Next-generation sequencing, assembly, annotation, and phylogenomic analysis of the complete mitochondrial genome of the painted lady butterfly Vanessa cardui (Linnaeus, 1758) (Insecta: Lepidoptera: Nymphalidae)

Abstract

Background: Vanessa butterflies, with 22 known species with local and cosmopolitan distributions, are good model organisms to study factors that contribute to the distribution and adaptation in the animal kingdom. Here, the complete mitochondrial genome of Vanessa cardui, a cosmopolitan member of Vanessa butterflies in Nymphalidae, was sequenced, assembled, annotated, and characterized. Results: The mitogenome was a midsize circular molecule with 15,299 bps containing regular 37 elements, including 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and an A + T-rich control region. The genes were organized by 11 intergenic and 13 overlapping spaces. The mitogenome showed a GC content of 19 % and a GC skew of -0.191724138, which was the lowest among the other sequenced Vanessa species. Out of 13 PCGs, only 7 start with ATG, and only 9 end with a TAA stop codon. Analysis of Relative Synonymous Codon Usage (RSCU) demonstrated that out of 66 codons, including stop codons, 25 codons were overrepresented, 7 were unbiased, and 34 were underrepresented. The tRNAs with the size range of 60 bps (tRNASer(AGN)) to 74 bps (tRNATrp) all showed typical cloverleaf secondary structures except for tRNASer(AGN), in which the D-loop was not seen. A Bayesian phylogenomic analysis of V. cardui's mitogenome and 42 other butterfly mitogenomes showed a well-resolved tree with 7 major clades. Conclusions: Studying Vanessa butterflies with different distribution ranges and their mitogenomes may provide insights into genetic factors influencing species distribution and adaptation. The complete mitogenome data provided better resolution in phylogenetic reconstructions for exploring the evolutionary history of the species. © The Author(s) 2025.