Fig. 1

Comparison between assemblies. a Stacked contigs from the previous honeybee genome assembly Amel_4.5 [34] and the long-read sequencing technologies used in this project. Sequences are sorted by length (x-axis) and the cumulative proportion of each assembly that is covered by the contigs is displayed on the y-axis. Dashed line indicates contig with length equivalent to N50. From the left: Amel_4.5, 10x Chromium-only (assembled using Supernova), PacBio-only (assembled using FALCON), Amel_HAv1 (PacBio contigs +10x scaffolding, see Methods) and Amel_HAv3 (Amel_HAv1 scaffolded using BioNano to produce AmelHA_v2, followed by Hi-C scaffolding). For 10x Chromium sequences, the full-length linked-read scaffolds are shown (i.e. including gaps). b Stacks from A super-imposed over the Amel_HAv3 scaffolds (i.e. including gaps). These scaffolds are chromosome-length and contain 51 gaps