| The genome sequence of the urochordate Ciona savignyi was determined with a standard whole genome shotgun strategy, but an extraordinarily high degree of polymorphism resulted in a fractured assembly wherein allelic sequences from the same genomic region assembled into separate contigs. Each locus of the sequenced individual is thus represented twice in the original assembly, and contigs contain no information to indicate which of the two 'haplomes' (haploid genomes) they belong to, or to which other contigs they are allelic. We have generated a global whole genome alignment of the C. savignyi assembly with itself in order to construct a highly contiguous and non-redundant reference sequence of the C. savignyi genome. Our C. savignyi reference sequence exhibits a threefold improvement in N50 and a sixfold reduction in contig breaks compared to the initial assembly, and has facilitated gene annotation of the C. savignyi genome. Sequence gaps and misassemblies have been dramatically reduced by utilizing information from both aligned alleles in a given region. The global alignment of the two haplomes allowed for genome-wide characterization of the heterozygosity of the sequenced individual. We demonstrate extreme per-base heterozygosity for insertions and deletions (16.6%), inversions (1.96%), mobile element activity (11.4%), and single nucleotide polymorphisms (SNPs; 4.5%). We show that the cause for the high rate of heterozygosity is a large effective population size rather than elevated mutation rates and, consistent with the large effective population size, we find evidence of strong purifying selection. These results constitute the first in-depth insight into the dynamics of highly polymorphic genomes and provide important empirical support of population genetic theory as it pertains to population size, heterozygosity, and natural selection. |
