bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.04.12.536482

Venomous Noodles: evolution of toxins in Nemertea through positive selection and gene duplication

Sonoda, G. G.·Tobaruela, E. C.·Norenburg, J. L.·Fabi, J. P.·Andrade, S. C. S.
View original source ↗Export metadata ↓

Abstract

Some, probably most and perhaps all, members of the phylum Nemertea are venomous, documented so far from marine and benthic specimens. Although the toxicity of these animals has been long known, systematic studies on characterization of toxins, mechanisms of toxicity and toxin evolution for this group are relatively scarce compared to other venomous groups. Here we present the first investigation of the molecular evolution of toxins in Nemertea. Using a proteo-transcriptomic approach, we described toxins in the body and poisonous mucus of the pilidiophoran Lineus sanguineus and the hoplonemertean Nemertopsis pamelaroeae. Using these new and publicly available transcriptomes, we investigated the molecular evolution of six selected toxin gene families. In addition, we have also characterized in silico the toxin genes found in the interstitial hoplonemertean, Ototyphlonemertes erneba, a first record for meiofaunal taxa. We identified 99 toxin transcripts in the pilidiophoran L. sanguineus, including previously known toxins, such as the alpha-nemertides and the Cytotoxins-A. However, for each of the hoplonemerteans, no more than 30 toxin transcripts were found. Genomic alignments and tree reconciliation methods supported the occurrence of at least one gene duplication in each analyzed toxin gene. Evidence of positive selection was observed in all investigated toxin genes. We hypothesized that an increased rate of gene duplications observed for Pilidiophora could be involved with the origin and expansion of toxin genes. Studies concerning the natural history of Nemertea are still needed to understand the evolution of their toxins. Nevertheless, our results show evolutionary mechanisms similar to those observed in other venomous groups.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sonoda, G. G., Tobaruela, E. C., Norenburg, J. L., Fabi, J. P., Andrade, S. C. S.. 2023-04-13. Venomous Noodles: evolution of toxins in Nemertea through positive selection and gene duplication. https://doi.org/10.1101/2023.04.12.536482

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ocean current models predict spatial structure for coastal biodiversity

Genomic diversity provides the raw material through which all evolutionary processes occur. Accurately describing how environmental features affect patterns of diversity shows promise in predicting the resilience of populations and entire communities to dynamic environments and novel stressors. Identifying the contribution of purely neutral responses to environmental effects can be difficult, especially across large spatial ranges with many covarying environmental features. Using an individual-based model of larvae carried by ocean currents, we predict patterns of neutral genomic diversity in a passively dispersed coastal species, suggesting large geographic regions of relative homogeneity with ancestry determined by the nearest "upstream" population with limited larval input. The genomic identity that dominates each region sharply transitions at the next such interruption, generating hierarchical structure and violating assumptions of isolation-by-distance. We call these upstream populations "lineage source regions" (LSRs), and we find strong concordance between LSR model predictions and an empirical population genomic survey of a keystone salt marsh mussel (Geukensia demissa). We quantitatively validate model performance and goodness-of-fit, updating baseline predictions of genomic diversity patterns from the classic isolation-by-distance model to this LSR framework. This spatially explicit coastal ancestry model has potential for generalization across passive dispersing species.

evolutionary biology↗
bioRxiv2026

Shared landscape, divergent genomes: Comparative population genomics of co-occurring flora in an isolated Australian mountain range

Understanding how landscape heterogeneity shapes genomic variation is key to conserving biodiversity and evolutionary potential. Yet conservation genomics is typically conducted at the single species level, limiting our ability to identify shared genomic patterns or understand how co-occurring taxa differ in their response to common environmental gradients. We assessed spatial patterns of genomic variation and their associations with geographic and environmental features among populations of nine co-existing plant species with contrasting life-histories and ecological traits across Gariwerd, a threatened biodiversity hotspot in south-eastern Australia. All species exhibited weak overall genetic structure, although the magnitude and spatial distribution of differentiation varied among species. Despite this variation, broadly consistent spatial trends were apparent, with higher genomic divergence largely concentrated in central zones and higher genomic diversity localised in southern regions of the landscape. Significant associations between genetic differentiation and geographic distance were observed in three species, while another species showed associations with environmental distance. These findings demonstrate that coexisting species can show overlapping spatial patterns in genomic variation while differing markedly in their associations with geographic and environmental variation across the same landscape. This comparative approach provides a basis for spatial prioritisation and conservation planning, while highlighting the complex eco-evolutionary processes operating across heterogeneous landscapes.

evolutionary biology↗
bioRxiv2026

BryoCAD: Extending Plant DNA Foundation Models Beyond Flowering Plants

Bryophytes exhibit diverse genome architectures and gene repertoires, yet their functional interpretation remains constrained by incomplete genomic annotations and limited experimental resources. Although DNA foundation models offer promising solutions, their applicability to evolutionarily divergent bryophytes remains largely unexplored. Here, we introduce BryoCAD, a DNA language model developed through continued pre-training of the angiosperm-specific PlantCAD2 model on 17 bryophyte genomes spanning hornworts, liverworts, and mosses. Across three representative bryophyte genomes and four gene-boundary motif recovery tasks, BryoCAD-Small improved mean zero-shot accuracy from 45.7% to 57.0%, a 24.8% relative increase over PlantCAD2-Small, while the over 200-fold larger Evo2-20B achieved a mean accuracy of only 39.3%. Remarkably, BryoCAD-Small outperformed PlantCAD2-Large in 11 of 12 motif-recovery comparisons across the three bryophytes, highlighting the benefits of lineage-specific adaptation over model scaling alone. These improvements extended to all six tested algal species, increasing mean accuracy from 26.3% to 37.5%, although performance varied across ferns and gymnosperms. BryoCAD also enhanced gene structure annotation: replacing PlantCAD2-Small with BryoCAD-Small increased transcript-level F1 scores from 0.578 to 0.625 in Marchantia polymorpha and from 0.485 to 0.530 in Physcomitrium patens. Together, our findings demonstrate that lineage-specific continued pre-training enhances genomic sequence interpretation and gene annotation across bryophytes, providing a transferable framework for extending DNA foundation models to evolutionarily diverse, understudied plant lineages.

evolutionary biology↗