| 1. |
- Abalde, Samuel, et al.
(författare)
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A Combined Transcriptomics and Proteomics Approach Reveals the Differences in the Predatory and Defensive Venoms of the Molluscivorous Cone Snail Cylinder ammiralis (Caenogastropoda: Conidae)
- 2021
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Ingår i: Toxins. - : MDPI AG. - 2072-6651. ; 13:9, s. 642-642
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Tidskriftsartikel (refereegranskat)abstract
- Venoms are complex mixtures of proteins that have evolved repeatedly in the animal kingdom. Cone snail venoms represent one of the best studied venom systems. In nature, this venom can be dynamically adjusted depending on its final purpose, whether to deter predators or hunt prey. Here, the transcriptome of the venom gland and the proteomes of the predation-evoked and defensive venoms of the molluscivorous cone snail Cylinder ammiralis were catalogued. A total of 242 venom-related transcripts were annotated. The conotoxin superfamilies presenting more different peptides were O1, O2, T, and M, which also showed high expression levels (except T). The three precursors of the J superfamily were also highly expressed. The predation-evoked and defensive venoms showed a markedly distinct profile. A total of 217 different peptides were identified, with half of them being unique to one venom. A total of 59 peptides ascribed to 23 different protein families were found to be exclusive to the predatory venom, including the cono-insulin, which was, for the first time, identified in an injected venom. A total of 43 peptides from 20 protein families were exclusive to the defensive venom. Finally, comparisons of the relative abundance (in terms of number of peptides) of the different conotoxin precursor superfamilies showed that most of them present similar abundance regardless of the diet.
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| 2. |
- Abalde, Samuel, et al.
(författare)
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Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus
- 2023
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Ingår i: Molecular Phylogenetics and Evolution. - 1055-7903 .- 1095-9513. ; 186, s. 107838-107838
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Tidskriftsartikel (refereegranskat)abstract
- The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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| 3. |
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| 4. |
- Abalde, Samuel, et al.
(författare)
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The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes
- 2023
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Ingår i: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group’s main clades and whose origin has been dated more than 400 million years ago.Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades.Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system.Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.
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| 5. |
- López‐Estrada, Estefany Karen, et al.
(författare)
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Mitogenomics and hidden‐trait models reveal the role of phoresy and host shifts in the diversification of parasitoid blister beetles (Coleoptera: Meloidae)
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:8, s. 2453-2474
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Tidskriftsartikel (refereegranskat)abstract
- Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the conse-quences of changes in two life history traits, host-type and phoresy, in the hypermeta-morphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most gen-era and tribes are bee- parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diver-sification rates and changes in host specificity and phoresy, using state-dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic-taxonomic ap-proach based on birth-death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermet-amorphic Meloidae was a nonphoretic bee- parasitoid, and that transitions towards a phoretic bee- parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee- parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee-and grasshopper- parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary suc-cess of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversifica-tion dynamics.
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| 6. |
- Maldonado, Manuel, et al.
(författare)
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On the dissolution of sponge silica: Assessing variability and biogeochemical implications
- 2022
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The dissolution of the biogenic silica that constitutes the skeletons of silicifying organisms is an important mechanism for regenerating dissolved silicon in the ocean. The silica skeletons deposited to the seafloor after the organisms die keep dissolving until becoming definitively buried. The low dissolution rate of sponge skeletons compared to that of diatom skeletons favors their burial and makes sponges (Phylum Porifera) to function as important silicon sinks in the oceans. However, it remains poorly understood whether the large variety of siliceous skeletons existing in the Porifera involves similar variability in their dissolution rates, which would affect the general conceptualization of these organisms as silicon sinks. Herein we investigated kinetics of silica dissolution for major types of skeletons in the three siliceous lineages of Porifera, following standardized digestion conditions in 1% sodium carbonate with orbital agitation at 85°C. The results are compared with those of a previous study conducted under identical conditions, which considered diatom silica, sponge silica, and lithogenic silica. Unexpectedly, the silica of homoscleromorph sponges dissolved only a bit slower than that of freshly cultured diatoms and as fast as diatom earth. However, the rest of sponge skeletons were far more resistant, although with some differences: the isolated spicules of hexactinellid sponges dissolved slightly faster than when forming frameworks of fused spicules, being hexactinellid frameworks as resistant to dissolution as the silica of demosponges, irrespective of occurring in the form of isolated spicules or frameworks. The experiments also indicated that the complexation of sponge silica with aluminum and with chitin does not increase its resistance to dissolution. Because the rapidly-dissolving homoscleromorph sponges represent less than 1% of extant sponges, the sponge skeletons are still conceptualized as important silicon sinks due to their comparative resistance to dissolution. Yet, the turnover of silica into dissolved silicon will always be faster in environments dominated by hexactinellids with isolated spicules than in environments dominated by other hexactinellids and/or demosponges. We discuss whether the time required for a given silica type to completely dissolve in 1% sodium carbonate could be a predictor of its preservation ratio in marine sediments.
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| 7. |
- Pardos-Blas, José Ramón, et al.
(författare)
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The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity
- 2021
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 10:5, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved inthe origin and diversification of venoms. Results: Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; ithas high contiguity (N50 = 93.53 Mb) and 86.6 Mb of the genome assembled into the 35 largest scaffolds or pseudochromosomes. On the basis of venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomesand located within repetitive regions. The genes encoding conotoxin precursors were normally structured into 3 exons,which did not necessarily coincide with the 3 structural domains of the corresponding proteins. Additionally, we found evidence in the L. ventricosus genome for a past whole-genome duplication event by means of conserved gene synteny withthe Pomacea canaliculata genome, the only one available at the chromosome level within Caenogastropoda. The whole-genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related to development, shell formation, and sex were located inthe genome. Conclusions: The new high-quality L. ventricosus genome should become a reference for assembling andanalyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.
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