Genome Report: Long read, high-coverage reference genomes of the Nymphalid butterflies Catonephele acontius and Catonephele numilia (Nymphalidae: Biblidinae)

Background Catonephele acontius and Catonephele numilia (Nymphalidae:Biblidinae:Epicalinii) are two butterfly species with wide distributions across the Neotropics including the Amazon. Here, we present and compare long-read high-coverage reference genomes for these two species to serve as a genomic resource for future studies on Biblidinae butterflies, a group that is the subject of ongoing studies of seasonal adaptation under climate change. Results We used PacBio HiFi and Isoseq reads to generate highly contiguous and well-annotated reference genomes. Five libraries were constructed for each species, four using RNA from different tissues and one High Molecular Weight (HMW) DNA from a wild-caught female. The DNA was sequenced using PacBio HiFi technology and the RNA was sequenced using long read PacBio IsoSeq technology. For C. numilia, 96Gb of raw HiFi data was generated and assembled to a size of 520Mbp (54x homozygous coverage) in 110 contigs. For C. acontius, 69Gb of raw HiFi data was generated and assembled to a size of 521Mb (39x homozygous coverage) in 90 contigs. Assemblies were then polished and decontaminated into 40 contigs for each species with an N50 of 21.329Mb for C. numilia (BUSCO completeness: 98.9%, duplication 0.3%, fragmentation 0.7% and missing 0.4%), and 19.927Mb for C. acontius (BUSCO completeness: 99.0%, duplication 0.5%, fragmentation 0.7% and missing 0.3%). Final assembly sizes were 519.6Mb for C. numilia, and 519.2Mb for C. acontius. Repeats were annotated, showing that both genomes consist of ∼40% transposable elements. IsoSeq transcriptome data from antennae, leg, ovary and digestive tissue was then used to structurally and functionally annotate gene models for the softmasked genome, uncovering ∼18,500 genes for each species, with 70% of them given functional annotation. Conclusions These reference assemblies join many published genomes in the Nymphalidae family but represent some of the first high-quality genomes from the Biblidinae subfamily. They provide a valuable resource to study the evolution of plastic and seasonal traits and will help investigate the genetic processes that may influence these species’ responses to rapid climate change.