continuity were achieved, with corrected misassemblies.
Conclusions:
- The developed multistep strategy effectively resolved the fractured assembly caused by high polymorphism.
- The new reference sequence provides a significantly improved and accurate genomic resource for Ciona savignyi research.
- This enhanced genome assembly will facilitate future studies in Ciona savignyi biology and evolution.
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