Periodic Reporting for period 1 - EVER (Evolution of VEnom Regulation)
Reporting period: 2019-07-01 to 2022-06-30
Animal venoms are complex secretions composed mostly by proteins and peptides that are used to subdue prey and predators. To produce this potent biochemical weapon, venomous animals possess specialized secretory glands which have evolved independently in the various animal lineages. How these glands evolved the ability to secrete venom remain mostly unknown. The project EVER investigated the genetic basis underlying the evolution of venom glands using a hierarchical approach.
First, we used publicly available datasets to perform large-scale comparative analyses of venom gland transcriptomes across multiple taxa. We found incredible similarities of global gene expression profiles among distantly related taxa, revealing that many animals have independently adopted similar molecular solutions to perform the same function.
In the second part of the project, we studied a group of marine snails, including the venomous cone snails. We compared gene expression across multiple tissues to shed light on the dynamics that led the venom gland to evolve from similar glands, with distinct physiological functions. We discovered that the ancestral venom gland used to have digestive functions, which other organs later took over, allowing the gland to specialise in producing toxins. This shift led to rapid changes in gene expression not just in the venom gland but throughout the digestive system, as these organs evolved together. On a molecular level, this functional divergence happened through the creation and duplication of genes and changes in the expression of already existing genes.
Finally, we closely studied the venom gland of cone snails using advanced imaging techniques. We found that different regions of the venom gland have varied gene expression profiles and tissue structures. This suggests that the venom gland evolved to work like an assembly line, with specific areas dedicated to making, processing, and secreting toxins.
First, we used publicly available datasets to perform large-scale comparative analyses of venom gland transcriptomes across multiple taxa. We found incredible similarities of global gene expression profiles among distantly related taxa, revealing that many animals have independently adopted similar molecular solutions to perform the same function.
In the second part of the project, we studied a group of marine snails, including the venomous cone snails. We compared gene expression across multiple tissues to shed light on the dynamics that led the venom gland to evolve from similar glands, with distinct physiological functions. We discovered that the ancestral venom gland used to have digestive functions, which other organs later took over, allowing the gland to specialise in producing toxins. This shift led to rapid changes in gene expression not just in the venom gland but throughout the digestive system, as these organs evolved together. On a molecular level, this functional divergence happened through the creation and duplication of genes and changes in the expression of already existing genes.
Finally, we closely studied the venom gland of cone snails using advanced imaging techniques. We found that different regions of the venom gland have varied gene expression profiles and tissue structures. This suggests that the venom gland evolved to work like an assembly line, with specific areas dedicated to making, processing, and secreting toxins.
The specific work carried out to achieve the objectives of the project is summarized below:
Objective 1: Convergent evolution of venom gland transcriptomes
In the first part of the project, we analysed publicly available gene expression (i.e. RNA-seq) datasets. We selected venomous species with either a well annotated genome or a high-quality transcriptome, and with RNA-seq data of venom glands and other body tissues. This resulted in a total of 109 samples (libraries) from 20 venomous species representing eight different origins of venom: five spiders, two scorpions, one bee, three wasps, one fly, two molluscs, four snakes, one fish, and one mammal. The results of this work have been published in the Proceedings of the National Academy of Sciences and presented as a talk at the European Venom Network (EUVEN) international conference in 2021 and as an invited keynote talk at the Venoms and Toxins in 2022.
Objective 2: Evolution of venom production in cone snails
We investigated the gene expression dynamics of venom glands in cone snails and their homologous oesophageal glands in related non-venomous snail species. To obtain the samples, in 2019 the researcher joined an expedition in New Caledonia organised by the Natural History Museum of Paris. In Kourmac, the researcher, with the assistance of colleagues from Italy and France, as well as local experts, collected tissue samples from 20 different species and eight different tissue types. The samples were processed for RNA extraction, which was then purified and sequenced on a high-throughput Illumina platform. After multiple steps of quality-filtering, we retained 150 libraries from 12 species: four cone snail species with the venom gland (Conus imperialis, C. marmoreus, C. virgo, and C. quercinus), five species with the homologous gland of Leiblein (Nassa serta, Murex tenuirostris, Oliva amethystine, Phos senticosus, and Vasum turbinellus), two species with the ancestral homologous oesophageal gland (Cymatium piliare and Polinices mammillata), and one species which has completely lost the gland (Mitra mitra). For each species, we performed de novo transcriptome assembly, differential gene expression analysis to identify tissue-specific genes, and Gene Ontology enrichment analysis to better understand the function of the homologous glands. Transcriptome dynamics along the phylogeny were investigated by performing ancestral gene expression reconstruction. The findings of this WP are in preparation for publication and have been presented as a poster at the Euro Evo-Devo conference in 2022.
Objective 3: Spatial transcriptomics of cone snail’s venom gland
We performed an in-depth analysis of the spatial patterns of gene expression in the venom gland of the Mediterranean cone snail, Lautoconus ventricosus. Cone snails have a peculiar venom gland consisting of a long, convoluted secretory duct which opens in the buccal cavity. At the proximal end of the duct, a voluminous muscular bulb contracts to push the venom through the duct and into a harpoon-shaped tooth which is used to inject the venom into another organism. Different sets of toxins are used against predators or prey and are secreted in distinct regions of the gland. How this additional specialisation of the venom gland is achieved remains unknown. To shed light on this aspect, the researcher obtained additional fundings through a ProFemmes Grant from the University of Lausanne to perform spatial transcriptomics. Tissue samples were collected from individuals kept in aquaria by collaborators at the University of Cadiz in Spain. The venom glands were processed and sequenced using the 10x Genomics Visium spatial transcriptomics platform. Additionally, three venom glands were prepared for transmission electron microscopy. For the latter, the venom duct was cut into seven parts to investigate structural differences progressing from the proximal to the distal region. The findings are in preparation for publication and have been presented as a poster at the Society of Molecular Biology and Evolution (SMBE) conference in 2023 and as an invited talk at the Lausanne Omics Days in 2024.
In addition to the work planned within the framework of this fellowship, the researcher joined the European Venom Network (EUVEN) COST Action CA19144 as a country representative for Switzerland and co-leader of the working group on web resources. The collaborative work resulted from this networking activity has been recently submitted for publication.
Objective 1: Convergent evolution of venom gland transcriptomes
In the first part of the project, we analysed publicly available gene expression (i.e. RNA-seq) datasets. We selected venomous species with either a well annotated genome or a high-quality transcriptome, and with RNA-seq data of venom glands and other body tissues. This resulted in a total of 109 samples (libraries) from 20 venomous species representing eight different origins of venom: five spiders, two scorpions, one bee, three wasps, one fly, two molluscs, four snakes, one fish, and one mammal. The results of this work have been published in the Proceedings of the National Academy of Sciences and presented as a talk at the European Venom Network (EUVEN) international conference in 2021 and as an invited keynote talk at the Venoms and Toxins in 2022.
Objective 2: Evolution of venom production in cone snails
We investigated the gene expression dynamics of venom glands in cone snails and their homologous oesophageal glands in related non-venomous snail species. To obtain the samples, in 2019 the researcher joined an expedition in New Caledonia organised by the Natural History Museum of Paris. In Kourmac, the researcher, with the assistance of colleagues from Italy and France, as well as local experts, collected tissue samples from 20 different species and eight different tissue types. The samples were processed for RNA extraction, which was then purified and sequenced on a high-throughput Illumina platform. After multiple steps of quality-filtering, we retained 150 libraries from 12 species: four cone snail species with the venom gland (Conus imperialis, C. marmoreus, C. virgo, and C. quercinus), five species with the homologous gland of Leiblein (Nassa serta, Murex tenuirostris, Oliva amethystine, Phos senticosus, and Vasum turbinellus), two species with the ancestral homologous oesophageal gland (Cymatium piliare and Polinices mammillata), and one species which has completely lost the gland (Mitra mitra). For each species, we performed de novo transcriptome assembly, differential gene expression analysis to identify tissue-specific genes, and Gene Ontology enrichment analysis to better understand the function of the homologous glands. Transcriptome dynamics along the phylogeny were investigated by performing ancestral gene expression reconstruction. The findings of this WP are in preparation for publication and have been presented as a poster at the Euro Evo-Devo conference in 2022.
Objective 3: Spatial transcriptomics of cone snail’s venom gland
We performed an in-depth analysis of the spatial patterns of gene expression in the venom gland of the Mediterranean cone snail, Lautoconus ventricosus. Cone snails have a peculiar venom gland consisting of a long, convoluted secretory duct which opens in the buccal cavity. At the proximal end of the duct, a voluminous muscular bulb contracts to push the venom through the duct and into a harpoon-shaped tooth which is used to inject the venom into another organism. Different sets of toxins are used against predators or prey and are secreted in distinct regions of the gland. How this additional specialisation of the venom gland is achieved remains unknown. To shed light on this aspect, the researcher obtained additional fundings through a ProFemmes Grant from the University of Lausanne to perform spatial transcriptomics. Tissue samples were collected from individuals kept in aquaria by collaborators at the University of Cadiz in Spain. The venom glands were processed and sequenced using the 10x Genomics Visium spatial transcriptomics platform. Additionally, three venom glands were prepared for transmission electron microscopy. For the latter, the venom duct was cut into seven parts to investigate structural differences progressing from the proximal to the distal region. The findings are in preparation for publication and have been presented as a poster at the Society of Molecular Biology and Evolution (SMBE) conference in 2023 and as an invited talk at the Lausanne Omics Days in 2024.
In addition to the work planned within the framework of this fellowship, the researcher joined the European Venom Network (EUVEN) COST Action CA19144 as a country representative for Switzerland and co-leader of the working group on web resources. The collaborative work resulted from this networking activity has been recently submitted for publication.
Research carried out during this fellowship has advanced our understanding of organ evolution beyond the classic model systems. Particularly, we have provided fascinating insights into the evolution of the venom gland in marine snails and the functional plasticity of their digestive system. The resources generated with the project EVER will be of immense value for answering additional biological research questions, as well as for data mining and discovery of natural compounds with potential therapeutic and biotechnological applications.
In addition to the work planned within the framework of this fellowship, the researcher joined the European Venom Network (EUVEN) COST Action CA19144. This role significantly enhanced the researcher's professional network and opened up new opportunities for collaboration across Europe. The Marie Curie fellowship, and the researcher’s involvement with the EUVEN COST Action, have had a profound impact on her career.
In addition to the work planned within the framework of this fellowship, the researcher joined the European Venom Network (EUVEN) COST Action CA19144. This role significantly enhanced the researcher's professional network and opened up new opportunities for collaboration across Europe. The Marie Curie fellowship, and the researcher’s involvement with the EUVEN COST Action, have had a profound impact on her career.