Characterization of the Complete Mitochondrial Genome and Evaluation of COI Barcoding in Philonis inermis (Coleoptera: Curculionidae: Cryptorhynchinae) Using Genome Skimming.

Abstract

Background: Philonis inermis is a Neotropical stem-galling weevil specialized on the invasive vine Passiflora foetida and represents a promising candidate for biological control. However, no genomic or barcoding data have previously been available for this genus, limiting its taxonomic resolution and risk assessment potential.

Methods: We used shallow whole-genome sequencing of two individuals reared under controlled conditions to assemble, annotate, and compare the complete mitochondrial genome of P. inermis with other Cryptorhynchinae. BUSCO analysis was performed to recover nuclear single-copy orthologs and additional multicopy markers. Cytochrome c oxidase subunit I (COI) sequences from 20 Colombian specimens were analyzed together with 24 Cryptorhynchinae barcodes from GenBank to evaluate intra- and interspecific divergence.

Results: The P. inermis mitogenome is 15,120 bp in length, AT-rich (77.0%), and contains 36 genes, including 13 protein-coding genes, 21 tRNAs, and two rRNAs. The tRNA-Ile was not detected, likely obscured within the variable control region, as reported for other cryptorhynchine weevils. Phylogenetic analysis based on mitogenomic sequences placed P. inermis as a well-supported clade closely related to Eucryptorrhynchus. COI barcode analysis revealed extremely low intraspecific divergence (pairwise K2P ≤ 0.006) and a pronounced barcode gap distinguishing P. inermis from other Cryptorhynchinae species. Genome-skimming assemblies yielded 196 single-copy orthologs, 28 duplicated BUSCOs, and a rich set of multicopy nuclear markers, including extensive rRNA fragments (18S, 28S, 5.8S, 16S) and core histones (H2A, H2B, H3, H4), which are provided as extended data for future phylogenomic applications.

Conclusion: This study presents the first complete mitochondrial genome for the genus Philonis and demonstrates the utility of COI barcoding for the current molecular identification of P. inermis, in a context where comparative mitogenomic data remain scarce. These genomic resources provide a foundation for future integrative taxonomic, comparative, and evolutionary studies, and support further evaluation of P. inermis as a potential biological control agent against P. foetida.