The fig wax scale, Ceroplastes rusci (Linnaeus, 1758), is a polyphagous, globally invasive pest native to Africa, causing severe economic losses. High-quality genomic resources for this species are lacking, limiting molecular research on its biology and management. Here, we report a high-quality chromosome-level genome assembly of C. rusci, with a total length of 426.70 Mb and a scaffold N50 of 24.19 Mb. Hi-C data anchored 99.96% of the assembly into 18 chromosomes. The genome contains 11,587 protein-coding genes (95.71% functionally annotated) with a BUSCO completeness of 95.3% (hemiptera_odb12). Repetitive elements account for 55.48% of the genome, of which 50.61% are unclassified repeats; among classified repetitive elements, LTR retrotransposons represent the dominant category. We also annotated 996 non-coding RNA loci and characterized SSRs and transposable elements. This chromosome-scale genome provides a key resource for studying the evolution, host adaptation, insecticide resistance, reproductive strategies, and symbiotic interactions of scale insects, and will support the development of precise monitoring and sustainable control strategies against this invasive pest.

The assembly of insect mitochondrial genomes remains challenging in certain taxa due to extreme AT biases and long repetitive regions. The family Diaspididae (Hemiptera: Coccomorpha) exemplifies this difficulty; despite more than 2,700 described species worldwide, no complete mitogenome has been reported prior to this study. Here, the complete mitogenome is presented of Aulacaspis yasumatsui, assembled using a hybrid approach combining second- and third-generation sequencing platforms. The A. yasumatsui mitogenome is the longest identified to date among scale insects, spanning 21,273 bp. It exhibits several extraordinary features, most notably the highest AT content (92%) yet recorded in Insecta, extensive gene rearrangements, the absence of half of the tRNA genes, and the first identified ultra-long repeat region (> 5,000 bp) in Coccomorpha. The leg degeneration and loss observed in Diaspididae evolution may have contributed to the emergence of such an extreme mitogenome structure. Comparative analysis of sequencing strategies revealed substantial coverage bias in Illumina data, which was effectively mitigated by Oxford Nanopore long reads. We propose a standardized pipeline tailored for efficient and accurate assembly of highly AT-rich and structurally complex mitogenomes. This study provides both methodological insights and a valuable genomic resource for future evolutionary and comparative studies on Diaspididae and other taxa with challenging mitogenomes.

Hemipteran insects typically rely on lineage-specific bacterial symbionts to meet their nutritional needs. However, soft scales (Hemiptera: Coccidae) are unique, with fungal rather than bacterial dominant symbionts. While bacterial symbioses in Hemiptera have been widely studied, fungal symbionts remain poorly understood. In this study, we investigated the red wax scale Ceroplastes rubens, a major pest of ornamental plants, by analysing 260 samples collected from 47 locations across 14 provinces in China between 2010 and 2023. We sequenced mitochondrial COI and nuclear 28S genes of the host and ITS and EF-1 alpha genes of its fungal symbiont, Ophiocordyceps (Hypocreales, Ophiocordycipitaceae). Phylogenetic reconstruction revealed four geographically distinct lineages of C. rubens in southern China, shaped by biogeographic barriers, host plant variation, and historical climate patterns. Each lineage harboured a specific Ophiocordyceps clade, exhibiting strong phylogenetic congruence. Cophylogenetic analyses revealed a significant association between the host and its fungal symbiont, supporting the parallel evolution hypothesis. Divergence time estimates suggested that the Ophiocordyceps symbiont associated with C. rubens originated after its host and subsequently underwent codiversification. This study provides the most comprehensive phylogenetic framework to date for scale insects and their fungal symbionts, offering novel insights into the evolution of obligate symbioses in Hemiptera.

Scale insects (Hemiptera: Coccoidea), comprising archaeococcoids and neococcoids, represent the fourth largest superfamily within the order Hemiptera and are recognized as significant agricultural and forestry pests. Despite the increasing availability of insect genomic data, systematic phylogenetic studies of scale insects at the family level have been limited due to challenges in specimen collection, identification, and sequencing. In this study, we sequenced the genomes of 46 species representing 20 families and integrated this data with publicly available sequences to encompass 22 families, representing 95% of Coccoidea taxa. Notably, 14 of these families are sequenced for the first time. This work establishes a robust phylogenetic framework for scale insects. Our findings clarified the phylogenetic relationships of archaeococcoids, confirming Matsucoccidae as the most primitive extant group of scale insects and identifying Putoidae as a transitional lineage between archaeococcoids and neococcoids. We further demonstrated that Xenococcidae belongs to the neococcoids, distinct from Pseudococcidae, and revealed that Coccidae form a paraphyletic group, with Aclerdidae nested within Coccidae. Using MCMCTree analysis, we estimated the divergence times of various Coccoidea families and proposed a comprehensive evolutionary framework for scale insects. This study addresses key gaps in the phylogenetic and evolutionary understanding of Coccoidea, providing a valuable genomic resource and advancing our knowledge of their phylogeny and evolutionary history.

The rapid advancement of high-throughput sequencing has led to a great increase in sequencing data, resulting in a significant accumulation of contamination, for example, sequences from non-target species may be present in the target species’ sequencing data. Insecta, the most diverse group within Arthropoda, still lacks a comprehensive evaluation of contamination prevalence in public databases and an analysis of potential contamination causes. In this study, COI barcodes were used to investigate contamination from insects and mammals in GenBank’s genomic and transcriptomic data across four insect orders. Among the 2796 WGS and 1382 TSA assemblies analyzed, contamination was detected in 32 (1.14%) WGS and 152 (11.0%) TSA assemblies. Key findings from this study include the following: (1) TSA data exhibited more severe contamination than WGS data; (2) contamination levels varied significantly among the four orders, with Hemiptera showing 9.22%, Coleoptera 3.48%, Hymenoptera 7.66%, and Diptera 1.89% contamination rates; (3) possible causes of contamination, such as food, parasitism, sample collection, and cross-contamination, were analyzed. Overall, this study proposes a workflow for checking the existence of contamination in WGS and TSA data and some suggestions to mitigate it.

The cottony cushion scale, Icerya purchasi, a polyphagous pest, poses a significant threat to the global citrus industry. The hermaphroditic self-fertilization observed in I. purchasi is an exceptionally rare reproductive mode among insects. In this study, we successfully assembled a chromosome-level genome sequence for I. purchasi using PacBio long-reads and the Hi-C technique, resulting in a total size of 1,103.38 Mb and a contig N50 of 12.81 Mb. The genome comprises 14,046 predicted protein-coding genes, with 462,722,633 bp occurrence of repetitive sequences. BUSCO analysis revealed a completeness score of 93.20%. The genome sequence of I. purchasi serves as a crucial resource for comprehending the reproductive modes in insects, with particular emphasis on hermaphroditic self-fertilization.

Additional file 5: Table S5. Annotation and gene organization of the mitochondrial genome of E. pela. N: minor strand; J: major strand. The tRNAs were annotated by different methods: MITOS2, ARWEN or aligning with the sequences of related species that were not annotated by software (ALIGN). Running ARWEN with the “-ps < num>” option.

In recent years, DNA barcoding has rapidly developed as a powerful tool in taxonomy, demonstrating its value in species identification and discovery of cryptic diversity. The number of barcoding sequences of various species continues to grow in the GenBank and BOLD databases; however, the accuracy of sequences and related raw information in public repositories is often questionable. In the present study, based on a dataset of 68,089 Hemiptera COI barcode sequences covering 3,064 species, 1,072 genera, and 48 families, we analyzed genetic differences within and between species and evaluated possible data errors in the insect barcodes. The results showed that errors in the barcode data are not rare, and most of them are due to human errors, such as specimen misidentification, sample confusion, and contamination. A significant portion of these errors can be attributed to inappropriate and imprecise practices in the DNA barcoding workflow. Herein, suggestions are provided to improve the practical operations and workflow of DNA barcoding to reduce human errors.

Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported. In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates. The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.

In the present study, a global presence/absence dataset including 2486 scale insect species in 157 countries was extracted to assess the establishment risk of potential invasive species based on a self-organizing map (SOM). According to the similarities in species assemblages, a risk list of scale insects for each country was generated. Meanwhile, all countries in the dataset were divided into five clusters, each of which has high similarities of species assemblages. For those countries in the same neuron of the SOM output, they may pose the greatest threats to each other as the sources of potential invasive scale insect species, and therefore, require more attention from quarantine departments. In addition, normalized ζi values were used to measure the uncertainty of the SOM output. In total, 9 out of 63 neurons obtained high uncertainty with very low species counts, indicating that more investigation of scale insects should be undertaken in some parts of Africa, Asia and Northern Europe.

A study of the mealybug genus Planococcus Ferris, 1950 (Hemiptera, Coccomorpha, Pseudococcidae) known from China is presented and 12 species are recognised. Of these, Planococcus camelliae Zhang, sp. nov. is described as new to science based on the morphology of the adult female, and P. bambusifolii (Takahashi, 1951) is recorded from China for the first time. Molecular analyses based on the mitochondrial gene cytochrome c oxidase subunit I (COI) of the new species and a key to species of the genus Planococcus in China are also given.

Six new species of Zaischnopsis Ashmead (Hymenoptera: Eupelmidae) from China are described, Zaischnopsis covid Jiang & Peng sp. nov., Zaischnopsis fuscolivida Tang & Peng sp. nov., Zaischnopsis lii Jiang & Peng sp. nov., Zaischnopsis pacis Jiang & Peng sp. nov., Zaischnopsis campaniformis Tang & Peng sp. nov., and Zaischnopsis zhongi Jiang & Peng sp. nov. All the new species are described and illustrated based on females, and partial mitochondrial cytochrome oxidase subunit I (COI) sequences are provided for the six new species as well as for the previously described Z. fumosa Peng & Xiang. Females of all the species of Zaischnopsis recorded from China are differentiated in a key.

As next-generation sequencing technology becomes more mature and the cost of sequencing continues to fall, researchers are increasingly using mitochondrial genomes to explore phylogenetic relationships among different groups. In this study, we sequenced and analyzed the complete mitochondrial genomes of Eupelmus anpingensis and Merostenus sp. We predicted the secondary-structure tRNA genes of these two species and found that 21 of the 22 tRNA genes in Merostenus sp. exhibited typical clover-leaf structures, with trnS1 being the lone exception. In E. anpingensis, we found that, in addition to trnS1, the secondary structure of trnE was also incomplete, with only DHU arms and anticodon loop remaining. In addition, we found that compositional heterogeneity and variable rates of evolution are prevalent in Chalcidoidea. Under the homogeneity model, a Eupelmidae + Encyrtidae sister group relationship was proposed. Different datasets based on the heterogeneity model produced different tree topologies, but all tree topologies contained Chalcididae and Trichogrammatidae in the basal position of the tree. This is the first study to consider the phylogenetic relationships of Chalcidoidea by comparing a heterogeneity model with a homogeneity model.

Complete mitochondrial genomes are valuable resources for different research fields such as genomics, molecular evolution and phylogenetics. The subfamily Lachninae represents one of the most ancient evolutionary lineages of aphids. To date, however, no complete Lachninae mitogenome is available in public databases. Here we report the Stomaphis sinisalicis mitogenome, representing the first complete mitogenome of Lachninae. The S. sinisalicis mitogenome is consist of 13 protein-coding genes (PCGs), two rRNA genes (rRNAs), 22 tRNA genes (tRNAs), a control region and a large tandem repeat region. Strikingly, the mitogenome exhibits a novel, highly rearranged gene order between trnE and nad1 compared with that of other aphids. The presence of repeat region in the basal Lachninae may further indicate it is probably an ancestral feature of aphid mitogenomes. Collectively, this study provides new insights on mitogenome evolution and valuable data for future comparative studies across different insect lineages.

Mutual relationships with symbionts play a crucial role in the evolution and ecology of plant-feeding hemipteran insects. However, there was no specific dominant bacterium observed in soft scales (Coccidae) in the previous studies, it is still unclear whether soft scales have specific primary symbionts. In this study, a nuclear ribosomal internal transcribed spacer (ITS)gene fragment was used to analyze the diversity of fungal communities in 28 Coccidae species based on next-generation sequencing (NGS). Furthermore, samples from different developmental stages of Ceroplastes japonicus were sequenced to illustrate the dynamics of fungal community. Our results showed that Coccidae-associated Ophiocordyceps fungi (COF) were prevalent in all 28 tested species with high relative abundance. Meanwhile, the first and second instars of C. japonicus, two important stages for growth and development, had high relative abundance of COF, while the relative abundances in other stages were low, ranging from 0.68% to 2.07%. The result of fluorescent in situ hybridization showed that the COF were widely present in hemolymph and vertically transmitted from mother to offspring. Our study confirms that the COF have intimate associations with the growth and development of soft scales, and provides new evidence to support that COF are primary fungal symbionts for Coccidae.

In this study, the complete mitochondrial genome of the pest aphid Greenidea ficicola was determined. The mitogenome was 17,361 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 long control region located between srRNA and tRNAIle, and a repeat region located between tRNAGlu and tRNAPhe. Thirteen protein-coding genes have typical ATN start codon and TAA termination codon. All tRNAs were predicted to contain typical clover-leaf secondary structures except tRNASer(gct). The length of lrRNA and srRNA are 1270 bp and 773 bp, respectively. Phylogenetic analysis shows that Greenideinae speices form a highly supported clade.

There have been few reports of complete mitochondrial genomes (mitogenomes) of scale insects, and it has been indicated that complex and novel structures in their mitogenomes may lead to difficulties in sequencing, assembly and annotation. Transfer RNAs (tRNAs) usually possess typical cloverleaf secondary structures, and truncated tRNAs are rarely found in insect mitogenomes. Here, we report a complete Saissetia coffeae mitogenome (15,389 bp) with high A+T content (84.7%) sequenced by next-generation sequencing (NGS) methods. Genes in the mitogenome were annotated, and nine tRNAs were not found using MITOS. Most of the detected tRNAs were significantly truncated without the dihydrouridine (DHU) arm or the TΨC (T) arm. In addition, the 9 “lost” tRNAs containing mismatched base pairs were retrieved based on the tRNA annotation workflow for Coccidae described in our study. The gene arrangement in the Saissetia coffeae mitogenome was significantly different from that in other hemipteran insects. Additionally, Bayesian and maximum likelihood trees based on the mitochondrial genes showed a long branch of the Saissetia lineage, indicating significant nonsynonymous substitutions or high evolutionary rates in the Saissetia lineage. We provide a reference mitogenome for the assembly and annotation of the Coccidae mitogenome and offer insights into the evolution of scale insects.

DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.

Institutional collaboration promotes development and technical advances in science. A social network analysis is often used to assess the evolutionary dynamics of institutional collaboration in many fields. However, there has been no social network analysis of the insect taxonomy field based on bibliometric data. To explore the evolutionary pattern of institutional collaboration in this field, a total of 21 095 articles were collected from the Web of Science between 1997 and 2016. According to author affiliations data, we found increasingly closer collaboration has occurred in this network over time. Due to economic development, social attention, and policies supporting science and research, developing countries such as China and Brazil have shown a strong upward tendency towards collaboration since 2001. However, the development of institutional collaboration reveals imbalance of taxonomic effort and requires careful attention to certain aspects. Several countries have published numerous research articles, whereas most countries have published a small number of papers. Most institutions have tended to collaborate with institutions from same country, neighbouring countries or continent. Some institutions in developing countries (e.g. China) have numerous collaborators, however these institutions only played a modest role in introducing new collaboration between their collaborators. More work needs be done to improve intermediary ability and to reduce the influence of geographical distance. This study offered a vision for understanding the evolutionary dynamics of institutional collaboration in the insect taxonomy field, and it also suggested further enhancement of institutional collaboration in some weak aspects.