Fig. 1

Comparison of our assembled scaffolds to a previously published T. forsythia sequence. The sequence KP715369 (black bar in the middle) aligns partially to our scaffold 1 (bottom) and partially to scaffold 2 (top). The sections named A to F represent the scaffolded contigs, gaps between them are indicated by vertical bars. Coverage tracks are shown for two different mapping strategies (allowing zero mismatches versus allowing only uniquely mapping reads); the differences between the two tracks highlight repetitive content found especially at the contig ends. Numbers of linking read pairs between contigs are indicated (based on the uniquely-mapping strategy) along with the numbers of unique mapping positions (read 1 / read 2). There were only 20 read pairs that supported the linkage of contig C to contig E as suggested by the alignment of KP715369. All adjacent contigs as scaffolded by us were supported by more than 5000 pairs for each link