Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae)

Simple Summary Swallowtail butterflies are renowned for their extensive morphological diversity, especially their wing color patterns, with around 600 described species. Given their morphological diversity and species richness, as well as their ecological habits, their phytophagous insect lineage is regarded to have evolved successfully. According to the NCBI database, sixty Papilionidae genomes have been reported, of which only two species have been assembled at the chromosome level. Currently, the paucity of high-quality genome data, especially for rarely seen and endemic butterflies, has hampered our knowledge of their evolution and biology at the genome level. Here, we report a chromosome-level genome assembly of Papilio elwesi, a butterfly species endemic to the Chinese mainland. The sequencing, assembly, and annotation of Papilio elwesi in this study enrich the available butterfly genome resources and lay the data foundation for future research. A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.