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PubMed2026

Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.

The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% using the Hymenoptera database and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,189 genes for A. andreniformis and 12,207 genes for A. florea, with ∼98% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, with the potential to offer new insights into the genetic basis of dwarf honey bee adaptations.

Male↗

PubMed1976

Control and management of insect populations by chemosterilants.

Chemosterilants, i.e., chemical compounds that interfere with the reproduction potential of sexually reproducing organisms, can be used in three new approaches to insect control. In the sterile-insect release technique, the principal problem is to develop compounds and methods for their application that would not result in introducing harmful residues into the environment. Because of the unusual and often unique circumstances connected with releasing large numbers of sterilized insects, the residue problem and its cost-benefit aspects must be examined individually for each intended control or eradication program. In the direct application technique, chemosterilants must meet the same efficiency and safety standards required from approved insecticides. Combined insecticidal and sterilizing activity is characteristic for some compounds now being investigated. In the genetic technique, chemosterilants may be used for inducing heritable changes in the insect's genome under laboratory conditions, and such procedures would not present any residue problems. Only the first two chemosterilant techniques are approaching practical application, and their safety aspects require detailed evaluation and assessment.

Chemosterilants↗

PubMed2025

Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.

Two invasive hemipteran adelgids are associated with widespread damage to several North American conifer species. Adelges tsugae, hemlock woolly adelgid, was introduced from Japan and reproduces parthenogenetically in North America, where it has rapidly decimated Tsuga canadensis and Tsuga caroliniana (the eastern and Carolina hemlocks, respectively). Adelges abietis, eastern spruce gall adelgid, introduced from Europe, forms distinctive pineapple-shaped galls on several native spruce species. While not considered a major forest pest, it weakens trees and increases susceptibility to additional stressors. Broad-spectrum insecticides that are often used to control adelgid populations can have off-target impacts on beneficial insects. Whole genome sequencing was performed on both species to aid in development of targeted solutions that may minimize ecological impact. Adelges abietis was sequenced using Illumina Linked-Read technology from 30 pooled individuals, with Hi-C scaffolding performed using data from a single individual collected from the same host plant. Adelges tsugae used Oxford Nanopore long-read sequencing from pooled nymphs. The assembled A. tsugae and A. abietis genomes, pooled from several parthenogenetic females, are 220.75 Mbp and 253.16 Mbp, respectively. Each consists of eight autosomal chromosomes, as well as two sex chromosomes (X1/X2), supporting the XX-XO sex determination system. The genomes are over 96% complete based on BUSCO assessment. Genome annotation identified 11,424 and 12,060 protein-coding genes in A. tsugae and A. abietis, respectively. Comparative analysis of proteins across 29 hemipteran species and 14 arthropod outgroups identified 31,666 putative gene families. Gene family evolution analysis with CAFE revealed lineage-specific expansions in immune-related aminopeptidases (ERAP1) and juvenile hormone binding proteins (JHBP), contractions in juvenile hormone acid methyltransferases (JHAMT), and conservation of nicotinic acetylcholine receptors (nAChR). These genes were explored as candidate families towards a long-term objective of developing adelgid-selective insecticides. Structural comparisons of proteins across seven focal species (Adelges tsugae, Adelges abietis, Adelges cooleyi, Rhopalosiphum maidis, Apis mellifera, Danaus plexippus, and Drosophila melanogaster) revealed high conservation of nAChR and ERAP1, while JHAMT exhibited species-specific structural divergence. The potential of JHAMT as a lineage-specific target for pest control was explored through virtual drug and pesticide screening.

adelgids↗

PubMed2005

AnoEST: toward A. gambiae functional genomics.

Here, we present an analysis of 215,634 EST and cDNA sequences of a major vector of human malaria Anopheles gambiae structured into the AnoEST database. The expressed sequences are grouped into clusters using genomic sequence as template and associated with inferred functional annotation, including the following: corresponding Ensembl gene prediction, putative orthologous genes in other species, homology to known proteins, protein domains, associated Gene Ontology terms, and corresponding classification into broad GO-slim functional groups. AnoEST is a vital resource for interpretation of expression profiles derived using recently developed A. gambiae cDNA microarrays. Using these cDNA microarrays, we have experimentally confirmed the expression of 7961 clusters during mosquito development. Of these, 3100 are not associated with currently predicted genes. Moreover, we found that clusters with confirmed expression are nonbiased with respect to the current gene annotation or homology to known proteins. Consequently, we expect that many as yet unconfirmed clusters are likely to be actual A. gambiae genes. [AnoEST is publicly available at http://komar.embl.de, and is also accessible as a Distributed Annotation Service (DAS).].

Animals↗

PubMed2026

Genomic profiling of digestion related enzymes in Anopheles aquasalis a major coastal neotropical malaria vector.

Digestive genes are fundamental for the development and survival of mosquitoes and can serve as a target for the development of strategies for mosquito control or vector-borne disease prevention. Genes related to digestion were identified in the genome of the neotropical malaria vector Anopheles aquasalis by similarity. We used reciprocal BLAST with annotated digestion proteins for Anopheles gambiae. Orthology and evolutionary analyses were performed using MEGA with a bootstrapped phylogenetic tree constructed by the neighbor-joining method, and copy number variation was measured by the standard deviation of the average copy number in each gene family. We identified 241 genes related to digestion in An. aquasalis: 56 genes related to carbohydrate digestion, 51 genes for lipid digestion, and 134 genes for protein digestion. Phylogenetic relationships with other anophelines show that An. aquasalis genes are closely related to those of neotropical mosquitoes Anopheles darlingi and Anopheles albimanus. Orthologous gene clusters are conserved in important families of all four species. Some of these conserved genes are of interest for studies on controlling mosquito vectors, such as larvicidal toxin receptor genes, alpha-amylase, alpha-glucosidase, and maltase; important target genes for transmission-blocking vaccines, such as aminopeptidase N1 and carboxypeptidase B; and the major intestinal serine proteases, such as trypsins and chymotrypsins, which can positively or negatively affect Plasmodium development in the midgut. These data provide a better understanding of digestion-related genes in American anopheline mosquitoes and may support further fundamental and applied studies aimed at malaria control.

Animals↗

PubMed2025

3D chromatin structures precede genome activation in Drosophila embryogenesis.

3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in Drosophila melanogaster throughout the first half of embryogenesis. These high-resolution contact maps reveal fine-scale features such as loops and boundaries delineating topologically associating domains. Notably, we observe that 3D chromatin structures form prior to zygotic genome activation and persist during successive mitotic cycles. Integrative analysis with 149 public chromatin immunoprecipitation sequencing (ChIP-seq) datasets identifies four classes of chromatin structuring elements, including a distinct group enriched for GAGA-associated factor (GAF) and Zelda binding, associated with developmental-gene regulation. These elements are mitotically retained and exhibit sequence and structure similarity between D. melanogaster and D. virilis. We propose that 3D chromatin organization in the pre-cellular embryo facilitates deployment of developmentally regulated genes during Drosophila embryogenesis.

Animals↗

PubMed2025

Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations.

Most genetic polymorphisms associated with complex traits are found in non-coding regions of the genome. Characterizing their effect presents a formidable challenge, and expression quantitative trait locus (eQTLs) mapping has been a key approach to do so. As comprehensive eQTL maps are available only for a few species, here we developed the Drosophila outbred synthetic population (Dros-OSP) and used it to characterize the landscape of transcriptional regulation in Drosophila melanogaster. We collected head and body transcriptomes and genomes from 1,286 outbred flies and mapped local and distant eQTLs for 98% of the genes. We characterized the network organization of the transcriptome across tissues and described the properties of local and distal eQTLs in terms of genetic diversity, heritability, connectivity, and pleiotropy. These results provide new insights into the genetic basis of transcriptional regulation in the fruit fly and offer a new mapping resource that will expand the possibilities currently available for the Drosophila community.

Animals↗

PubMed2025

The first chromosome-level genome of the lappet moth Trabala vishnou (Lepidoptera: Lasiocampidae).

Trabala vishnou (Lefèbvre, 1827) (Lepidoptera: Lasiocampidae) is a destructive leaf-eating pest that causes severe damage to forest ecosystems, leading to substantial economic losses. Herein, we sequenced and assembled a high-quality chromosome-level genome of T. vishnou using a combination of Illumina reads, PacBio HiFi reads, and High throughput Chromosome Conformation Capture (Hi-C) technologies. The genome size is 561.86 Mb and spans 25 chromosomes, exhibiting a high level of contiguity (scaffold/contig N50 = 21.75 Mb/20.67 Mb). Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis a 99.5% completeness score for this genome assembly. Repeat elements constitute 62.66% of the genome. A total of 1,630 non-coding RNAs and 12,895 protein-coding genes have been identified within the genome. The first chromosome-level genome of T. vishnou serves as a valuable reference for elucidating the evolution of functional traits in Lasiocampidae family and will facilitate the development of strategies for controlling defoliating pests.

Animals↗

PubMed2025

Chromosome-level genome assembly of the longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae).

The longhorn beetle Arhopalus rusticus (Coleoptera: Cerambycidae) is a widely distributed wood-boring pest of conifers. Here, we assembled a chromosome-level genome of A. rusticus using Illumina, Oxford Nanopore, and Hi-C sequencing technologies. The assembled genome is 1180.40 Mb, with a scaffold N50 of 125.01 Mb, and BUSCO completeness of 93.6%. All contigs were assembled into ten pseudo-chromosomes. The genome contains 69.87% repeat sequences. We identify 18, 377 protein-coding genes in the genome, of which 11,368 were functionally annotated. This genome provides a valuable resource for understanding the ecology, genetics, and evolution of A. rusticus, as well as for controlling wood-boring pests.

Animals↗

PubMed2025

Chromosome-level genome assembly of the large carpenter bee Xylocopa dejeanii Lepeletier, 1841 (Hymenoptera: Apidae).

Xylocopinae, a diverse bee subfamily comprising over 1,000 bee species, and also a major model system for studying the pollination and evolution of sociality. The lack of chromosome-level genome assembly resources for the Xylocopinae limits our research of their biology and evolution. Here, we provided the first pseudo-chromosomes genome assembly of the Xylocopa dejeanii combined PacBio CLR long reads, Illumina sequences, and Hi-C data. The final genome is 194.44 Mb located in 16 chromosomes. Our assembly includes 141 scaffolds, with a scaffold N50 length of 13.15 Mb. BUSCO analysis revealed 99.00% completeness. Genome annotation identified 28.27 Mb of repetitive elements, 10,970 protein-coding genes, and 432 ncRNAs. This high-quality X. dejeanii assembly advances our understanding of Xylocopinae genomics and provides new insights into bee evolution.

Animals↗

PubMed2025

The Fire Ant Social Chromosome Exerts a Major Influence on Genome Regulation.

Supergenes underlying complex trait polymorphisms ensure that sets of coadapted alleles remain genetically linked. Despite their prevalence in nature, the mechanisms of supergene effects on genome regulation are poorly understood. In the fire ant Solenopsis invicta, a supergene containing over 500 individual genes influences trait variation in multiple castes to collectively underpin a colony level social polymorphism. Here, we present results of an integrative investigation of supergene effects on gene regulation. We present analyses of ATAC-seq data to investigate variation in chromatin accessibility by supergene genotype and STARR-seq data to characterize enhancer activity by supergene haplotype. Integration with gene co-expression analyses, newly mapped intact transposable elements (TEs), and previously identified copy number variants (CNVs) collectively reveals widespread effects of the supergene on chromatin structure, gene transcription, and regulatory element activity, with a genome-wide bias for open chromatin and increased expression in the presence of the derived supergene haplotype, particularly in regions that harbor intact TEs. Integrated consideration of CNVs and regulatory element divergence suggests each evolved in concert to shape the expression of supergene encoded factors, including several transcription factors that may directly contribute to the trans-regulatory footprint of a heteromorphic social chromosome. Overall, we show how genome structure in the form of a supergene has wide-reaching effects on gene regulation and gene expression.

Animals↗

PubMed2015

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Adaptation, Biological↗

PubMed2025

Sexual selection, genomic evolution and population fitness in Drosophila pseudoobscura.

Sexual selection shapes the genome in unique ways. It is also likely to have significant fitness consequences, such as purging deleterious mutations from the genome or conversely maintaining genetic load in a population via sexual conflict. Here, we examined what the influence of sexual selection has on genomic variation potentially underlying population fitness using experimentally evolved Drosophila pseudoobscura populations. Sexual selection was manipulated by keeping replicate lines in elevated polyandry or strict monogamy for approximately 200 generations followed by individual-based sequencing. Using pi (π), fixation index (Fst)and recombination rate measures, we confirmed signatures of selection were not dispersed but mainly localized to the third and X chromosome. Overall mutational load was similar between lines but our analysis of the distribution of fitness effects revealed considerable variation between lines and chromosomes. Furthermore, we found that the distribution of transposable elements differs between the lines, with a higher load in monogamous lines. Our results suggest that complex interactions between purifying selection and sexual conflict are shaping the genome, particularly on chromosome 3 and the sex chromosome; sexual selection influences divergence across chromosomes but in a more complex way than proposed by simple 'purging' of deleterious loci.

Animals↗

PubMed2026

Convergence and conflict among telomere-specialized transposons across 60 million years of Drosophilid evolution.

The Drosophila telomere is one of the best-studied examples of active transposable elements (TEs) benefiting, rather than harming, the host genome. All Drosophila species lack telomerase, and most species instead have telomeres composed of head-to-tail arrays of specialized retrotransposons. These TEs ostensibly act as mutualists by elongating chromosome ends, but evidence from species closely related to Drosophila melanogaster suggests that telomeric transposons may also antagonize their host genome. Importantly, the limited number of Drosophila species characterized thus far has precluded our ability to delineate idiosyncrasies from universal evolutionary forces and genetic mechanisms that shape the history of these TEs. Here, we have surveyed long-read genome assemblies of more than 100 species of Drosophila, identifying a total of 396 telomeric TE families. Our findings show that these telomere-specialized elements evolve dynamically and also undergo striking convergent evolution: The complete loss of telomeric TEs has occurred repeatedly across the genus, whereas individual telomeric TE lineages have repeatedly lost one of their two protein-coding genes. These elements have also repeatedly undergone horizontal transfer between distantly related Drosophila lineages and have repeatedly captured host gene fragments that promote their selfish suppression of host TE-silencing systems. Furthermore, telomere specialization itself appears to have evolved convergently, as some nontelomeric families have gained the ability to target their insertions to telomeres. These results provide unprecedented resolution into the evolution of these unusual TEs and highlight several novel mechanisms by which they evolve in conflict both with each other and their host genome despite the essential telomere function they provide.

Animals↗

PubMed2026

Escape and survival: transposon adaptations in the face of insect host silencing.

Transposable elements (TEs) are mobile genetic sequences that have long resided within host genomes. Over this shared history, a continuous process of co-evolution has forged a diverse array of dynamic TE-host interactions. In an evolutionary arms race, hosts must silence TEs to protect genome integrity from deleterious mutations by TE insertions, while TEs must evade this silencing to survive. TE adaptations to host genomes have recently gained prominence, following many discoveries in eukaryotic genomes. Here, I discuss TE strategies to evade host silencing and ensure their long-term persistence within host genomes, focusing on insects as the primary model system. Furthermore, by describing host silencing, I postulate potential evasive mechanisms that may drive TE adaptation within host genomes.

Journal Article↗

PubMed2024

Activity, structure, and diversity of Type II proline-rich antimicrobial peptides from insects.

Apidaecin 1b (Api), the first characterized Type II Proline-rich antimicrobial peptide (PrAMP), is encoded in the honey bee genome. It inhibits bacterial growth by binding in the nascent peptide exit tunnel of the ribosome after the release of the completed protein and trapping the release factors. By genome mining, we have identified 71 PrAMPs encoded in insect genomes as pre-pro-polyproteins. Having chemically synthesized and tested the activity of 26 peptides, we demonstrate that despite significant sequence variation in the N-terminal sequence, the majority of the PrAMPs that retain the conserved C-terminal sequence of Api are able to trap the ribosome at the stop codons and induce stop codon readthrough-all hallmarks of Type II PrAMP mode of action. Some of the characterized PrAMPs exhibit superior antibacterial activity in comparison with Api. The newly solved crystallographic structures of the ribosome complexed with Api and with the more active peptide Fva1 from the stingless bee demonstrate the universal placement of the PrAMPs' C-terminal pharmacophore in the post-release ribosome despite variations in their N-terminal sequence.

Animals↗

PubMed1992

The nucleotide sequence of an infectious insect-transmissible clone of the geminivirus Panicum streak virus.

The infectious genome of a Kenyan isolate of Panicum streak virus (PSV) has been cloned and sequenced. Infection of host plants was done using an Agrobacterium binary vector containing a partial repeat of the genome. Progeny virus from resultant infections proved to be transmissible by the leafhopper Cicadulina mbila (Naude). Comparisons of the amino acid sequences of PSV DNA-encoded proteins with those of previously characterized geminiviruses infecting monocotyledonous plants, including maize streak virus, revealed high levels of identity. The evolutionary relationship between PSV and other geminiviruses infecting monocotyledons is discussed.

Amino Acid Sequence↗

PubMed2026

Museum specimens reveal the genomic consequences of long-term population decline in an insect pollinator.

Global insect pollinator populations are under threat, with reported declines attributed to increasing habitat loss, pesticide use, and disease. Tracking how genetic diversity has changed over time could reveal the rate and extent of these declines, and the adaptive capacity of affected species-providing an important complement to habitat-based conservation efforts. However, few studies have been able to reconstruct suitable historical baselines to link genomic changes with population change. Here, we use whole genome data from 101 museum specimens of the declining moss carder bumblebee (Bombus muscorum) collected across Britain and Ireland between 1894 and 2019 to reveal a dramatic drop in genetic diversity over the last century. We find a substantial (∼24.6%) reduction in genome-wide heterozygosity across Britain during this period. In England and Wales, where habitat fragmentation is most pronounced, we observe a 2.86-fold increase in runs of homozygosity, commensurate with population fragmentation and isolation. Our results reveal the extent to which human-induced environmental change can lead to severe decadal-scale genomic erosion in a functionally important insect. Identified using DNA from historic museum collections, our approach has widespread applicability for insect conservation and understanding the evolutionary consequences of environmental change.

Animals↗