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Modica, M. V.

Publications and source records attributed to Modica, M. V..

3 recordsLinked to original sources

Evolution of venom production in marine predatory snails

Venom-secreting glands are highly specialised organs evolved throughout the entire animal kingdom to synthetise and secrete toxins for predation and defence. Venom is extensively studied for its toxin components and application potential; yet, how animals become venomous remains poorly understood. Venom systems therefore offer a unique opportunity to understand the molecular mechanisms underlying functional innovation. Here, we conducted a multi-species multi-tissue comparative transcriptomics analysis of 12 marine predatory gastropods, including species with venom glands and species with homologous non-venom producing glands, to examine how specialised functions evolve through gene expression changes. We found that while the venom gland specialised for the mass production of toxins, its homologous glands retained the ancestral digestive functions. The functional divergence and specialisation of the venom gland was achieved through a redistribution of its ancestral digestive functions to other organs, specifically the oesophagus. This entailed concerted expression changes and accelerated transcriptome evolution across the entire digestive system. The increase in venom gland secretory capacity was achieved through the modulation of an ancient secretory machinery, particularly genes involved in endoplasmic reticulum stress and unfolded protein response. This study shifts the focus from the well-explored evolution of toxins to the lesser-known evolution of the organ and mechanisms responsible for venom production. As such, it contributes to elucidating the molecular mechanisms underlying organ evolution at a fine evolutionary scale, highlighting the specific events that lead to functional divergence.

evolutionary biology↗

SeqLengthPlot: An easy-to-use Python-based Tool for Visualizing and Retrieving Sequence Lengths from fasta files with a Tunable Splitting Point

MotivationAccurate sequence length profiling is essential in bioinformatics, particularly in genomics and proteomics. Existing tools like SeqKit and the Trinity toolkit, among others provide basic sequence statistics but often fall short in offering comprehensive analytics and plotting options. For instance, SeqKit is a very complete and fast tool for sequence analyses, that delivers useful metrics (e.g., number of sequences, average, minimum, maximum length), and can returns the range of sequence shorter or longer (one side, not both at once) on a given lengths. Similarly, Trinitys utility pearl-based scripts provide detailed contig length distributions (e.g., N50, median, and average lengths) but do not encompass the total number of sequences nor offer graphical representations of data. ResultsGiven that key sequence analysis tasks are distributed among separate tools, we introduce SeqLengthPlot: an easy-to-use Python-based script that fills existing gaps in bioinformatics tools on sequence length profiling, crucial. SeqLengthPlot generates comprehensive statistical summaries, filtering and automatic sequences retriving from the input FASTA (nucleotide and proteins) file into two distinct files based on a tunable, user-defined sequence length, as well as the plots or dynamic visualizations of the corresponding sequences. Availability and implementationThe detailed SeqLengthPlot pipeline is available on GitHub at https://github.com/danydguezperez/SeqLengthPlot, released under the GPL-3.0 license. Additional datasets used as sources or compiled as use cases are publicy available through the Mendeley Data repository: DATASET_Ss_SE.1: http://dx.doi.org/10.17632/pmxwfjyyvy.1, DATASET_Ss_SE.2: http://dx.doi.org/10.17632/3rtbr7c9s8.1, DATASET_Ss_SE.3: http://dx.doi.org/10.17632/wn5kbk5ryy.1, DATASET_Ss_SE.4: http://dx.doi.org/10.17632/sh79mdcm2c.1 and DATASET_Ss_SE.5: http://dx.doi.org/10.17632/zmvvff35dx.1.

bioinformatics↗

The proteotranscriptomic characterization of venom in the white seafan Eunicella singularis elucidates the evolution of Octocorallia arsenal

All the members of the phylum Cnidaria are characterized by the production of venom in specialized structures, the nematocysts. Venom of jellyfish (Medusozoa) and sea anemones (Anthozoa) has been investigated since the 1970s, revealing a remarkable molecular diversity. Specifically, sea anemones harbour a rich repertoire of neurotoxic peptides, some of which have been developed in drug leads. However, venoms of the vast majority of Anthozoa species remain uncharacterized, particularly in the class Octocorallia. To fill this gap, we applied a proteo-transcriptomic approach to investigate the venom composition in Eunicella singularis, a gorgonian species common in Mediterranean hard-bottom benthic communities. Our results highlighted the peculiarities of the venom of E. singularis with respect to sea anemones, which is reflected in the presence of several toxins with novel folds, worthy of functional characterization. A comparative genomic survey across the octocoral radiation allowed us to generalize these findings and provided insights into the evolutionary history, molecular diversification patterns and putative adaptive roles of venom toxins. A comparison of whole-body and nematocyst proteomes revealed the presence of different cytolytic toxins inside and outside the nematocysts. Two instances of differential maturation patterns of toxin precursors were also identified, highlighting the intricate regulatory pathways underlying toxin expression.

evolutionary biology↗