Biology subjects

Frandsen, P. B.

Publications and source records attributed to Frandsen, P. B..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparative genome analyses suggest a common blueprint for obligate endoparasitism in Strepsiptera

The twisted-wing parasites (order Strepsiptera) are well-known for their unusual life histories as obligate endoparasites of a wide variety of other insect orders. Here, we present the first high-quality genome assembly of a leafhopper-parasitizing strepsipteran species. We sequenced the genome of Elenchus koebelei using PacBio HiFi technology, yielding a primary assembly of 63.7Mb in 96 contigs, with an N50 of 1.60Mb and a BUSCO completeness score of 82.3%. In total, we recovered 8,167 protein-coding gene annotations, and 34.2% of the genome annotated as repeats. For the first time, we compare the genome content of three strepsipteran species and find that they are remarkably consistent in broad structure, with approximately 600 insect universal single-copy orthologs that appear to be completely missing from the order. These similarities imply a conserved genomic blueprint for strepsipteran parasitic strategy and/or differences that must be investigated at the post-translational level.

genomics↗

bioRxiv2026

Genomics and CT imaging reveal diversity in silk genes and gland morphology of webspinners

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

evolutionary biology↗

bioRxiv2026

Satellite DNA dynamics across phylogenetic scales in ground beetles and other insects

Satellite DNAs (satDNAs) are tandemly repeated sequences that can comprise large fractions of eukaryotic genomes. For decades, we have known that satellite DNAs are among the most rapidly evolving genomic components, yet few studies have examined their dynamics across broad evolutionary frameworks--likely in part because their rapid evolution complicates or precludes homology identification. We investigated satDNA dynamics across 50 ground beetle (Carabidae) species, sampling above and below the species level in the subgenus Plataphus of Bembidion. We used RepeatExplorer2 and a novel homology detection pipeline, which we validated using species of Drosophila for which satDNAs are well-documented, to study satDNA dynamics in a comparative framework. We show that satDNAs comprise large genomic fractions (mean = 25.7%, range = 3.2%-53%), with individual satDNA motifs accounting for >30% of total DNA within some species. We quantify major satDNA turnover among closely related species which drives extensive repatterning of repeat content over short evolutionary scales. To place our findings in a broader context, we also surveyed satDNA diversity across the beetle suborder (Adephaga), the beetle order (Coleoptera), and the next six largest insect orders (Lepidoptera, Diptera, Hymenoptera, Hemiptera, Orthoptera, Trichoptera), representing 400 additional species. While satDNA abundance was significantly elevated in the focal subgenus (Plataphus), high genomic proportions were also found in species across Adephaga, Coleoptera, Hymenoptera, and Diptera. Conversely, satDNA proportions were notably reduced in Lepidoptera and Trichoptera. Our investigation of satDNA dynamics at narrow and broad taxonomic scales provides a quantitative illustration of satDNA turnover across a well-sampled clade. It also identifies new high-potential systems for gaining mechanistic insights into the drivers and impacts of satDNA evolution, and raises questions regarding potential links between satDNA turnover, speciation, and core strategies of chromosome and genome architecture in diverse clades.

evolutionary biology↗

bioRxiv2025

Comparative genomic analyses of trans-ithmanian reef fishes reveals different molecular targets of environmental adaptation in different families.

The extent to which selection acts upon the same molecular targets when faced with the same environmental changes has important implications for our understanding of the repeatability and predictability of evolutionary processes. Replicated natural experiments are well positioned to provide insight, however often these involve closely related species or populations of the same species. Given that the similarity of genetic background makes the same molecular change more likely, it is essential to evaluate the extent to which molecular parallelism occurs in more distantly related species. The rise of the Isthmus of Panama presents an ideal natural experiment to investigate the prevalence of parallel molecular changes in distantly related lineages exposed to the same environmental regimes of temperature, salinity and primary productivity in the two newly formed oceans. Here, we generate high-quality reference genomes for two replicate pairs of geminate reef fishes, one in the family Pomacentridae and one in the Serranidae. Comparative analyses of positive selection in protein-coding genes and of gene family evolution revealed multiple signals of potentially adaptive divergence between geminate species in response to environmental regime. Common targets of selection between families included MAPK signalling (MAP3K10), solute transport (SLC46A2) and reproduction (ZPL3L), as well as expansions in immune and MAPK related gene families. Overall, however, we found minimal evidence of parallelism between families either at the gene level or when considering higher functional categories. Our findings suggest that phylogenetic constraints may limit the levels of molecular parallelism in distant lineages even when faced with comparable selective pressures. Significance StatementUnderstanding the extent to which species exposed to similar environmental conditions may adapt using similar genetic solutions has important implications for our understanding of evolutionary processes and how we may expect species to adapt in the future. However, systems where multiple, independent lineages are faced with the same shift in conditions are rare. The rise of the Isthmus of Panama provides a unique, natural experiment where multiple marine species have been divided and exposed to radically different environmental conditions. Here, we generate genomes for separated species in two distantly related families of reef fishes and compare genome-wide patterns of divergence. Our analyses identified signals of selection in protein-coding genes and shifts in gene family size consistent with adaptation to the distinct environments, however the specific genes and pathways involved predominantly differed between the families, revealing that, even under shared selective pressures, molecular mechanisms may differ across more distant lineages.

evolutionary biology↗

bioRxiv2025

WntA expression and wing transcriptomics illuminate the evolution of stripe patterns in skipper butterflies

Skippers (Hesperiidae) form a distinct lineage of butterflies where the developmental mechanisms of color patterning have seldom been studied. The wing patterns of skippers often consist of median stripes, and classic comparative morphology studies suggest these elements are homologous to the Central Symmetry System (CSS) found in nymphalid butterflies. Consistent with this hypothesis, we show here that expression of the signaling ligand gene WntA, a marker of the CSS in nymphalids, prefigures the position of the main wing patterns of the silver-spotted skipper Epargyreus clarus. Notably, WntA expression is associated with different color outputs in the forewing vs. hindwing, validating a theory of pattern homology from the mid-twentieth century. To further gain insights into the genes associated with this patterning process, we generated an annotated genome for E. clarus and performed an RNAseq study profiling gene expression along the proximo-distal (P-D) axis of early pupal wings. These data suggest that the transcription factor genes lobe, u-shaped, and odd-paired are expressed in restricted P-D sections of the wing similarly to WntA, indicating they may participate in the patterning of the CSS. In addition, inverted expression patterns of dachsous and four-jointed, as well as the expression of transcription factors with roles in specifying proximal (homothorax, tiptop/teashirt) and distal (vestigial, scalloped) section of ths Drosophila wing disk, suggest a deep conservation of wing P-D patterning process between Diptera and Lepidoptera. This work highlights the developmental homology between the CSS of Hesperiidae and Nymphalidae, and enriches our knowledge of patterning mechanisms in lepidopteran wings. Summary StatementThis study reveals how skipper butterfly wing stripes share deep developmental origins with other butterflies, offering fresh insight into wing pattern evolution.

developmental biology↗

bioRxiv2025

Whole genome assembly and annotation of the acorn weevil, Curculio nanulus (Coleoptera: Curculionidae)

The acorn weevil Curculio nanulus (Coleoptera: Curculionidae) is a seed predator that lays its eggs inside developing acorns and hickory nuts in the western United States. The female weevil uses her elongated rostrum to excavate a hole into the seed, creating a protected site for oviposition. Natural history traits among Curculio species--such as host-specificity and variation in larval diapause--suggest a dynamic evolutionary relationship with their host plants. These traits are best studied through a comparative genomic framework, but such analyses cannot currently be undertaken due to the lack of whole genome assemblies for Curculio species. To address this gap, we generated a whole genome assembly for C. nanulus using PacBio HiFi sequencing. The resulting assembly is [~]1.5 Gbp in length, with high contiguity (contig N50 = 7.7 Mbp) and gene completeness (USCO score: 97.46%). To enable comparative analysis, we also assembled the genome of the pecan weevil, Curculio caryae, using publicly available PacBio HiFi reads. For both species, we annotated repetitive elements and protein-coding genes, and compared these features with those of other weevil genomes. Our results reveal a marked expansion of repetitive elements within Curculio and its close relatives. These genomic resources provide a foundation for investigating seed predation, co-speciation, and host-parasite evolutionary dynamics in Curculio and related taxa, as well as their impacts on forest ecology.

genomics↗

bioRxiv2025

First Genomic Insights into an Aeshnidae Dragonfly: Unveiling the Genome of a Holarctic Species, Aeshna juncea

Temperature oscillations in the Arctic may present a unique opportunity to study how insect species respond to such changes. Aeshna juncea, a Holarctic species of the family Aeshnidae thrives in this environment; molecular adaptations that allow it to survive in the Arctic have yet to be evaluated. Here, we present the first assembled and annotated draft genome assembly and annotation of A. juncea. The assembly is both highly contiguous and complete. This resource is presented and used here to provide further evidence that transposons and unclassified repetitive elements are a major driver behind genome size variation in Odonata and show that the effective population size of A. juncea populations from Alaska went through bottlenecks during the most recent ice age. We believe this genome will be an important resource in understanding how species like Aeshna juncea survive in Arctic habitats.

evolutionary biology↗

bioRxiv2025

Selecting a Window Size for the Analysis of Whole Genome Alignments using AIC

AO_SCPLOWBSTRACTC_SCPLOWThe variation of evolutionary histories along the genome presents a challenge for phylogenomic methods to identify the non-recombining regions and reconstruct the phylogenetic tree for each region. To address this problem, many studies used the non-overlapping window approach, often with an arbitrary selection of fixed window sizes that potentially include intra-window recombination events. In this study, we proposed an information theoretic approach to select a window size that best reflects the underlying histories of the alignment. First, we simulated chromosome alignments that reflected the key characteristics of an empirical dataset and found that the AIC is a good predictor of window size accuracy in correctly recovering the tree topologies of the alignment. Due to the issue of missing data in empirical datasets, we then designed a stepwise non-overlapping window approach and applied this method to the genomes of erato-sara Heliconius butterflies and great apes. We found that the best window sizes for the butterflies chromosomes ranged from <125bp to 250bp, which are much shorter than those used in a previous study even though this difference in window size did not significantly change the most common topologies across the genome. On the other hand, the best window sizes for great apes chromosomes ranged from 500bp to 1kb with the proportion of the major topology (grouping human and chimpanzee) falling between 60% and 87%, consistent with previous findings. Additionally, we observed a notable impact of stochastic error and concatenation when using small and large windows, respectively. For instance, the proportion of the major topology for great apes was 50% when using 250bp windows, but reached almost 100% for 64kb windows. In conclusion, our study highlights the challenges associated with selecting a window size in non-overlapping window analyses and proposes the AIC as a more objective way to select the optimal window size for whole genome alignments.

evolutionary biology↗

bioRxiv2025

Gene family evolution reveals dietary adaptations in butterflies and moths

Butterflies and moths (Lepidoptera) are a hyperdiverse lineage of nearly 160,000 described species and their evolutionary success is postulated to be tightly correlated with the radiation of their primary host -- angiosperms. Previous studies found that a significant number of emergent gene families are specific to Lepidoptera, with many genes linked to odorant receptors and peptidases, suggesting that such genetic innovations may be linked to their diversification. Here, we use genomic resources to identify lineage-specific gene families in four nested lepidopteran clades (e.g. Lepidoptera, Glossata, Ditrysia, and Apoditrysia). Among nearly a hundred gene families specific to each group, a handful of gene families have specific and interpretable functions. We found that many digestion-related gene families emerged early in the evolution of Lepidoptera, followed by genes associated with detoxification and immunity. This result aligns with the evolutionary transition in ancient Lepidoptera diets to terrestrial plants, highlighting the emergence of detoxification mechanisms in the megadiverse Ditrysia as a critical adaptation driven by the proliferation of plant chemical defenses. We also found gene families originating from horizontal gene transfer (HGT) events, likely introduced from bacteria and fungi to the common ancestors of Lepidoptera and Ditrysia, respectively. These HGT-derived genes likely played a pivotal role in supporting the dietary transition from algae, diatoms, and aquatic plant debris to fungi and primitive terrestrial plants, ultimately enabling the adaptation to the most dominant angiosperm species.

evolutionary biology↗

bioRxiv2024

Environmental DNA vs. Community Science: Strengths and Limitations for Urban Odonata Surveys

The study of insect decline remains a major frontier in insect biodiversity and conservation. Despite growing concern about accelerating rates of insect decline generally, relatively little data has been compiled about species of aquatic insects. Data is particularly lacking on the distribution of aquatic insects in urban ecosystems. Here, we compare environmental DNA (eDNA) metabarcoding and community science observation as means of monitoring Odonata within an urban system in Southwest Idaho. We show that the distribution of Odonata across this urban landscape is not uniform and that both monitoring methods have different strengths and weaknesses. We found that eDNA metabarcoding was very sensitive to the identification of genera from underrepresented families in the region, but was unable to distinguish between closely related genera, particularly from localities where eDNA could accumulate more damage. On the other hand, community science observations effectively identified the presence of genera from more speciose families but missed the presence of relatively rare species, and those that had a short flight season. These findings suggest that, in our study system, eDNA and community science are highly complementary of each other. In cases where only one method is employed for a monitoring or conservation project, care should be given to account for the biases of each approach.

ecology↗

bioRxiv2024

Elevational and Oceanic Barriers Shape the Distribution, Dispersal and Diversity of Aotearoa's Kapokapowai (Uropetala) Dragonflies

Mountains and islands provide an opportunity for studying the biogeography of diversification and population fragmentation. Aotearoa (New Zealand) is an excellent location to investigate both phenomena due to alpine emergence and oceanic separation. While it would be expected that separation across oceanic and elevation gradients are major barriers to gene flow in animals, including aquatic insects, such hypotheses have not been thoroughly tested in these taxa. By integrating population genomic from sub-genomic Anchored-Hybrid Enrichment sequencing, ecological niche modeling, and morphological analyses from scanning-electron microscopy, we show that tectonic uplift and oceanic vicariance are implicated in speciation and population structure in Kapokapowai (Uropetala) dragonflies. Although Te Moana o Raukawa (Cook Strait), is likely responsible for some of the genetic structure observed, speciation has not yet occurred in populations separated by the strait. We find that the altitudinal gradient across K[a] Tiritiri-o-te-Moana (the Southern Alps) is not impervious but it significantly restricts gene flow between aforementioned species. Our data support the hypothesis of an active colonization of K[a] Tiritiri-o-te-Moana by the ancestral population of Kapokapowai, followed by a recolonization of the lowlands. These findings provide key foundations for the study of lineages endemic to Aotearoa.

evolutionary biology↗

bioRxiv2024

Environment and diet shape the geography-specific Drosophila melanogaster microbiota composition

Geographic and environmental variation in the animal microbiota can be directly linked to the evolution and wild fitness of their hosts but often appears to be disordered. Here, we sought to better understand patterns that underlie wild variation in the microbiota composition of Drosophila melanogaster. First, environmental temperature predicted geographic variation in fly microbial communities better than latitude did. The microbiota also differed between wild flies and their diets, supporting previous conclusions that the fly microbiota is not merely a reflection of diet. Flies feeding on different diets varied significantly in their microbiota composition, and flies sampled from individual apples were exceptionally depauperate for the Lactic Acid Bacteria (LAB), a major bacterial group in wild and laboratory flies. However, flies bore significantly more LAB when sampled from other fruits or compost piles. Follow-up analyses revealed that LAB abundance in the flies uniquely responds to fruit decomposition, whereas other microbiota members better indicate temporal seasonal progression. Finally, we show that diet-dependent variation in the fly microbiota is associated with phenotypic differentiation of fly lines collected in a single orchard. These last findings link covariation between the flies dietary history, microbiota composition, and genetic variation across relatively small (single-orchard) landscapes, reinforcing the critical role that environment-dependent variation in microbiota composition can play in local adaptation and genomic differentiation of a model animal host. SIGNIFICANCE STATEMENTThe microbial communities of animals influence their hosts evolution and wild fitness, but it is hard to predict and explain how the microbiota varies in wild animals. Here, we describe that the microbiota composition of wild Drosophila melanogaster can be ordered by temperature, humidity, geographic distance, diet decomposition, and diet type. We show how these determinants of microbiota variation can help explain lactic acid bacteria (LAB) abundance in the flies, including the rarity of LAB in some previous studies. Finally, we show that wild fly phenotypes segregate with the flies diet and microbiota composition, illuminating links between the microbiota and host evolution. Together, these findings help explain how variation in microbiota compositions can shape an animals life history.

microbiology↗

bioRxiv2024

Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower cellular freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes tandem array structure and consequently poor resolution of these repetitive regions. Here we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B and show that AFP copies expanded under low temperature, but also decreased with depth, which reduces freezing point via pressure. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which Zoarcoidei AFP arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

evolutionary biology↗

bioRxiv2023

Phylogenomics recovers multiple origins of portable case-making in caddisflies (Insecta: Trichoptera), the world's most common underwater architects

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16,000 described species. They play an outsized role in freshwater ecology and environmental engineering in streams, rivers, and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programs. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case-making, have been unanswered due to the lack of a well-resolved phylogenetic tree. To shed light on these questions in Trichoptera, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 206 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with a set of 33 carefully selected fossils. The first caddisflies originated in the Permian and the major suborders began to diversify in the Triassic. Ancestral state reconstruction and diversification analysis revealed that portable case-making evolved in three separate lineages and shifts in diversification occurred in concert with key evolutionary innovations other than case-making.

evolutionary biology↗

bioRxiv2023

Evolution of Opsin Genes in Caddisflies (Insecta: Trichoptera)

Insects have evolved complex and diverse visual systems in which light-sensing protein molecules called opsins couple with a chromophore to form photopigments. Insect photopigments group into three major gene families based on wavelength sensitivity: long wavelength (LW), short wavelength (SW), and ultraviolet wavelength (UV). Here, we identified 123 opsin sequences from whole genome assemblies across 25 caddisfly species (Insecta: Trichoptera). We discovered the LW opsins have the most diversity across species and form two separate clades in the opsin gene tree. Conversely, we observed a loss of the SW opsin in half of the trichopteran species in this study, which might be associated with the fact that caddisflies are active during low-light conditions. Lastly, we found a single copy of the UV opsin in all the species in this study, with one exception: Athripsodes cinereus has two copies of the UV opsin and resides within a clade of caddisflies with colorful wing patterns. SignificanceWhile opsin evolution in some insect groups has been well-characterized, it has never been studied across caddisflies. Our findings provide insight into the diversity of opsins in caddisflies and form a basis for further research into the evolutionary drivers and complex visual systems in Trichoptera.

genomics↗

bioRxiv2023

Newly Sequenced Genomes Reveal Patterns of Gene Family Expansion in select Dragonflies (Odonata: Anisoptera)

Gene family evolution plays a key role in shaping patterns of biodiversity across the tree of life. In Insecta, adaptive gene family turnover has broadly been tied to vision, diet, pesticide resistance, immune response and survival in extreme environments. Patterns of gene family evolution are of particular interest in Odonata (dragonflies and damselflies), which represents the first lineage to fly, and one of the most exceptional groups of predators. Previous work in Odonata found expansions of opsin genes are correlated with the diversification of the herbivorous insects that Odonata prey upon, but general trends in gene family turnover has not been studied in this order. Here, we show that two families of suborder Anisoptera (dragonflies), Libellulidae and Petaluridae, have expanded gene repertoire related to their unique life history and diversification patterns. These results are an important step towards understanding why Libellulidae is, generally, a species rich family of short lived species that are highly tolerant to poor water quality, while Petaluridae is a species poor family of habitat and behavioral specialists. Specifically, Libellulidae share expanded gene families related to immune response, desiccation response, and processing of free radicals, which all potentially enable many Libellulidae to inhabit low quality water bodies. Likewise, Petaluridae show unique patterns of gene turnover in gene families implicated in sensory perception, which could be tied to the unique semi-terrestrial lifestyle of the nymphs of this family. Furthermore, Odonata as a whole has a gene gene turnover rate that is an order of magnitude smaller than other studied insect orders, potentially contributing to the relatively low species diversity in the order Odonata compared to other insects. These results offer important hypotheses for the consideration of evolutionary drivers across Insecta.

evolutionary biology↗

bioRxiv2023

New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)

Nearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.

evolutionary biology↗

bioRxiv2022

Uncovering hidden genetic diversity: allelic resolution of insect and spider silk genes

Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we show that there is extensive variation--both in terms of length and repeat motif order--between alleles of silk genes within individual arthropods. Further, this variation exists across two deep, independent origins of silk which diverged more than 500 million years ago--(1) the insect clade containing caddisflies and butterflies and (2) spiders. This remarkable convergence in previously overlooked patterns of allelic variation across multiple origins of silk suggests mechanisms for the generation and maintenance of structural protein-coding genes. Future genomic efforts to connect genotypes to phenotypes should account for such allelic variation.

genomics↗