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At least 19 recordsLinked to original sources

PubMed2026

Identification of Specific Virulence Factors of Pseudomonas Strains in the Biocontrol of the Potato Pest Tecia solanivora.

Tecia solanivora (The Guatemalan potato tuber moth) is a major potato pest, responsible for up to 20% of crop losses and a significant economic impact. Certain Pseudomonas exhibit insecticidal activity and produce virulence factors with cytotoxic and antimicrobial properties, positioning them as promising candidates for biological control. This study evaluated seven Pseudomonas strains with insecticidal activity and identified key virulence factors involved. The strains demonstrated varying degrees of insecticidal activity, with Pseudomonas protegens strains CHA0 and 59C being the most lethal, causing over 75% mortality and triggering a systemic melanization response in the insects. Genomic analysis revealed 175 virulence-related genes shared across all strains and 16 genes specific to the highly insecticidal ones, including genes for antimicrobial compounds and insect toxins. Mutational analysis confirmed the roles of hydrogen cyanide, 2,4-diacetylphloroglucinol, pyoluteorin, Fit toxin, and two-partner secretion systems in P. protegens CHA0 insecticidal activity. This strain also exhibited insecticidal effects on adult T. solanivora and delayed egg hatching and pupal emergence. In microcosm assays, P. protegens CHA0 reduced tuber damage caused by T. solanivora larvae by up to 38%. These results suggest that P. protegens CHA0 is a promising biocontrol agent, providing a sustainable alternative to chemical pesticides to control T. solanivora.

Animals↗

PubMed2026

Adaptation to Plant Defence in an Agricultural Insect Pest: Integrating Genome Scans and Gene Expression in the Soybean Aphid Reveals Multi-Genic Pathways.

In agroecosystems, intense selection pressures cause species to adapt and spread, often leading to the evolution and persistence of pests. Understanding how pests rapidly adapt can help develop sustainable strategies for their management and improve agroecosystem health. Pest adaptation involves stable variations in DNA sequence, as well as dynamic shifts in gene expression, often mediated by non-coding regulatory elements. We examined adaptation to plant defences in the soybean aphid, Aphis glycines, in which virulent aphids have overcome plant defences and avirulent aphids have not. Previous data with laboratory colonies suggested that virulent aphids have higher overall gene expression, including transposable elements, some of which influence gene regulation. However, we lack information on how genetic variation in natural populations impacts adaptation and potentially gene regulation. We integrated population genome scans of field-collected, soybean aphid populations with gene expression profiles of virulent and avirulent laboratory colonies to uncover connections between genetic differentiation and gene regulation for virulence. Genome scan methods found 2144 single nucleotide polymorphisms (SNPs) with significant genetic differentiation (i.e., outliers) in field-collected populations. These SNPs were near 1004 genes, representing 5.16% of the effective number of genes. Based on previous RNA-Seq data with laboratory colonies, we found 3160 genes and 147 long non-coding RNAs (lncRNAs) with differential expression among virulent and avirulent biotypes. By integrating both data sets, we identified 16 genes and 5 long non-coding RNAs with differential expression and that were associated with an outlier SNP (within 10 kbp). We validated SNPs with additional field collected aphids and found an aphid clone with stronger virulence than our laboratory virulent colony, surviving on 2 different aphid-resistant soybean varieties. This new virulent clone had fixed allele differences at 9 SNPs compared to our avirulent and other virulent colony. Field collected soybean aphids matching the phenotype of this new virulent clone had significant genetic differentiation with 3 outlier SNPs near genes related to zinc transport and lachesin compared to field collected avirulent aphids. Our entire data reinforced the importance of a potential multi-genetic response to overcome plant defence and generates new insights into complex genetic and regulatory mechanisms involved in insect-plant interactions.

Animals↗

PubMed2025

Improving spliced alignment by modeling splice sites with deep learning.

MOTIVATION: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands sophisticated modeling of splice sites, but current aligners use simple models, which may affect their accuracy given dissimilar sequences. RESULTS: We implemented minisplice to learn splice signals with a one-dimensional convolutional neural network (1D-CNN) and trained a model with 7,026 parameters for vertebrate and insect genomes. It captures conserved splice signals across phyla and reveals GC-rich introns specific to mammals and birds. We used this model to estimate the empirical splicing probability for every GT and AG in genomes, and modified minimap2 and miniprot to leverage pre-computed splicing probability during alignment. Evaluation on human long-read RNA-seq data and cross-species protein datasets showed our method greatly improves the junction accuracy especially for noisy long RNA-seq reads and proteins of distant homology. AVAILABILITY AND IMPLEMENTATION: https://github.com/lh3/minisplice.

Journal Article↗

PubMed2026

Long-read, high-coverage reference genome of the nymphalid butterfly Catonephele acontius (Nymphalidae: Biblidinae).

Catonephele acontius (Nymphalidae:Biblidinae:Epicalinii) is a butterfly species with a wide distribution across the Neotropics including the Amazon. Here, we present a long-read high-coverage reference genome for this species to serve as a genomic resource for future studies on Biblidinae butterflies, a group that is the subject of ongoing studies of seasonal adaptation under climate change. We used PacBio HiFi and IsoSeq reads to generate a highly contiguous and well-annotated reference genome. Five libraries were constructed, 4 using RNA from different tissues and 1 using high molecular weight (HMW) DNA from a wild-caught female. The DNA was sequenced using PacBio HiFi technology, and the RNA was sequenced using long read PacBio IsoSeq technology. About 20 Gb of raw HiFi data were generated and assembled to an initial size of 520.7 Mb (39 × homozygous coverage) in 90 contigs. The assembly was then polished and decontaminated into 40 contigs with an N50 of 19.927 Mb (BUSCO completeness: 99.0%; duplication: 0.5%; fragmentation: 0.7%; and missing: 0.3%). Final assembly size was 519.2 Mb. Repeats were annotated, showing that the genome consisted of 40.4% transposable elements. IsoSeq transcriptome data from antennae, leg, ovary, and digestive tissue was then used to structurally and functionally annotate gene models for the softmasked genome, uncovering ∼18,500 genes, with 70% of them given functional annotation. This reference assembly joins many published genomes in the Nymphalidae family but represents one of the first high-quality genomes from the Biblidinae subfamily. It provides a valuable resource to study the evolution of plastic and seasonal traits and will help investigate the genetic processes that may influence these species' responses to rapid climate change.

Animals↗

PubMed2025

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.

The investigation of chromatin organization in single cells holds great promise for identifying causal relationships between genome structure and function. However, analysis of single-molecule data is hampered by extreme yet inherent heterogeneity, making it challenging to determine the contributions of individual chromatin fibers to bulk trends. To address this challenge, we propose ChromaFactor, a novel computational approach based on non-negative matrix factorization that deconvolves single-molecule chromatin organization datasets into their most salient primary components. ChromaFactor provides the ability to identify trends accounting for the maximum variance in the dataset while simultaneously describing the contribution of individual molecules to each component. Applying our approach to two single-molecule imaging datasets across different genomic scales, we find that these primary components demonstrate significant correlation with key functional phenotypes, including active transcription, enhancer-promoter distance, and genomic compartment. Also, we find that some bulk trends exist at the single-cell level, but only in a small fraction of cells, suggesting that critical changes in genome organization may be driven by specific rare subpopulations rather than occurring uniformly across all cells. ChromaFactor offers a robust tool for understanding the complex interplay between chromatin structure and function on individual DNA molecules, pinpointing which subpopulations drive functional changes and fostering new insights into cellular heterogeneity and its implications for bulk genomic phenomena.

Animals↗

PubMed2025

Population genomics of Aedes albopictus across remote Pacific islands for genetic biocontrol considerations.

Remote Pacific islands (RPI) are characterized by ecological isolation, diverse endemic species, and vulnerability to invasive organisms due to globalization-driven connectivity. Among these species, Aedes albopictus, a highly invasive vector of flaviviruses, has spread extensively across the RPI via human-mediated dispersal, posing significant health and economic burdens. While the population structure and the degree of gene flow between mosquito populations can inform the dispersal pathways critical for disease vector management, the population genetics of Ae. albopictus in Northern RPI remains understudied. The present work investigated the population structure and connectivity of Ae. albopictus populations from Guam, Hawaiian Islands, and the Republic of the Marshall Islands (RMI) to inform disease and vector-based biosecurity risks and develop targeted management strategies. This is the first assessment to develop and analyze whole genome sequences of Ae. albopictus for RPI, enabling more accurate estimates of differentiation, admixture, and ancestry. We found distinct genetic clustering between regions, distinct ancestry of populations across RPI, and potential invasions that originated from Hawaii and spread into the RMI, and invasions from North America that spread to Guam. These findings can inform biosecurity protocols to limit the invasion of Ae. albopictus and their associated diseases within Hawaii and around the Pacific. Given the significant degree of genetic differentiation, we found between islets, islands, and regions, the genome data from this study can be used to enable the development of locally confined geographically isolated gene drives. These drives may be used to prevent and control outbreaks of dengue, chikungunya, and Zika, diseases that have had devastating consequences in these remote island communities.

Animals↗

PubMed2026

Annotated genome assemblies of two temperate North American dung beetles, Canthon chalcites and Phanaeus vindex.

Dung beetles serve as cultivators of their natural habitats, improving soil health and functions in both natural and anthropogenic environments. Despite their ecological importance, whole genome sequences for Scarabaeinae are limited. Here, we present the draft annotated genome assemblies for 2 temperate species of North American dung beetles collected from eastern Tennessee: Canthon chalcites and Phanaeus vindex. Both genome assemblies were generated from PacBio long reads and have high completeness, with BUSCO scores of 98.1% and 98.6% for C. chalcites and P. vindex, respectively. For C. chalcites, the BRAKER3 pipeline predicted 12,799 genes, and the gene set was 93.7% complete. For P. vindex, the BRAKER3 predicted 12,252 genes, and the gene set was 94.9% complete. From the annotated gene sets, orthologous protein sequence analyses among C. chalcites, P. vindex, the dung beetle species Onthophagus taurus, and the more evolutionarily distant beetle Tribolium castaneum indicated that there are 260 unique protein clusters for C. chalcites and 210 unique protein clusters for P. vindex. These 2 draft genomes provide valuable data for comparative genomics, evolution, and phylogenic studies for dung beetle species.

Animals↗

PubMed2025

Exploring the genetics of social behaviour in C. calcarata.

Studies investigating social evolution often focus on species that are obligately eusocial, where presumably all of the adaptive genetic changes associated with sociality have already been completed. To fully understand eusociality, we must study species with facultative social behaviour. The small carpenter bee Ceratina calcarata is an ideal model for studying the genetics and molecular biology of eusocial evolution as it can exhibit both subsocial behaviour with parental care and social behaviour facilitated by the altruistic dwarf eldest daughter. Here, we sequenced the genomes of subsocial and social C. calcarata to identify mutations and genes associated with social behaviour and used these data to test several hypotheses related to the evolution of eusociality. Many single nucleotide polymorphisms that had high levels of genetic differentiation (Fst) between social and subsocial C. calcarata were in or near genes or regions important for regulating gene expression. These results are consistent with the Genetic Toolkit Hypothesis of eusocial evolution. Our findings suggest that the low behavioural complexity observed in C. calcarata may involve modulation of existing regulatory genes and gene networks to generate phenotypes associated with social behaviour.

Animals↗

PubMed2025

Genome assembly and annotation of the parasitoid jewel wasp Nasonia oneida.

The jewel wasp, Nasonia (Hymenoptera: Pteromalidae), is a well-established model system for evolutionary genetics and host-microbial interactions. Here, we present the genome of N. oneida, a species lacking prior genomic characterization, using 10× Genomics linked-read (400× coverage), Illumina short-read (120× coverage), and transcriptome data (30× coverage). The assembled genome size is 267 Mb, comprising 4,675 scaffolds, with a scaffold N50 of 1 Mb and 98.40% Benchmarking Universal Single-Copy Orthologues (BUSCOs) completeness score. Annotation revealed 32.29% (86.46 Mb) of repetitive sequences and 14,221 protein-coding genes. Comparative genomics of N. oneida with 15 other hymenopteran species validated the presence of 5,939 gene families shared among them, including 3643 single-copy and 2296 multicopy gene families. This study provides the first de novo assembly of N. oneida, providing a significant addition to the growing repertoire of molecular tools for comparative genomics and functional studies to understand the evolution of closely related species as well as the evolution of parasitic wasps.

Animals↗

PubMed2025

Large-scale Genome Analyses Provide Insights into Hymenoptera Evolution.

The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, stinger, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.

Animals↗

PubMed2026

Draft genome assembly of the green-bronze dung beetle, Onthophagus orpheus.

Dung beetles (Coleoptera: Scarabaeinae) are ecologically important insects, yet genomic resources for this diverse lineage remain limited. Here, we present a high-quality genome assembly for Onthophagus orpheus, an understudied species that is abundant in urban forests in the eastern United States. The assembled genome is a scaffold-level assembly, with a high degree of genic completeness as assessed by Benchmarking Universal Single-Copy Ortholog (BUSCO) analyses, indicating robust representation of conserved protein-coding genes. Structural and functional annotation recovered a comprehensive gene set consistent with expectations for coleopteran genomes. This genome assembly provides an important resource for future work on the behavioral ecology and population genetics of Onthophagus orpheus, specifically, and Scarabaeidae more broadly.

Onthophagus↗

PubMed2026

Genome-wide scans reveal candidate genes associated with wing morph differentiation in Tetrix japonica.

Wing dimorphism is an important dispersal-related trait in insects, but its genomic basis remains poorly understood in pygmy grasshoppers. Here, we integrated genome-wide single-nucleotide polymorphism (SNP) analyses, population structure inference, selection scans, and functional annotation to investigate genomic differentiation between long- and short-winged Tetrix japonica. Principal component analysis (PCA), ADMIXTURE, and phylogenetic analyses revealed weak genome-wide separation between morphs, indicating differentiation on a largely shared genetic background. Genome-wide scans based on the fixation index (FST), nucleotide diversity ratios, and Tajima's D, using 50-kb non-overlapping windows and empirical top-5% outlier thresholds, identified multiple candidate regions across seven chromosomes. The broader long- and short-winged candidate sets spanned 9.35 Mb and 9.37 Mb and directly overlapped 82 and 77 genes, respectively. Candidate genes were associated with signaling/hormone regulation, membrane transport, metabolism, cytoskeletal organization, extracellular matrix structure, and development. Short-winged candidate genes were significantly enriched for ABC-type transporter activity and ATP hydrolysis activity. Because all individuals originated from a single laboratory-maintained population with weak genome-wide structure, these regions should be regarded as candidate loci from a screening-stage analysis that require validation in independent populations and by functional assays, rather than as confirmed targets of selection.

Animals↗

PubMed2026

Genome-guided stage- and tissue-resolved transcriptome analysis of Serrodes campana identifies sex-biased antennal expression and candidate chemosensory-related genes.

Serrodes campana is an erebid moth of ecological and forestry relevance; its larvae are mainly associated with the soapberry tree, Sapindus mukorossi, whereas adults exhibit fruit-piercing behavior. However, stage- and tissue-resolved transcriptomic resources for this species remain limited. Here, using a chromosome-level reference genome, we performed a genome-guided transcriptome analysis of S. campana based on 12 RNA-seq libraries representing major developmental stages and key adult tissues. Global transcriptomic analyses revealed pronounced transcriptional differentiation across developmental stages and tissue types. Tissue-enriched gene sets and functional enrichment analyses identified distinct molecular signatures associated with developmental, sensory, and pheromone-associated tissues. Comparative analysis of female and male antennae further revealed sex-biased expression of several candidate chemosensory-related genes. Among 153 curated chemosensory-related candidate genes, most odorant receptor genes showed strong antennal enrichment, whereas other major chemosensory gene families displayed broader but still tissue-preferential expression patterns. In addition, an exploratory comparison of female terminal abdominal gland tissue and male terminal abdominal coremata revealed divergent expression profiles and highlighted candidate genes potentially associated with pheromone-related physiology, reproduction, and tissue-specific signaling. Together, this study provides the first genome-guided stage- and tissue-resolved transcriptomic resource for S. campana and offers a useful foundation for future studies of chemosensory detection, sex-biased gene expression, and pheromone-associated biology in this species.

Animals↗

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↗