Overview of generation of the Ciona savignyi reference sequence. (a) The initial whole-genome shotgun (WGS) assembly is represented; black horizontal lines represent contigs, which are connected into supercontigs by gray arcs. (b) Dashed purple lines represent unique anchor between allelic contigs. (c) Two separate bins are represented by red and yellow supercontigs. (d) A single bin is represented; supercontigs in the bin have been assigned to sub-bin A (green) or B (blue). Purple lines denote alignments between allelic contigs in sub-bins A and B. (e) An allelic pair of ordered hypercontigs is represented. Red brackets denote regions where alignment to the opposite allele has bridged a supercontig boundary. (f) The reference sequence contains sequence from allele A (green) and allele B (blue).