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Philosophical Transactions of the Royal... May 2021As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities...
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Topics: Animals; Databases, Genetic; Gene Expression Profiling; Genome; Genomics; Mollusca; Transcriptome
PubMed: 33813885
DOI: 10.1098/rstb.2020.0157 -
International Journal of Molecular... Jul 2020Chitin, being the second most abundant biopolymer after cellulose, has been gaining popularity since its initial discovery by Braconot in 1811. However, fundamental... (Review)
Review
Chitin, being the second most abundant biopolymer after cellulose, has been gaining popularity since its initial discovery by Braconot in 1811. However, fundamental knowledge and literature on chitin and its derivatives from insects are difficult to obtain. The most common and sought-after sources of chitin are shellfish (especially crustaceans) and other aquatic invertebrates. The amount of shellfish available is obviously restricted by the amount of food waste that is allowed; hence, it is a limited resource. Therefore, insects are the best choices since, out of 1.3 million species in the world, 900,000 are insects, making them the most abundant species in the world. In this review, a total of 82 samples from shellfish-crustaceans and mollusks (n = 46), insects (n = 23), and others (n = 13)-have been collected and studied for their chemical extraction of chitin and its derivatives. The aim of this paper is to review the extraction method of chitin and chitosan for a comparison of the optimal demineralization and deproteinization processes, with a consideration of insects as alternative sources of chitin. The methods employed in this review are based on comprehensive bibliographic research. Based on previous data, the chitin and chitosan contents of insects in past studies favorably compare and compete with those of commercial chitin and chitosan-for example, 45% in , 36.6% in (cicada sloughs), and 26.2% in . Therefore, according to the data reported by previous researchers, demonstrating comparable yield values to those of crustacean chitin and the great interest in insects as alternative sources, efforts towards comprehensive knowledge in this field are relevant.
Topics: Animals; Chemical Fractionation; Chitin; Chitosan; Crustacea; Insecta; Mollusca; Refuse Disposal
PubMed: 32679639
DOI: 10.3390/ijms21144978 -
Biochimica Et Biophysica Acta. Proteins... Jan 2021The discovery of enzyme-derived d-amino acid-containing peptides (DAACPs) that have physiological importance in the metazoan challenges previous assumptions about the... (Review)
Review
The discovery of enzyme-derived d-amino acid-containing peptides (DAACPs) that have physiological importance in the metazoan challenges previous assumptions about the homochirality of animal proteins while simultaneously revealing new analytical challenges in the structural and functional characterization of peptides. Most known DAACPs have been identified though laborious activity-guided purification studies or by homology to previously identified DAACPs. Peptide characterization experiments are increasingly dominated by high throughput mass spectrometry-based peptidomics, with stereochemistry rarely considered due to the technical challenges of identifying l/d isomerization. This review discusses the prevalence of enzyme-derived DAACPs among animals and the physiological consequences of peptide isomerization. Also highlighted are the analytical methods that have been applied for structural characterization/discovery of DAACPs, including results of several recent studies using non-targeted discovery methods for revealing novel DAACPs, strongly suggesting that more DAACPs remain to be uncovered.
Topics: Amino Acids; Amphibians; Animals; Antimicrobial Cationic Peptides; Arthropods; Conotoxins; Mammals; Mollusca; Oligopeptides; Opioid Peptides; Peptides, Cyclic; Phylogeny; Stereoisomerism
PubMed: 33002629
DOI: 10.1016/j.bbapap.2020.140553 -
Database : the Journal of Biological... Sep 2021Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities...
Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We also integrated a series of analysis and visualization tools, such as BLAST, MUSCLE, GENEWISE and LASTZ. In particular, a phylogenetic tree was implemented in this database to visualize the evolutionary relationships between species. The original version contains 616 species whose mitochondrial genomes have been sequenced. The database provides comprehensive information and analysis platform for researchers interested in understanding the biological characteristics of mollusks. Database URL: http://modb.ytu.edu.cn/.
Topics: Animals; Biological Evolution; Genome, Mitochondrial; Humans; Mollusca; Phylogeny
PubMed: 34510194
DOI: 10.1093/database/baab056 -
ELife Nov 2020Sea slugs increase the longevity of the chloroplasts they steal from algae by limiting the harmful side-effects of photosynthesis.
Sea slugs increase the longevity of the chloroplasts they steal from algae by limiting the harmful side-effects of photosynthesis.
Topics: Animals; Aplysia; Chloroplasts; Gastropoda; Photosynthesis; Theft
PubMed: 33215989
DOI: 10.7554/eLife.64057 -
Journal of Evolutionary Biology Jan 2021Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin...
Pteropods, a group of holoplanktonic gastropods, are regarded as bioindicators of the effects of ocean acidification on open ocean ecosystems, because their thin aragonitic shells are susceptible to dissolution. While there have been recent efforts to address their capacity for physiological acclimation, it is also important to gain predictive understanding of their ability to adapt to future ocean conditions. However, little is known about the levels of genetic variation and large-scale population structuring of pteropods, key characteristics enabling local adaptation. We examined the spatial distribution of genetic diversity in the mitochondrial cytochrome c oxidase I (COI) and nuclear 28S gene fragments, as well as shell shape variation, across a latitudinal transect in the Atlantic Ocean (35°N-36°S) for the pteropod Limacina bulimoides. We observed high levels of genetic variability (COI π = 0.034, 28S π = 0.0021) and strong spatial structuring (COI Φ = 0.230, 28S Φ = 0.255) across this transect. Based on the congruence of mitochondrial and nuclear differentiation, as well as differences in shell shape, we identified a primary dispersal barrier in the southern Atlantic subtropical gyre (15-18°S). This barrier is maintained despite the presence of expatriates, a gyral current system, and in the absence of any distinct oceanographic gradients in this region, suggesting that reproductive isolation between these populations must be strong. A secondary dispersal barrier supported only by 28S pairwise Φ comparisons was identified in the equatorial upwelling region (between 15°N and 4°S), which is concordant with barriers observed in other zooplankton species. Both oceanic dispersal barriers were congruent with regions of low abundance reported for a similar basin-scale transect that was sampled 2 years later. Our finding supports the hypothesis that low abundance indicates areas of suboptimal habitat that result in barriers to gene flow in widely distributed zooplankton species. Such species may in fact consist of several populations or (sub)species that are adapted to local environmental conditions, limiting their potential for adaptive responses to ocean changes. Future analyses of genome-wide diversity in pteropods could provide further insight into the strength, formation and maintenance of oceanic dispersal barriers.
Topics: Animal Distribution; Animal Shells; Animals; Gastropoda; Oceans and Seas; Phenotype; Zooplankton
PubMed: 33150701
DOI: 10.1111/jeb.13735 -
Food Research International (Ottawa,... Nov 2020Extensive biodiversity and availability of marine and estuarine molluscs, along with their their wide-range of utilities as food and nutraceutical resources developed... (Review)
Review
Extensive biodiversity and availability of marine and estuarine molluscs, along with their their wide-range of utilities as food and nutraceutical resources developed keen attention of the food technologists and dieticians, particularly during the recent years. The current review comprehensively summarized the nutritional qualities, functional food attributes, and bioactive properties of these organisms. Among the phylum mollusca, Cephalopoda, Bivalvia, and Gastropoda were mostly reported for their nutraceutical applications and bioactive properties. The online search tools, like Scifinder/Science Direct/PubMed/Google Scholar/MarinLit database and marine natural product reports (1984-2019) were used to comprehend the information about the molluscs. More than 1334 secondary metabolites were reported from marine molluscs between the periods from 1984 to 2019. Among various classes of specialized metabolites, terpenes were occupied by 55% in gastropods, whereas sterols occupied 41% in bivalves. The marketed nutraceuticals, such as Cadalmin green mussel extract (Perna viridis) and Lyprinol® (Perna canaliculus) were endowed with potential anti-inflammatory activities, and were used against arthritis. Molluscan-derived therapeutics, for example, ziconotide was used as an analgesic, and elisidepsin was used in the treatment of cancer. Greater numbers of granted patents (30%) during 2016-2019 recognized the increasing importance of bioactive compounds from molluscs. Consumption of molluscs as daily diets could be helpful in the enhancement of immunity, and reduce the risk of several ailments. The present review comprehended the high value compounds and functional food ingredients from marine and estuarine molluscs.
Topics: Animals; Anti-Inflammatory Agents; Bivalvia; Ecosystem; Food Ingredients; Prospective Studies
PubMed: 33233216
DOI: 10.1016/j.foodres.2020.109637 -
Integrative and Comparative Biology Nov 2021Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study... (Review)
Review
Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study genomic-phenotype connections in a climate change framework. Recent advances in genomic sequencing technologies and genome assembly approaches finally allow the relatively cheap and tractable assembly of high-quality mollusc genome resources. After a brief review of these issues and advances, we use a case-study approach to provide some concrete examples of phenotypic plasticity and genomic adaptation in molluscs in response to environmental factors expected to be influenced by climate change. Our goal is to use molluscs as a "common currency" to demonstrate how organismal and evolutionary biologists can use natural systems to make phenotype-genotype connections in the context of changing environments. In parallel, we emphasize the critical need to collaborate and integrate findings across taxa and disciplines in order to use new data and information to advance our understanding of mollusc biology in the context of global environmental change. We end with a brief synthetic summary of the papers inspired by the 2021 SICB Symposium "Genomic Perspectives in Comparative Physiology of Molluscs: Integration across Disciplines".
Topics: Animals; Biological Evolution; Climate Change; Ecosystem; Genome; Mollusca; Plastics
PubMed: 34435639
DOI: 10.1093/icb/icab186 -
Biomolecules Dec 2019The n-3 and n-6 polyunsaturated fatty acid (PUFA) families are essential for important physiological processes. Their major source are marine ecosystems. The fatty acids... (Review)
Review
The n-3 and n-6 polyunsaturated fatty acid (PUFA) families are essential for important physiological processes. Their major source are marine ecosystems. The fatty acids (FAs) from phytoplankton, which are the primary producer of organic matter and PUFAs, are transferred into consumers via food webs. Mollusk FAs have attracted the attention of researchers that has been driven by their critical roles in aquatic ecology and their importance as sources of essential PUFAs. The main objective of this review is to focus on the most important factors and causes determining the biodiversity of the mollusk FAs, with an emphasis on the key relationship of these FAs with the food spectrum and trophic preference. The marker FAs of trophic sources are also of particular interest. The discovery of new symbioses involving invertebrates and bacteria, which are responsible for nutrition of the host, deserves special attention. The present paper also highlights recent research into the molecular and biochemical mechanisms of PUFA biosynthesis in marine mollusks. The biosynthetic capacities of marine mollusks require a well-grounded evaluation.
Topics: Animals; Bacteria; Diet; Fatty Acids; Mollusca; Symbiosis
PubMed: 31835867
DOI: 10.3390/biom9120857 -
Acta Biomaterialia Apr 2022Biomineralization integrates complex physical and chemical processes bio-controlled by the living organisms through ionic concentration regulation and organic molecules...
Biomineralization integrates complex physical and chemical processes bio-controlled by the living organisms through ionic concentration regulation and organic molecules production. It allows tuning the structural, optical and mechanical properties of hard tissues during ambient-condition crystallisation, motivating a deeper understanding of the underlying processes. By combining state-of-the-art optical and X-ray microscopy methods, we investigated early-mineralized calcareous units from two bivalve species, Pinctada margaritifera and Pinna nobilis, revealing chemical and crystallographic structural insights. In these calcite units, we observed ring-like structural features correlated with a lack of calcite and an increase of amorphous calcium carbonate and proteins contents. The rings also correspond to a larger crystalline disorder and a larger strain level. Based on these observations, we propose a temporal biomineralization cycle, initiated by the production of an amorphous precursor layer, which further crystallizes with a transition front progressing radially from the unit centre, while the organics are expelled towards the prism edge. Simultaneously, along the shell thickness, the growth occurs following a layer-by-layer mode. These findings open biomimetic perspectives for the design of refined crystalline materials. STATEMENT OF SIGNIFICANCE: Calcareous biominerals are amongst the most present forms of biominerals. They exhibit astonishing structural, optical and mechanical properties while being formed at ambient synthesis conditions from ubiquitous ions, motivating the deep understanding of biomineralization. Here, we unveil the first formation steps involved in the biomineralization cycle of prismatic units of two bivalve species by applying a new multi-modal non-destructive characterization approach, sensitive to chemical and crystalline properties. The observations of structural features in mineralized units of different ages allowed the derivation of a temporal sequence for prism biomineralization, involving an amorphous precursor, a radial crystallisation front and a layer-by-layer sequence. Beyond these chemical and physical findings, the herein introduced multi-modal approach is highly relevant to other biominerals and bio-inspired studies.
Topics: Animals; Bivalvia; Calcium Carbonate; Crystallization; Pinctada; Proteins
PubMed: 35041900
DOI: 10.1016/j.actbio.2022.01.024