Genome quality assessment

We generated k-mer counts from the PacBio HiFi reads using meryl (https://github.com/marbl/meryl). The k-mer counts were then used in GenomeScope2.0 (Ranallo-Benavidez et al. 2020) to estimate genome features including genome size, heterozygosity, and repeat content. To obtain general contiguity metrics, we ran QUAST (Gurevich et al. 2013). To evaluate genome quality and functional completeness we used BUSCO (Manni et al. 2021) with the Insecta ortholog database (insecta_odb10) which contains 1,367 genes. Assessment of base level accuracy (QV) and k-mer completeness was performed using the previously generated meryl database and merqury (Rhie et al. 2021). We further estimated genome assembly accuracy via BUSCO gene set frameshift analysis using the pipeline described in Korlach et al. (2017).

Measurements of the size of the phased blocks is based on the size of the contigs generated by HiFiasm on HiC mode. We follow the quality metric nomenclature established by (Rhie et al. 2020), with the genome quality code x.y.P.Q.C, where, x = log10[contig NG50]; y = log10[scaffold NG50]; P = log10 [phased block NG50]; Q = Phred base accuracy QV (quality value); C = % genome represented by the first “n” scaffolds, following a karyotype of 2n = 60 estimated as the median number of chromosomes from other species in the Family Papilionidae (Genome on a Tree—GoaT; tax_tree [Battus philenor]). Quality metrics for the notation were calculated on the assembly for haplotype 1.