The Complete Mitochondrial Genome of <i>Conopomorpha sinensis</i> (Lepidoptera: Gracillariidae) Sample from Taiwan

<h4>Background</h4>The litchi fruit borer, <i>Conopomorpha sinensis</i> (Lepidoptera: Gracillariidae), is a devastating pest affecting litchi and longan production across Asia. Although a reference mitochondrial genome (mitogenome) has been published, its utility is limited by the lack of precise geographical data and raw sequencing data.<h4>Methods</h4>In this study, we sequenced and characterized the complete mitogenome of <i>C. sinensis</i> collected from Taiwan using a hybrid assembly of Illumina and Oxford Nanopore technologies.<h4>Results</h4>The assembled mitogenome is 17,301 bp in length with a mean sequencing depth of 19,155-fold, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an AT-rich control region. Notably, we identified a rare tRNA gene rearrangement (<i>trnR-trnA-trnN-trnS1-trnE-trnF</i>) that deviates from the ancestral lepidopteran ditrysian pattern. Comparative analysis revealed a 94.65% overall sequence identity with the reference mitogenome, though the PCGs remained highly conserved at 99.35%. Variant analysis demonstrated that this divergence is predominantly driven by structural variations (228 indels) rather than nucleotide substitutions (2 SNPs) across the entire mitogenome; furthermore, 94.7% of the indels were identified in the control region and intergenic spacers. Subtle differences in codon usage were also observed in the <i>ND6</i> start codon (ATT vs. ATA) and <i>COX1</i> stop codon (TAA vs. T). Phylogenetic and molecular clock analyses robustly clustered the Taiwan specimen within the <i>C. sinensis</i> clade. Molecular dating estimates that the <i>Conopomorpha</i> lineage originated during the Late Cretaceous (~77.23 Ma). Notably, the divergence between the Taiwan specimen and the reference lineage was estimated to be negligible (<0.01 Ma) within the protein-coding regions, demonstrating a high degree of purifying selection that maintains coding-sequence stability across geographically distinct specimens, even as substantial variation accumulates in non-coding genomic regions.<h4>Conclusions</h4>These findings provide high-resolution genomic resources and a temporal framework for the evolutionary study of Gracillariidae, offering foundational tools for targeted pest management.