Genome assembly and completeness assessment
Long reads derived from Sequel System were assembled using the HGAP4
assembler (https://www.pacb.com/support/software-downloads/). To
construct consensus sequences from draft contigs from HGAP4, Racon
(Vaser, Sovic, Nagarajan, & Sikic, 2016) with minimap (Li, 2016) was
employed. Racon treatment was repeated until the output FASTA file
showed no difference from that of the previous run. In this case, four
repeats were sufficient to obtain final results. Then, in order to
polish the assembly, Pilon (Walker et al., 2014) was utilized with
Illumina short reads. The final assembly was submitted to BUSCO v3
software (Waterhouse et al., 2018) to assess the completeness of the
assembly. For comparison, the latest genome assembly of 4 lepidopteran
species, including B. mori , Papilio xuthus , Danaus
plexippus and Plutella xylostella , was also sumitted to BUSCO.