More extensive mitochondrial genome (mitogenome) sequence varieties are required to improve our understanding of Lepidoptera phylogeny and mitogenome evolution. However, only a limited mitogenome diversity is currently available in the lepidopteran superfamily Yponomeutoidea. This study reports the 15,350-bp complete mitogenome of the hawthorn moth Scythropia crataegella (Linnaeus, 1767), the first species in the family Scythropiidae in Yponomeutoidea. S. crataegella has the typical gene content and arrangement found in Lepidoptera. Having the A/T-biased genetic composition in whole mitogenome of S. crataegella (85.3%) A/T-only-containing codons, such as TTA, ATT, TTT, ATA, AAT, and TAT account for 53.21% of protein-coding genes. Including S. crataegella, all Yponomeutoidea species have a TTAGTAT conserved sequence motif at the trnS2 and ND1 junction, a mitochondrial transcription termination peptide binding site. Yponomeutoidea gene sequence divergences were highly variable, ranging from 8.47% (srRNA) to 19.95% (ND6), indicating a substantial substitution force difference among Yponomeutoidea mitochondrial genes. Phylogenetic analysis placed Scythropiidae, represented by S. crataegella, as a sister Glyphipterigidae group, represented by Acrolepiopsis assectella; however, this group’s nodal support was markedly low (bootstrap support = 30%). An extended taxon diversity is essential for further robust Yponomeutoidea phylogenetic inference. Adding a new Yponomeutoidea familial member benefits future mitogenome-based extensive phylogenetic study for this superfamily.
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