Genome Biology and Evolution

Transposable elements are a highly diverse group of selfish genomic elements, prevalent across the tree of life, whose uncontrolled propagation poses a threat to genome stability. Recent studies have explored the evolution of Drosophila melanogaster transposable elements, their co-evolution with the host genome, and mechanisms that regulate their activity. However, little is known about their cross-species evolutionary patterns. Long terminal repeat (LTR) retrotransposons are the most active group of transposable elements in Drosophila. They are broadly separated into retroelements, which are active in the germline, and insect endogenous retroviruses that are active in the soma. Somatic elements are hypothesised to infect the germline through their acquisition of virus-derived proteins such as Envelope and sORF2, thus multiplying through successive generations. In this study, we curated the sequences of LTR retrotransposons in 249 drosophilid genomes, allowing us to study their evolution across these species and highlight their varying degrees of conservation. Furthermore, we reveal multiple instances of Envelope protein loss or inactivation that suggest shifts in the expression pattern of these transposons, likely accompanied by adopting different transcriptional control mechanisms. We contrast this with the evolutionary history of sORF2, which we found to be much more stable. Lastly, we examined variations in transposon LTR regions responsible for transcriptional regulation and use predictive modelling to suggest six transcription factors likely involved in their tissue-specific expression. Altogether, we reveal complex, interspecies evolutionary patterns of Gypsy-family LTR retrotransposons and highlight examples of their co-evolution with their host genome.

Organisms cope with environmental changes by modifying gene expression. To understand how regulatory networks controlling expression plasticity evolve, we analyzed RNAseq data from Saccharomyces cerevisiae, Saccharomyces paradoxus, and their F1 hybrids at multiple timepoints after transferring cells from standard laboratory conditions to five environments (low phosphorus, low nitrogen, hydroxyurea shock, heat stress, and cold stress) and during the diauxic shift. In each of the six datasets, we identified genes that changed expression following the transition to the new environment and used hierarchical clustering to identify genes that increased or decreased in expression. We then compared these classifications between orthologs to identify genes with divergent plasticity. For some genes, plasticity was more extreme in one species than the other, and for others, expression of orthologs changed in opposite directions when acclimating to the same environment. Most cases of plasticity divergence were seen only in one environment and were attributable primarily to trans-regulatory divergence. Using environment-specific regulatory networks inferred from data in Yeastract, we found that divergent plasticity of environment-specific transcription factors generally did not predict divergent plasticity of their target genes. We also found that, as a group, genes with conserved plasticity tended to have more regulatory interactions than genes with divergent plasticity. Interesting patterns of expression divergence were also observed for five transcription factors in the pleiotropic drug resistance network and their target genes that might contribute to phenotypic divergence. Together, these findings show how environment-specific trans-regulatory divergence and combinatorial gene regulation shape the evolution of expression plasticity.

The origin of eukaryotes is a key event in the evolution of cellular life hypothesized to involve a symbiotic integration between a member of the Asgard archaea and the Alphaproteobacteria. Recent work has provided evidence for additional genetic input from other prokaryotes to the eukaryotic proteome yet the extent and sources of these contributions remain debated. Here we aimed to further resolve the prokaryotic origins of eukaryotic genes to inform our understanding of eukaryogenesis. Specifically, we developed a phylogenetic framework to investigate the origins of eukaryotic gene families associated with metabolism and informational processing for comparison. We found that informational processing genes were predominantly derived by archaea whereas eukaryotic metabolism is highly chimeric in its origin. In contrast to previous studies, we report a substantial number of archaeal origins of diverse metabolic enzymes including key metabolic regulators. This highlights an overlooked participation of archaeal metabolism and pinpoints potential metabolic integrations during eukaryogenesis. Apart from the alphaproteobacterial contributions to the eukaryotic metabolism, we found an additional dominant phylogenetic signal of genes potentially derived from Myxococcota, especially for gene families associated with lipid metabolism. By systematically analysing the origins of eukaryotic metabolism, this research offers novel insights into the origin of eukaryotic membranes and refine our current models for the origin of the eukaryotic cell.

Co-evolution between genes can occur for a variety of reasons, including co-expression of genes, epistatic interactions between them, physical interactions of gene products and many others. Co-evolutionary partners of a gene are therefore of great interest in identifying potential factors that contribute to any phenotype of interest. State-of-the-art approaches to detect these interactions use correlations of evolutionary rates across a broader phylogeny, and so by necessity identify interactions only among genes that are present across long evolutionary time periods. This makes the methods unwieldy when interest lies in a single focal organism in which the genes of interest may have evolved in the recent evolutionary past. Here, we present a new approach to calculating evolutionary rate correlations which focuses on extracting maximum coverage for a single focal species, while retaining signals of co-evolution across large clades. We show how this approach is able to identify potential interactions even in highly studied species and highly studied genes, with a focus on the D. melanogaster sex-determiner, Sxl, using data from 72 species of Dipterans.

The field of genetics of bird migration advances, driven by exponential refinements of sequencing and tracking technologies. In willow warblers (Phylloscopus trochilus), a complex repeat-rich region named MARB (Migration Associated Repeat Block) has recently been found to correlate with the routes taken by individual birds from Europe to their African wintering grounds. However, the genomic location of this region remains unknown. Here, we characterized MARB using a combination of approaches to understand how it evolved. We describe the region using long-read genome assemblies of two willow warbler subspecies (P. t. trochilus and P. t. acredula), two related species, the common chiffchaff (P. collybita) and the greenish warbler (P. trochiloides), and whole genome sequencing data from 76 willow warblers. Finally, we applied karyotyping and fluorescent in situ hybridization techniques on willow warbler spermatocytes to cytogenetically locate MARB. Due to the many repeats, we cannot order scaffolds in silico, but probe hybridization on the karyotype shows that MARB constitutes a single locus (~27.5 Mb) spanning most of the 11th largest chromosome in the willow warbler genome. Interestingly, the MARB regions of all species share several characteristics such as relatively high GC content (50%), a high density of specific repeat families and notably, more than 800 olfactory receptor sequences. Regions homologous to MARB may exist in several migrant bird genomes, though currently unassembled due to their complexity. Resolving these in species with similar migratory polymorphisms to willow warblers will be essential to determine whether MARB influences migratory behaviour across species.

Sexual selection arises from individual differences in reproductive success, which can drive the maintenance of genetic polymorphisms in genes subject to balancing selection by the pleiotropic effects that trade-off between survival and reproduction. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored on genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and detected genomic regions affected by introgression. Regions with signatures of selection from multiple statistics were located on eleven chromosomes. In particular, a region spanning 4.25 to 6.80 Mb on chromosome 18 showed high genetic diversity that could not be explained by sex differentiation or introgression from O. latipes in Eastern Japan. This pattern suggests that balancing selection maintains genetic polymorphisms in O. sakaizumii. Specifically, because a previously reported quantitative trait locus associated with female mating behavior overlaps with this region, we infer that sexual selection contributes to the maintenance of genetic polymorphism at this locus.

Immunoglobulin genes are a central component of jawed-vertebrate adaptive immunity. A previous study showed that the blunt-snouted clingfish Gouania willdenowi lacks immunoglobulin genes and T-cell receptor gamma/delta loci, while retaining T-cell receptor alpha/beta genes, MHC genes, and RAG1 /RAG2. Here I extend that observation to the family Gobiesocidae using all seven chromosome-level Gobiesocidae genome assemblies currently available. Manual tblastn and synteny-guided searches found no convincing immunoglobulin heavy-chain or light-chain loci in G. willdenowi, Gouania pigra, Gobiesox punctulatus, Apletodon dentatus, Lepadogaster candolii, Lepadogaster purpurea, or Diplecogaster bimaculata. Thus, the absence of antibody genes is best interpreted as a root-level character of clingfishes. The latest seven-species screen of 40 additional immune-associated genes shifts the broader interpretation in the same direction: the B-cell/adaptive core genes CD79A, CD79B, CIITA, TNFRSF13B, and TNFSF13B lack strong tblastn support in all sampled Gobiesocidae, and 37 of the 40 tested targets show an all-zero binary pattern at the presence threshold. Only IL21R.1, TYROBP, and TNFRSF11A show strong hits in one or more species. I therefore interpret the principal immune-gene erosion as occurring at or near the Gobiesocidae root rather than as a recent Gouania-specific process, while keeping weak, paralog-sensitive, and patchy loci provisional. RAG2 comparisons show a shared Gobiesocidae PHD-domain C-to-S replacement in the zinc-binding motif, with apparently intact RAG2 coding sequence. A family-wide TRG/TRD screen did not recover TRGV V segments or accepted TRDC constant-region exons, but it did detect TRGC-like constant exons in several genomes. These TRGC-like sequences are probably not canonical TRG constant exons without further validation, so I treat the gamma/delta system as eroded or rearranged rather than as a complete root-level loss equivalent to the Ig loss. The RAG2 variant provides a plausible molecular context for antigen-receptor remodeling, but it is not evidence that RAG genes are pseudogenized, because TCR alpha/beta, MHC genes, and RAG1 /RAG2 are retained. Gobiesocidae are therefore best described as a vertebrate family with ancestral loss of canonical immunoglobulin genes and associated root-level erosion of B-cell and immune-related genes, not as a lineage lacking adaptive immunity in its entirety. HighlightsO_LISeven chromosome-level Gobiesocidae genomes lack convincing canonical IgH and IgL loci. C_LIO_LIThe strongest non-Ig losses map to the B-cell/adaptive core: CD79A, CD79B, CIITA, TNFRSF13B, and TNFSF13B. C_LIO_LITCR alpha/beta, MHC genes, and RAG1 /RAG2 are retained, so Gobiesocidae should not be described as lacking adaptive immunity in full. C_LIO_LIA shared Gobiesocidae RAG2 PHD-domain C-to-S variant provides candidate molecular context for antigen-receptor remodeling. C_LI

Recent advances in genome imputation have enabled the application of state-of-the-art statistical methods--originally developed for present-day genomes--to ancient genomes. One class of such methods, known as local ancestry inference (LAI), can model an individuals genome as a mosaic of tracts assigned to different putative ancestral sources, revealing patterns of genetic ancestry across the genome. However, most LAI methods have been designed to study recent admixture events in human history, and they generally assume large panels of present-day genomes. Despite the recent availability of high-quality imputed ancient genomes, it remains unknown to what degree LAI inference is reliable for such datasets. Ancient DNA is often characterized by heterogeneous geographic and temporal sampling, varying degrees of divergence between ancient source proxies and admixing populations, and complex demographic histories. Here, we performed an extensive set of population genetic simulations to evaluate the accuracy of four popular LAI methods-RFMix, FLARE, MOSAIC and simpLAI-under different demographic scenarios, various temporal sampling schemes, sample sizes, and admixture dates. We quantify the accuracy of these methods as a function of different parameters in practically relevant scenarios, and provide general guidelines for future studies utilizing LAI in ancient DNA research.

Recent studies have reported consistent inter-population differences in GC content at polymorphic sites in multiple species, including humans. Specifically, populations that experienced recent bottlenecks exhibit lower average GC content (GC%) at common polymorphic sites compared to non-bottlenecked groups--an observation previously interpreted as indication of rapid evolution of base composition. In this study, we investigate the evolutionary and technical factors driving these patterns across humans, mice, maize, and silkworm. We find that GC% at polymorphic sites is highly sensitive to the allele frequency threshold applied. Relaxing this threshold reduces inter-population differences to negligible levels in humans and significantly attenuates similar signals in other species. We further observe substantial GC% variation across allele frequency bins, a pattern driven by the differential abundance of different mutation types. We demonstrate that these observations are collectively driven by an interaction between demographic history and a universal excess of strong-to-weak mutations relative to weak-to-strong mutations, which is counteracted by GC-biased gene conversion (gBGC) over long evolutionary timescales. Forward-in-time simulations with realistic parameters recapitulate observed patterns of GC% variation across both populations and allele frequency bins. Overall, our findings reveal that the base composition at polymorphic sites is strongly shaped by the interaction between demographic history, mutation bias, and gBGC, and does not represent stable, genome-wide trends. Consequently, inter-population differences in GC content--especially at common variants--should not be interpreted as evidence of ongoing divergence in base composition or shifts in mutation patterns.

Fungal genomics has expanded rapidly over the past 30 years, and recently the pace and breath has further quickened for many taxa, although many taxonomic gaps persist. With three decades of rapid growth, fungal genomics now merits a re-examination of its history, progress, and unresolved taxonomic gaps. Here, we review the development of fungal genomics from early efforts such as the Fungal Genome Initiative to current progress driven by third-generation long-read sequencing. We have compiled and summarised publicly available fungal genomes to highlight trends in assembly quality, adoption of long-read technologies, and taxonomic representation. Notably, substantial phylogenetic gaps remain, particularly outside Dikarya, and significant challenges persist for unculturable taxa. This review identifies priorities for the fungal community, including: (1) coordinated efforts to close major taxonomic gaps across the fungal tree of life; (2) improved repository metrics to facilitate identification of high-quality assemblies; and (3) improved and standardised genome annotation which is lacking for most assemblies. Together, these steps will support the development of reliable genomic resources that capture the full breadth of diversity across the fungal kingdom, generating foundational data for comparative genomics, evolutionary biology, functional studies, genetic studies and applied research.

Arthropods exhibit an exceptional diversity of life histories, where developmental modes involve moulting stage progressions with changes ranging from the bare minimal to the dramatically transformative. While this variability drives many research questions aiming to understand evolutionary and developmental underpinnings of life history differences, it can complicate comparative analyses across taxa. However, this can be approached by applying a framework that defines metamorphosis as a post-embryonic stage progression characterised by substantial changes in morphology and adaptive landscape. Employing this framework with a phylogenomic dataset spanning 26 orders and encompassing four independently arising metamorphic lineages, we explore gene repertoire evolutionary dynamics potentially associated with metamorphosis in Pancrustacea. The approach contrasts gene family evolutionary dynamics inferred to have occurred in the last common ancestors of the metamorphic Insecta, Copepoda, Eucarida, and Thecostraca, with those of their sister lineages, as well as of descendent and ancestral nodes. The results reveal that the metamorphosis ancestors are characterised by an elevated number of gene family births and expansions. Expanded gene families share a set of commonly enriched biological processes across all metamorphosis ancestors, suggesting functional convergence by independent evolution of distinct gene families involved in embryonic and post-embryonic development and nervous system differentiation. Evolutionary modelling further highlights a subset of these families exhibiting signatures of adaptive, lineage-specific gene family size increases associated with metamorphic development. These families include genes implicated in neural and sensory development, segmentation, and moulting. These findings support a model of the evolution of pancrustacean metamorphosis where distinct gene families from a common functional toolkit expand and are co-opted into facilitating transitions to multi-phasic life cycles. This reframes the role of moulting in arthropod diversification to be recognised as an important reservoir of genetic change that can potentiate truly remarkable life history transitions.

To preserve homeostasis in the face of continual chemical insult, animals evolved dedicated molecular systems that detect, detoxify, and eliminate foreign compounds. Collectively, these enzymes, transporters, and regulatory pathways constitute the chemical defensome. In cetaceans, the loss of two key nuclear receptors (NR1I2/PXR and NR1I3/CAR) suggests a profound rearrangement of the chemical defense systems. Therefore, we investigated the gene inventory of the chemical defensome in Cetacea and two other major marine mammal lineages (Pinnipedia and Sirenia), using their closest terrestrial relatives to understand the extent and patterns of chemical defensome remodelling. We demonstrate large-scale gene loss in chemical defensome genes of cetaceans, as well as smaller scale gene loss in the other two marine mammal lineages, indicating possible convergent evolution. Gene loss occurred predominantly in phase I and phase II biotransformation enzymes, including CYPs, FMOs, SULTs, and GSTs. Many of the lost genes in cetaceans are known to be regulated by PXR and/or CAR, while genes lost in multiple marine mammal lineages are often not regulated by these transcription factors. We hypothesize that the transition to aquatic environments, often accompanied by corresponding changes in feeding habits, led to convergent loss of chemical defensome genes, and loss of PXR and CAR in cetaceans accelerated these losses. These findings reveal systematic erosion of chemical defense capabilities across marine mammal lineages, suggesting that adaptation to marine life involves trade-offs in detoxification capacity that may have significant implications for these species responses to increasing chemical pollution in present-day ocean environments.

Holcosus orcesi, the Orces Blue Whiptail, is a Critically Endangered lizard endemic to the upper Jubones River basin in southern Ecuador. Restricted to a narrow elevational range within semi-arid Andean shrublands, it represents one of the few montane members of a predominantly lowland lineage. Here we present the first high-quality reference genome for H. orcesi, generated using Oxford Nanopore Technologies long-read sequencing. The assembly spans 1.68 Gb across only 91 contigs, with an N50 of 76.2 Mb and a BUSCO completeness of 96.8%, making it among the most contiguous and complete squamate genomes to date. Structural annotation predicted 25,682 genes, of which 85% showed homology to known proteins and 45% were assigned Gene Ontology terms. Repetitive elements accounted for 46.3% of the genome, with LINEs representing the predominant class. This genome provides a foundational resource for future evolutionary, comparative and conservation-genomic research of H. orcesi and other mountain reptiles, enabling studies of population genomics, local adaptation, and genomic erosion in isolated populations. By expanding the genomic representation of tropical montane reptiles, this work helps address longstanding phylogenetic and geographic gaps in global biodiversity genomics and provides a foundation for evidence-based conservation of H. orcesi and related taxa.

Mosquitoes are classified into two subfamilies, each monophyletic, and typically considered to both be ancient, having diverged more than 100 million years ago based on previous divergence analyses. A recent publication challenged this view with phylogenomic results primarily from the third codon position and UCEs. Utilizing alternative fossil placement and these phylogenomic data, these authors find that the Culicidae and Chaoboridae diverged in the lower Cretaceous, and that one mosquito subfamily, the Anophelinae, is nested within the Culicinae. These results are in stark contrast to previous results from diverse data sources, ranging from other genomic data, to morphology, to fossils. Here, we briefly detail the substantial evidence that supports two monophyletic subfamilies of extant mosquitoes, along with fossil evidence that supports the ancient divergence of these lineages.

There are some disputed hypotheses for the recurrent observations of insular gigantism and dwarfism, like the island rule: small organisms would become larger on islands, while large organisms would become smaller. But, why is the latter? In addition, not all the observations fit this rule. Here I propose a causal model. Following the Island Biogeography Theory (IBT), insular aspects influence the census N. Observations suggest that variation in N is associated with variation in effective population size (Ne). The body size of insular colonisers might change, following Damuths law, as Ne can decrease at a differential rate from the island area A, resulting in a distinctive effective density [Formula]. Interestingly, a prediction of the drift-barrier hypothesis is that Ne is affecting mutation rates. Consequently, body mass, genome size and {micro} may be predicted to some extent by island area, as they are influenced by De and Ne. Falsification of the latter hypothesis is feasible by determining changes in genomic features of insular species. We now have the opportunity to interrogate the extensive data available. Here I ask: (i) How is decreasing island area predicting average body sizes? (ii) To which levels does this prediction apply (species, cells, genomes)? (iii) How well does the model fare on predicting {micro} over paradigmatic case studies? The resolution of these questions may provide a more reliable diagnosis of the evolutionary causes for somatic size variation. Significance statementNaturalists have long reported that insular species tend to become unusually large or small compared to their mainland relatives. Despite the familiarity of this "island rule", there is still no broad mechanistic explanation for why these changes occur so consistently across different groups of organisms. This work proposes that an important neutral factor can be the change in effective density of isolated populations. By combining the expectations of Damuths law, the IBT model, and the nearly-neutral theory it offers unified predictions on how sudden constraints in island area can influence not only the evolution of body size, but also the direction of changes in genome size and evolutionary rates.

Pattersons D statistic, also known as the ABBA-BABA statistic, is widely used to detect the presence of archaic genome-wide introgression between two non-sister taxa. Requiring only a single lineage from each of four taxa where one taxon acts as an outgroup to determine the ancestral allele, Pattersons D, counts the imbalance between the number of biallelic sites where either the second and third taxa (ABAB site) or the first and third taxa (BABA site). When there is no introgression, these counts are expected to be equal, and a discordance between counts suggests introgression from the third taxon into either the first or second. Pattersons D is limited to the detection of genome-wide introgression and exhibits a high false-positive rate when applied to smaller genomic segments. Here, we present a new method, D STatistic with Allelic Rarefaction (D*), to address these limitations. D* uses multiple lineages and does not require an outgroup to calculate the imbalance between the number of alleles found exclusively in the second and third taxa and the number of alleles found exclusively in the first and third taxa. D* employs a rarefaction technique to correct for unequal sample-size and allows multiallelic sites. We use simulations to show that D* has better precision and recall for detecting introgressed segments of DNA when compared to similar methods under a wide variety of model parameters and in the presence of technical artifacts common to ancient DNA analyses. We conclude with an analysis of Denisovan DNA introgression in modern day Papuans. Precompiled executables, the manual, and source code can be found at https://github.com/TQ-Smith/DSTAR

Protein evolutionary rates vary widely across proteins and among sites within proteins, reflecting multiple molecular, cellular, and functional constraints. While protein-level properties, such as expression and essentiality, and site-level structural and functional constraints, are known to influence evolutionary rates, how these constraints combine across scales to determine site-specific evolutionary rates remains unclear. Moreover, because many protein features are strongly correlated, it is difficult to disentangle their individual contributions to evolutionary rate variance, and unified predictive models that integrate these properties are still lacking. Here, we use neural networks to predict protein evolutionary rates across multiple scales based on multiple molecular and cellular features. At the protein level, integrating molecular and cellular descriptors explains substantial variance in evolutionary rates across proteins in multiple eukaryotic species, including nearly 50% of the variance in humans and substantial fractions of the variance in other eukaryotic species. The model also allows us to identify proteins whose evolutionary rates deviate from expectations based on their molecular and cellular properties. At the site level, we found that structural and functional features explain a comparable fraction of the variance in relative evolutionary rates. By integrating protein-level and site-level predictors, the model explains up to 37% of the variance in site-specific evolutionary rates across proteins. Our analysis demonstrates that constraints at these two scales combine largely additively, with protein-level properties setting the overall evolutionary context and site-level properties shaping variation within proteins. Together, these results provide a quantitative framework for understanding protein evolution across biological scales.

Whole genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects. The resulting morphological, physiological, and fitness consequences and how they affect the survival probability of newly polyploid lineages are intensively studied, but very little is known about the effect of genome doubling on the short-term evolvability of populations. Understanding the effect of polyploidization on the adaptive potential of populations is of crucial importance to predict the future of polyploid populations. In this paper, I investigate the immediate consequences of genome doubling on the genetic variance of populations. To do so, I performed numerical iterations and simulations of how the genetic variance of a quantitative trait changes after polyploidization, under different genetic architectures (additivity, dominance, and epistasis). I found that genetic variance generally decreases after genome doubling. Non-additive gene actions can make autotetraploid populations genetically more diverse than their diploid progenitors in rare cases, notably with overdominance and directional epistasis. By collecting estimates from the agronomic literature, I found that both dominance and epistatic variance contribute to the genetic variance of polyploid populations. These results bring new insights into the adaptive potential of newly formed tetraploid populations, and call for further experimental investigations of how polyploidization is associated with a short-term decrease in evolvability.

Parasites are ubiquitous drivers of host evolution by exerting strong selective pressure on natural populations. Understanding the genetic basis of host susceptibility to infection is important to know how host-pathogen interactions shape patterns of resistance and diversity in natural populations. We conducted a genome-wide association study (GWAS) to identify host genetic variants associated with infection by helminth and blood pathogens in spatially structured populations of Bank voles (Myodes glareolus; (Schreber, 1780). We genotyped 182 individuals sampled from ten sites in central Europe using quaddRAD sequencing, retaining 30,206 high-quality single-nucleotide polymorphisms (SNPs). Associations between SNP genotypes and parasite infection status were tested using mixed models controlling for relatedness, with host body mass included as a covariate. Across parasite taxa, we identified twelve SNPs exceeding genome-wide significance with the strongest signals detected for the intestinal nematode Heligmosomum mixtum. The variants identified are all intergenic, intronic, upstream or downstream of genes, with none predicted to alter coding sequences. These genes are not classical immunity genes but some are implicated in cytokine production, PI3K/AKT signalling and p38 MAPK pathway, suggesting that selective pressure from pathogens does not only act on known immunity genes, but on broader regulatory and metabolic networks. This finding suggests that variation in gene expression may be important for the differences in host susceptibility or resistance to parasitic infections.

The pea aphid (Acyrthosiphon pisum) is an important model organism for studying complex biological traits, including wing polyphenism and host-symbiont interactions, yet its regulatory genomic landscape remains largely uncharacterized. Here we present the first genome-wide chromatin accessibility map of the pea aphid, generated using the assay for transposase-accessible chromatin followed by sequencing (ATAC-seq). We profiled open chromatin regions (OCRs) in adult brains and late-stage embryos from winged and wingless morphs maintained under solitary or crowded conditions. We also paired ATAC-seq with RNA-seq in embryonic samples to examine the relationship between chromatin accessibility and gene expression. Libraries showed a high abundance of reads from the aphid endosymbionts Spiroplasma and Buchnera, reflecting preferential Tn5 transposase insertion into nucleosome-free bacterial DNA. After computational removal of these reads, the remaining aphid-mapping libraries displayed hallmarks of high-quality ATAC-seq data. We identified a consensus set of 37,127 OCRs enriched at promoters and distal regulatory elements, with substantial overlap with computationally predicted enhancers and enrichment for transcription factor binding motifs. Tissue identity was the dominant driver of chromatin variation, accounting for 85% of variance along the first principal component, with 19,513 differentially accessible regions distinguishing brain from embryo samples. By contrast, differences associated with wing morph or crowding treatment were modest. Promoter accessibility was significantly and positively correlated with gene expression genome-wide. Together, these data constitute a foundational regulatory genomics resource for the pea aphid and establish a framework for mechanistic studies of gene regulation in this ecologically and economically important insect.