Soft scale insects (Hemiptera, Coccidae) are important pests of various agricultural and horticultural crops and ornamental plants. They have negative impacts on agriculture and forestry. The tribe Coccini represents one of the most ancient evolutionary lineages of soft scale insects. However, no complete Coccini mitochondrial genome (mitogenome) is available in public databases. Here, we described the complete mitogenome of Coccus hesperidum L., 1758. The 15,566 bp mitogenome of C. hesperidum had a high A+T content (83.4%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Only seven tRNAs had the typical clover-leaf secondary structure and the remaining tRNAs lacked the DHU arm, TψC arm or both. Moreover, a comparative analysis of all reported scale insect mitogenomes from GenBank database was performed. The mitogenomes of scale insects showed high similarities in base composition and A+T content. Additionally, our phylogenetic analysis confirmed the monophyly of Coccomorpha and revealed that the archaeococcoids were the most basal lineage within Coccomorpha, while Ericerus pela and Didesmococcus koreanus, belonging to Coccidae, were often mixed with Aclerdidae, making Coccidae a paraphyletic group. These findings expand the mitogenome database of scale insects and provide new insights on mitogenome evolution for future studies across different insect groups.

The phylum Acanthocephala is an important monophyletic group of parasites, with adults parasitic in the digestive tracts of all major vertebrate groups. Acanthocephalans are of veterinary, medical, and economic importance due to their ability to cause disease in domestic animals, wildlife, and humans. However, the current genetic data for acanthocephalans are sparse, both in terms of the proportion of taxa surveyed and the number of genes sequenced. Consequently, the basic molecular phylogenetic framework for the phylum is still incomplete. In the present study, we reported the first complete mitochondrial genome from a representative of the family Pseudoacanthocephalidae Petrochenko, 1956. The mitogenome of Pseudoacanthocephalus bufonis (Shipley, 1903) is 14,056 bp in length, contains 36 genes (12 protein-coding genes (PCGs) (lacking atp8), 22 tRNA genes, and 2 rRNA genes (rrnL and rrnS)) and two non-coding regions (NCR1 and NCR2), and displayed the highest GC-skew in the order Echinorhynchida. Phylogenetic results of maximum likelihood (ML) and Bayesian inference (BI) using the amino acid sequences of 12 protein-coding genes in different models provided further evidence for the resurrection of the family Pseudoacanthocephalidae and also supported that the order Echinorhynchida is paraphyletic. A monophyletic clade comprising P. bufonis and Cavisoma magnum suggests a close affinity between Pseudoacanthocephalidae and Cavisomatidae. Our phylogenetic analyses also showed that Polymorphidae has a closer relationship with Centrorhynchidae than Plagiorhynchidae in the monophyletic order Polymorphida.

Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.

Metazoan oxidative phosphorylation (OXPHOS) complexes are composed of subunits encoded by mitochondrial and nuclear genes, requiring continuous mitonuclear coevolution to ensure functional compatibility. However, mitochondrial and nuclear genomes exhibit separate inheritance patterns, leading to their distinct or even conflicting evolutionary histories. This study aimed to analyse phylogenetic signals among mitochondrial genes, nuclear-encoded OXPHOS genes, and general nuclear genes across 53 beetle species. Two major cases of mitonuclear discordance were detected. The nuclear-encoded OXPHOS genes supported mitochondrial phylogenetic signals in noterids, indicating that in noterids the evolutionary history of OXPHOS complexes diverged from the phylogenetic history. Conversely, nuclear-encoded OXPHOS genes aligned with the phylogenetic history of rhysodines, and this mitonuclear discordance suggests that mitochondrial genomes exhibited clear signatures of genetic introgression. By integrating phylogenetic reconstructions and reticulate evolutionary network analyses, we attributed the mitonuclear discordance in noterids to incomplete lineage sorting. In contrast, the mitochondrial genomes of rhysodines underwent introgressive hybridization events. Although mitonuclear incompatibility is typically resolved by nuclear compensatory mechanisms, our findings indicate that nuclear compensation exhibits limited efficacy at the gene level, yet locally adaptive residues persist. This was further supported by the weak correlation between nuclear-encoded OXPHOS genes and mitochondrial genes, with no robust mitonuclear coevolutionary signals detected. These findings collectively suggest a loose mitonuclear interaction in beetles. The decoupling of mitochondrial and nuclear evolutionary trajectories may serve as an evolutionary “buffer” to accommodate genomic conflicts while maintaining essential OXPHOS systems.

Creophilus Leach and Platydracus Thomson are two genera whose members were formerly included in a poorly defined Staphylinus. Both include large-sized rove beetles that can be frequently found in carrion, faeces, and other such rotting materials worldwide. But there are not yet mitochondrial genomes in public databases, which deters scientists from further studies that involve species of these two genera. Here we present the first complete mitochondrial genomes of two typical Palaearctic species, Creophilus maxillosus and Platydracus impotens, which are also the first for the two genera. Additionally, we included the new mitogenomic data in a phylogenetic context using maximum likelihood phylogenetic analyses. Our results confirm the results of previous studies but show that the position of Creophilus, and therefore the monophyly of Staphylinina, could be affected by dataset constitution and model selection.

The ground beetle represents one of the largest families in Coleoptera and is the main object of various ecological studies. However, the phylogeny of Carabidae remains unresolved, with insufficient publicly available mitogenomic data and persistent issues of misidentifications. In this study, six complete mitochondrial genomes (mitogenomes) from the genus Harpalus are reported, ranging from 16,066 to 16,948 bp in length and containing 37 typical genes and a control region. Combined with previously reported mitogenomic data, we found all protein‐coding genes (PCGs) initiated with standard start codons ATN or TTG and ended with TAN or an incomplete stop codon single T. Evolutionary rate analysis (Ka/Ks) revealed atp8 was the fastest‐evolving gene, whereas cox1 was the slowest. Additionally, 13 cases of suspected misidentifications in public Carabidae mitogenomes from GenBank were identified, with potential corrections suggested. Bayesian inference and maximum likelihood approaches were used to infer the phylogenetic relationships within Carabidae based on 121 mitogenomes and various datasets. The results confirmed the distinct separation of Cicindelidae from Carabidae. Within Carabidae, most subfamilies were supported as monophyletic, except Licininae and Platyninae. However, inter‐subfamily relationships remain poorly resolved, with Carabinae and Nebriinae consistently occupying basal positions and Harpalinae s. l. positioned terminally across different topologies. Our results provided more insights into the phylogenetic relationships within Carabidae, while expanding mitogenomic and genomic data across carabid lineages is crucial to resolve the uncertain phylogenetic relationships within this important beetle clade.