Figure 3

Repeat positions in the assembly. A. Four available Picea abies BAC sequences. Contigs assembled within each of the nine test pools were mapped to the 4 BACs (horizontal grey lines) available for the P. abies genome. Multiple hits to the same BAC regions from different FPs were identified (color bars). Multiple hits from the same FP were also common, although they are not shown here because of a lack of resolution. B. Library repeats mapped to contigs assembled from two different sequencing pipelines: whole genome sequencing versus FP sequencing. From both WGS and FP assemblies (available from the database of genome assembly lock v. 1.0), random subsets of 1000 contigs (min length 5000 bp) were aligned against the repeat library presented for spruce genome in [7]. Horizontal coordinates reflect percent identity of contig BLAST hits against sequences from the repeat library. Vertical axes represent the total length of each contig, so that hit points are rescaled and placed proportionally to the length of the respective contig. Filled boxes represent length of a contig hit to a repeat sequence, at the appropriate position relative to the contig length. The hit lengths range from 18 bp (invisible) to over 3000 bp. C. Example contig likely assembled to full original length, with read coverage, vector fragments, and repeat regions. Horizontal axis: length of the contig in base pairs. Vertical axis: read coverage; brown color: unique read mapping; red color: redundant read mapping. Letters S and E: 3′ and 5′ termini of the vector sequence, respectively (~40 bp long). Boxes: repeat regions in the contig. Height denotes original length in the repeat library, width represents locally aligned region of the repeat. A, B, C.