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Philosophical Transactions of the Royal... May 2021The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct...
The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Topics: Animals; Genome; Genomics; Mollusca; Phylogeny
PubMed: 33813889
DOI: 10.1098/rstb.2020.0161 -
Proceedings of the National Academy of... Nov 2021Macromolecular function commonly involves rapidly reversible alterations in three-dimensional structure (conformation). To allow these essential conformational changes,... (Comparative Study)
Comparative Study
Macromolecular function commonly involves rapidly reversible alterations in three-dimensional structure (conformation). To allow these essential conformational changes, macromolecules must possess higher order structures that are appropriately balanced between rigidity and flexibility. Because of the low stabilization free energies (marginal stabilities) of macromolecule conformations, temperature changes have strong effects on conformation and, thereby, on function. As is well known for proteins, during evolution, temperature-adaptive changes in sequence foster retention of optimal marginal stability at a species' normal physiological temperatures. Here, we extend this type of analysis to messenger RNAs (mRNAs), a class of macromolecules for which the stability-lability balance has not been elucidated. We employ in silico methods to determine secondary structures and estimate changes in free energy of folding (ΔG) for 25 orthologous mRNAs that encode the enzyme cytosolic malate dehydrogenase in marine mollusks with adaptation temperatures spanning an almost 60 °C range. The change in free energy that occurs during formation of the ensemble of mRNA secondary structures is significantly correlated with adaptation temperature: ΔG values are all negative and their absolute values increase with adaptation temperature. A principal mechanism underlying these adaptations is a significant increase in synonymous guanine + cytosine substitutions with increasing temperature. These findings open up an avenue of exploration in molecular evolution and raise interesting questions about the interaction between temperature-adaptive changes in mRNA sequence and in the proteins they encode.
Topics: Animals; Computer Simulation; Evolution, Molecular; Malate Dehydrogenase; Molecular Structure; Mollusca; RNA, Messenger; Thermotolerance
PubMed: 34728561
DOI: 10.1073/pnas.2113324118 -
Marine Drugs Feb 2016The marine environment is an important source of structurally-diverse and biologically-active secondary metabolites. During the last two decades, thousands of compounds... (Review)
Review
The marine environment is an important source of structurally-diverse and biologically-active secondary metabolites. During the last two decades, thousands of compounds were discovered in marine organisms, several of them having inspired the development of new classes of therapeutic agents. Marine mollusks constitute a successful phyla in the discovery of new marine natural products (MNPs). Over a 50-year period from 1963, 116 genera of mollusks contributed innumerous compounds, Aplysia being the most studied genus by MNP chemists. This genus includes 36 valid species and should be distinguished from all mollusks as it yielded numerous new natural products. Aplysia sea hares are herbivorous mollusks, which have been proven to be a rich source of secondary metabolites, mostly of dietary origin. The majority of secondary metabolites isolated from sea hares of the genus Aplysia are halogenated terpenes; however, these animals are also a source of compounds from other chemical classes, such as macrolides, sterols and alkaloids, often exhibiting cytotoxic, antibacterial, antifungal, antiviral and/or antifeedant activities. This review focuses on the diverse structural classes of secondary metabolites found in Aplysia spp., including several compounds with pronounced biological properties.
Topics: Animals; Aplysia; Aquatic Organisms; Biological Products; Drug Discovery; Humans; Mollusca; Secondary Metabolism
PubMed: 26907303
DOI: 10.3390/md14020039 -
ELife Jun 2019Cephalopod mollusks evolved numerous anatomical novelties, including arms and tentacles, but little is known about the developmental mechanisms underlying cephalopod...
Cephalopod mollusks evolved numerous anatomical novelties, including arms and tentacles, but little is known about the developmental mechanisms underlying cephalopod limb evolution. Here we show that all three axes of cuttlefish limbs are patterned by the same signaling networks that act in vertebrates and arthropods, although they evolved limbs independently. In cuttlefish limb buds, is expressed anteriorly. Posterior transplantation of -expressing cells induced mirror-image limb duplications. Bmp and Wnt signals, which establish dorsoventral polarity in vertebrate and arthropod limbs, are similarly polarized in cuttlefish. Inhibition of Bmp2/4 dorsally caused ectopic expression of which marks the ventral sucker field, and ectopic sucker development. Cuttlefish also show proximodistal regionalization of , , , , and expression, which delineates arm and tentacle sucker fields. These results suggest that cephalopod limbs evolved by parallel activation of a genetic program for appendage development that was present in the bilaterian common ancestor.
Topics: Animals; Cephalopoda; Extremities; Gene Expression Regulation, Developmental; Hedgehog Proteins; Homeodomain Proteins; Mollusca; Organogenesis; Phylogeny; Vertebrates
PubMed: 31210127
DOI: 10.7554/eLife.43828 -
Nature Sep 2011Evolutionary relationships among the eight major lineages of Mollusca have remained unresolved despite their diversity and importance. Previous investigations of...
Evolutionary relationships among the eight major lineages of Mollusca have remained unresolved despite their diversity and importance. Previous investigations of molluscan phylogeny, based primarily on nuclear ribosomal gene sequences or morphological data, have been unsuccessful at elucidating these relationships. Recently, phylogenomic studies using dozens to hundreds of genes have greatly improved our understanding of deep animal relationships. However, limited genomic resources spanning molluscan diversity has prevented use of a phylogenomic approach. Here we use transcriptome and genome data from all major lineages (except Monoplacophora) and recover a well-supported topology for Mollusca. Our results strongly support the Aculifera hypothesis placing Polyplacophora (chitons) in a clade with a monophyletic Aplacophora (worm-like molluscs). Additionally, within Conchifera, a sister-taxon relationship between Gastropoda and Bivalvia is supported. This grouping has received little consideration and contains most (>95%) molluscan species. Thus we propose the node-based name Pleistomollusca. In light of these results, we examined the evolution of morphological characters and found support for advanced cephalization and shells as possibly having multiple origins within Mollusca.
Topics: Animals; Bivalvia; Expressed Sequence Tags; Gastropoda; Gene Expression Profiling; Genes; Genome; Genomics; Models, Biological; Mollusca; Phylogeny
PubMed: 21892190
DOI: 10.1038/nature10382 -
TheScientificWorldJournal 2012The geographical distribution of the Rissoidae in the Atlantic Ocean and Mediterranean Sea was compiled and is up-to-date until July 2011. All species were classified... (Review)
Review
The geographical distribution of the Rissoidae in the Atlantic Ocean and Mediterranean Sea was compiled and is up-to-date until July 2011. All species were classified according to their mode of larval development (planktotrophic and nonplanktotrophic), and bathymetrical zonation (shallow species--those living between the intertidal and 50 m depth, and deep species--those usually living below 50 m depth). 542 species of Rissoidae are presently reported to the Atlantic Ocean and the Mediterranean Sea, belonging to 33 genera. The Mediterranean Sea is the most diverse site, followed by Canary Islands, Caribbean, Portugal, and Cape Verde. The Mediterranean and Cape Verde Islands are the sites with higher numbers of endemic species, with predominance of Alvania spp. in the first site, and of Alvania and Schwartziella at Cape Verde. In spite of the large number of rissoids at Madeira archipelago, a large number of species are shared with Canaries, Selvagens, and the Azores, thus only about 8% are endemic to the Madeira archipelago. Most of the 542-rissoid species that live in the Atlantic and in the Mediterranean are shallow species (323), 110 are considered as deep species, and 23 species are reported in both shallow and deep waters. There is a predominance of nonplanktotrophs in islands, seamounts, and at high and medium latitudes. This pattern is particularly evident in the genera Crisilla, Manzonia, Onoba, Porosalvania, Schwartziella, and Setia. Planktotrophic species are more abundant in the eastern Atlantic and in the Mediterranean Sea. The results of the analysis of the probable directions of faunal flows support the patterns found by both the Parsimony Analysis of Endemicity and the geographical distribution. Four main source areas for rissoids emerge: Mediterranean, Caribbean, Canaries/Madeira archipelagos, and the Cape Verde archipelago. We must stress the high percentage of endemics that occurs in the isolated islands of Saint Helena, Tristan da Cunha, Cape Verde archipelago and also the Azores, thus reinforcing the legislative protective actions that the local governments have implemented in these islands during the recent years.
Topics: Animals; Atlantic Ocean; Demography; Genetic Variation; Mediterranean Region; Mollusca
PubMed: 22693430
DOI: 10.1100/2012/164890 -
Philosophical Transactions of the Royal... May 2021Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is...
Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. DNA extraction methods that employ the detergent hexadecyltrimethylammoniumbromide (CTAB) to remove these contaminants importantly facilitate molecular-level study of molluscs. Molluscan pigments may stain DNA samples and interfere with spectrophotometry, necessitating gel electrophoresis or fluorometry for accurate quantification. RNA can reliably be extracted but the 'hidden break' in 28S rRNA of molluscs (like most protostomes) causes 18S and 28S rRNA fragments to co-migrate electrophoretically. This challenges the standard quality control based on the ratio of 18S and 28S rRNA, developed for deuterostome animals. High-AT content in molluscan rRNA prevents the effective purification of polyadenylated mRNA. Awareness of these matters aids the continuous expansion of molecular malacology, enabling work also with museum specimens and next-generation sequencing, with the latter imposing unprecedented demands on DNA quality. Alternative methods to extract nucleic acids from molluscs are available from literature and, importantly, from communications with others who study the molecular biology of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Topics: Animals; DNA; Genomics; Mollusca; Nucleic Acids; RNA
PubMed: 33813891
DOI: 10.1098/rstb.2020.0162 -
PloS One 2022Oysters and blue mussels are important hydrobiological resources for aquaculture. In Chile, they are farming on the Chiloé island, where around 18% of the world's...
Oysters and blue mussels are important hydrobiological resources for aquaculture. In Chile, they are farming on the Chiloé island, where around 18% of the world's mussels are produced, however, their nutritional dynamics are largely unknown. For this reason, the objective of this study was to determine the proximal biochemical composition and the fatty acid profile in the Chilean oyster (Ostrea chilensis), the Pacific oyster (Crassostrea gigas) and the Chilean mussel (Mytilus chilensis), to perform an intra and interspecific comparison. Shellfish sampled in winter were characterized by a high protein content, followed by medium values for lipid content and a low carbohydrate content compared to similar species in Europe. Also, oysters and mussels were found to be rich in omega-3 long chain polyunsaturated fatty acid (n-3 LC-PUFA), so they can be considered excellent functional food option for a healthy human diet. Their high contribution of n-3 LC-PUFA ranged between 5.2-12.9 μg FA mg-1 dry weight with high n-3/n-6 ratios, which depends on both the species and the on-growing location. Both taxa can be considered a plausible option to promote a healthy diet of marine origin in future generations. Also, these results could benefit the projection and development of aquaculture of these mollusks.
Topics: Animals; Bivalvia; Chile; Crassostrea; Fatty Acids; Humans; Mytilus; Ostrea
PubMed: 35797370
DOI: 10.1371/journal.pone.0270825 -
Scientific Reports Jan 2022The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host's ecology. Of...
The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host's ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, β-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.
Topics: Animals; Bacteria; Energy Metabolism; Fatty Acids; In Situ Hybridization, Fluorescence; Microbiota; Mollusca; Phylogeny; Ribotyping; Symbiosis
PubMed: 34997021
DOI: 10.1038/s41598-021-03973-7 -
ELife Jan 2023Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary...
Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary distance that separates vertebrates from cephalopods, it is evident that higher cognitive features have evolved separately in these clades despite the similarities that they share. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Despite significant progress in genome and transcriptome sequencing, the molecular identities of cell types in cephalopods remain largely unknown. We here combine single-cell transcriptomics with in situ gene expression analysis to uncover cell type diversity in the European squid . We describe cell types that are conserved with other phyla such as neurons, muscles, or connective tissues but also cephalopod-specific cells, such as chromatophores or sucker cells. Moreover, we investigate major components of the squid nervous system including progenitor and developing cells, differentiated cells of the brain and optic lobes, as well as sensory systems of the head. Our study provides a molecular assessment for conserved and novel cell types in cephalopods and a framework for mapping the nervous system of .
Topics: Animals; Decapodiformes; Loligo; Mollusca; Cephalopoda; Chromatophores
PubMed: 36594460
DOI: 10.7554/eLife.80670