Characterization of mitochondrial genomes in six newly sequenced species and analysis of gene rearrangements across Encyrtidae (Hymenoptera, Chalcidoidea)

Encyrtidae plays a significant ecological and agricultural role in the biological control of pests. However, the limited mitogenome data and unresolved phylogenetics impede the evolutionary research. We sequenced and annotated the complete mitogenomes of six Encyrtidae species ( Blastothrix speciosa , Encyrtus aurantii , Lamennaisia ambigua , Lamennaisia nobilis , Cheiloneurus chinensis , and Tassonia gloriae ). All six mitogenomes exhibit the typical circular structure, containing 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). They show a strong AT bias (81.3–83.8%) and vary in length from 15,397 bp to 17,160 bp. Conserved family-specific gene rearrangements, likely synapomorphic for Encyrtidae, were identified in this study using Drosophila yakuba as the ancestral reference species. Species-specific variations, mainly in tRNAs and a few PCGs, appear shaped by positive selection, tRNA structural flexibility, and host adaptation, a pattern that is consistent with the “duplication-random loss” model. Phylogenetic analyses based on the concatenated sequences of 13 PCGs via Maximum Likelihood and Bayesian Inference yielded highly congruent topologies, confirming Encyrtus monophyly and the congruence between molecular clustering and morphological taxonomy. This study enriches Encyrtidae mitogenome resources, clarifies the evolutionary rules and gene rearrangements mechanisms, and provides molecular evidence for Encyrtidae systematics and adaptive evolution research.