The PDF file includes:

• Note S1. Genome assembly, mtDNA assembly, HaploMerger results, and BUSCO analysis.
• Note S2. HiRise scaffolding and misassembly correction.
• Note S3. Linkage group correction of misassemblies.
• Legend for note S4
• Note S5. RBH of orthologs.
• Note S6. Whole-genome sequencing and RNA-based linkage map.
• Note S7. MP spanning.
• Note S8. Alignment between P. napi and P. rapae.
• Note S9. Syntenic block support of scaffold joins.
• Note S10. SNP generation from nextRAD library sequence.
• Note S11. Comparison of P. napi versus B. mori collinear blocks within Lepidoptera genomes.
• Note S12. Estimation of genomic rearrangements.
• Note S13. Lepidopteran synteny cutoff selection.
• Table S1. Read data used in assembly and analysis.
• Legend for table S2
• Table S3. Lepidopteran phylogeny calibrations.
• Legend for table S4
• Fig. S1. Chromosomal assembly validation figures.
• Fig. S2. Alignment of P. rapae scaffolds to P. napi chromosomes.
• Fig. S3. Example of criteria used to determine napi-like and mori-like joins.
• Fig. S4. Permutation analysis of chromosomal terminal ends.
• Fig. S5. Repetitive element distribution across chromosomes.
• Fig. S6. Insert size distribution.
• Fig. S7. The mtDNA of P. napi.
• Fig. S8. Chronogram of lepidopteran genomes with node labels.
• Fig. S9. Comparative assessment of genome assemblies and chromosomal evolution across, using a BLAST-like approach.
• References (69–85)

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Other Supplementary Material for this manuscript includes the following:

• Note S4 (.zip format). Functional annotation summary.
• Table S2 (Microsoft Excel format). Genomic data from Lepbase used in the comparative assessment of genome assemblies.
• Table S4 (.tsv format). GO term enrichment in syntenic blocks.