The Complete Mitochondrial Genome of Evergestis extimalis (Scopoli, 1763) and Its Phylogenetic Implications

The fennel shoot borer, Evergestis extimalis (Scopoli) (Lepidoptera: Crambidae: Glaphyriinae), is a widespread and economically significant pest across the Qinghai–Tibet Plateau. However, its geographic distribution, comprehensive genomic resources and the phylogenetic position have not been systematically examined. Our findings reveal a broad distribution for E. extimalis, spanning extensive regions across Asia, Europe, and North America. Furthermore, we present the first complete mitochondrial genome (mitogenome) of this species and conduct extensive phylogenetic analyses to clarify its evolutionary relationships within Crambidae. The circular mitogenome is 15,301 bp in length and exhibits typical lepidopteran organization, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and an AT-rich control region. Comparative analysis of E. junctalis revealed conserved gene arrangement and high structural similarity. Among the 13 PCGs, nad6 exhibited the highest nucleotide diversity, whereas cox1 was the most conserved. Most PCGs were under purifying selection (Ka/Ks < 1) except atp8, nad2, and nad6. The AT-rich region (367 bp) contained tandem repeat motifs characteristic of Pyraloidea. Phylogenetic reconstruction based on concatenated sequences of 13 PCGs and 2 rRNAs from 58 species strongly supported the monophyly of Crambidae and revealed Glaphyriinae as a sister group to Odontiinae. Our results confirm the basal divergence between the “PS clade” (Pyraustinae + Spilomelinae) and the “non-PS clade” (Glaphyriinae, Odontiinae, Crambinae, Scopariinae, Schoenobiinae, and Acentropinae) but reveal discordant relationships within the “CAMMSS clade” (Crambinae, Acentropinae, Midilinae, Musotiminae, Schoenobiinae, and Scopariinae) compared to earlier nuclear gene-based studies. This study fills a significant gap in Glaphyriinae mitogenomics and provides valuable genomic resources for future population genetics on this economically important pest.