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The Ciona savignyi genome was sequenced by whole genome shotgun from a single individual with a high level of heterozygosity. Based on targeted finishing of homologous regions, the estimated rate of substitution between the two haplotypes is 6%, the ... total heterozygosity including indels is at least 19%, and these rates vary significantly between regions. The assembly of Ciona savignyi therefore required extensive adaptation of existing strategies for whole genome assembly.
Novel algorithms attempted to recognize read-read overlaps between reads of opposite haplotype based on context and, by excluding such overlaps, to construct contigs and scaffolds which represent sequence from only one of the haplotypes. These scaffolds (CON records) are assigned the accession numbers CH000001-CH003011. Because there are two haplotypes, many regions of the Ciona savignyi genome are represented exactly twice within these scaffold records. To remove this redundancy, the two haplotypes were merged by constructing paired scaffold assemblies, which reference the same contigs as the separate haplotype assembly, but which switch frequently between haplotypes at homologous positions in order to choose the best-assembled haplotype at each region. These scaffolds are assigned the accession numbers CH003012-CH003447.  more

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