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Genes Dec 2022In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed...
In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.
Topics: Animals; Phylogeny; Gastropoda; DNA Barcoding, Taxonomic; Biodiversity; Base Sequence
PubMed: 36553540
DOI: 10.3390/genes13122273 -
Philosophical Transactions of the Royal... May 2021Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations....
Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such as and , such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropod (356.6 Mb, 1.59% heterozygosity) and the bivalve (1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40-50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified by , while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified by . A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Topics: Animals; Benchmarking; Gastropoda; Genome; Genomics; Mytilus; Nanopores
PubMed: 33813888
DOI: 10.1098/rstb.2020.0160 -
Biological Reviews of the Cambridge... Dec 2020Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO... (Review)
Review
Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.
Topics: Animals; Aquaculture; Biomimetics; Hydrogen-Ion Concentration; Mollusca; Seawater
PubMed: 32737956
DOI: 10.1111/brv.12640 -
Infectious Diseases of Poverty May 2022Bulinus globosus, the main intermediate snail host of Schistosoma haematobium. The increased contacts between Africa and China could even lead to large-scale...
BACKGROUND
Bulinus globosus, the main intermediate snail host of Schistosoma haematobium. The increased contacts between Africa and China could even lead to large-scale dissemination of B. globosus in China. Temperature is the key factor affecting fresh-water snail transmission. This study predicted potential risk of colonization of B. globosus in the mainland of China under climate change.
METHODS
We investigated minimum and maximum temperatures for B. globosus eggs, juveniles and adult snails kept under laboratory conditions to find the most suitable range by pinpointing the median effective temperatures (ET50). We also assessed the influence of temperature on spawning and estimated the accumulated temperature (AT). The average air temperatures between 1955 and 2019 in January and July, the coldest and hottest months in China, respectively, were collected from national meteorological monitoring stations and investigated in a geographic information system (GIS) using empirical Bayesian Kriging to evaluate the theoretical possibility for distribution of B. globosus in southern China based on temperature.
RESULTS
The effective minimum temperature (ET50) for eggs, juveniles, adult snails and spawning were 8.5, 7.0, 7.0, 14.9 °C, respectively, with the corresponding maximum values (ET50) of 36.6, 40.5, 40.2 and 38.1 °C. The AT was calculated at 712.1 ± 64.9 °C·d. In 1955, the potential B. globosus distribution would have had a northern boundary stretching from the coastal areas of Guangdong Province and Guangxi Autonomous Region to southern Yunnan Province. Since then, this line has gradually moved northward.
CONCLUSIONS
Annual regeneration of B. globosus can be supported by the current climate conditions in the mainland of China, and a gradual expansion trend from south to north is shown in the study from 2015 to 2019. Thus, there is a potential risk of colonization of B. globosus in the mainland of China under climate change.
Topics: Animals; Bayes Theorem; Bulinus; China; Climate Change; Schistosoma haematobium; Snails
PubMed: 35562755
DOI: 10.1186/s40249-022-00980-2 -
Marine Drugs Nov 2020Respiratory diseases place an immense burden on global health and there is a compelling need for the discovery of new compounds for therapeutic development. Here, we... (Review)
Review
Respiratory diseases place an immense burden on global health and there is a compelling need for the discovery of new compounds for therapeutic development. Here, we identify research priorities by critically reviewing pre-clinical and clinical studies using extracts and compounds derived from molluscs, as well as traditional molluscan medicines, used in the treatment of respiratory diseases. We reviewed 97 biomedical articles demonstrating the anti-inflammatory, antimicrobial, anticancer, and immunomodulatory properties of >320 molluscan extracts/compounds with direct relevance to respiratory disease, in addition to others with promising bioactivities yet to be tested in the respiratory context. Of pertinent interest are compounds demonstrating biofilm inhibition/disruption and antiviral activity, as well as synergism with approved antimicrobial and chemotherapeutic agents. At least 100 traditional medicines, incorporating over 300 different mollusc species, have been used to treat respiratory-related illness in cultures worldwide for thousands of years. These medicines provide useful clues for the discovery of bioactive components that likely underpin their continued use. There is particular incentive for investigations into anti-inflammatory compounds, given the extensive application of molluscan traditional medicines for symptoms of inflammation, and shells, which are the principal molluscan product used in these preparations. Overall, there is a need to target research toward specific respiratory disease-related hypotheses, purify bioactive compounds and elucidate their chemical structures, and develop an evidence base for the integration of quality-controlled traditional medicines.
Topics: Animals; Anti-Inflammatory Agents; Antiviral Agents; COVID-19; Coronavirus Infections; Drug Discovery; Humans; Inflammation; Medicine, Traditional; Mollusca; Pandemics; Pneumonia, Viral; Respiratory Tract Diseases
PubMed: 33228163
DOI: 10.3390/md18110570 -
PeerJ 2022In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons...
In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet and the periwinkle shared similar microbiota. The microbiota of the chiton keyhole limpet and scurrinid limpet differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of and negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities.
Topics: Animals; Mollusca; Gastropoda; Microbiota; Polyplacophora; Gammaproteobacteria; Biofilms; Mucus
PubMed: 36172502
DOI: 10.7717/peerj.13642 -
Ecology Jul 2021Parasites can harm hosts and influence populations, communities, and ecosystems. However, parasites are reciprocally affected by population- and community-level...
Parasites can harm hosts and influence populations, communities, and ecosystems. However, parasites are reciprocally affected by population- and community-level dynamics. Understanding feedbacks between infection dynamics and larger-scale epidemiological and ecological processes could improve predictions and reveal novel control methods. We evaluated how exploitative resource competition among hosts, a fundamental aspect of population biology, influences within-host infection dynamics of the widespread human parasite Schistosoma mansoni in its intermediate host, Biomphalaria glabrata. We added size-dependent consumption of shared resources to a parameterized bioenergetics model to predict a priori the growth, parasite production, and survival of an infected focal host coexisting with an uninfected conspecific competitor in an experiment that varied competitor size. The model quantitatively anticipated that competitors disrupt growth and parasite production and that these effects increase with competitor size. Fitting the model to these data improved its match to host survivorship. Thus, resource competition alters infection dynamics, there are strong size asymmetries in these effects, and size-asymmetric resource competition effects on infection dynamics can be accurately predicted by bioenergetics theory. More broadly, this framework can assess parasite transmission and control in other contexts, such as in resource competitive host communities, or in response to eutrophication, food supplementation, or culling.
Topics: Animals; Biomphalaria; Ecosystem; Host-Parasite Interactions; Humans; Parasites; Schistosoma mansoni; Snails
PubMed: 33950517
DOI: 10.1002/ecy.3383 -
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 -
Proceedings of the National Academy of... Jan 2020In contrast to the Hox genes in arthropods and vertebrates, those in molluscs show diverse expression patterns with differences reported among lineages. Here, we...
In contrast to the Hox genes in arthropods and vertebrates, those in molluscs show diverse expression patterns with differences reported among lineages. Here, we investigate 2 phylogenetically distant molluscs, a gastropod and a polyplacophoran, and show that the Hox expression in both species can be divided into 2 categories. The Hox expression in the ventral ectoderm generally shows a canonical staggered pattern comparable to the patterns of other bilaterians and likely contributes to ventral patterning, such as neurogenesis. The other category of Hox expression on the dorsal side is strongly correlated with shell formation and exhibits lineage-specific characteristics in each class of mollusc. This generalized model of decoupled dorsoventral Hox expression is compatible with known Hox expression data from other molluscan lineages and may represent a key characteristic of molluscan Hox expression. These results support the concept of widespread staggered Hox expression in Mollusca and reveal aspects that may be related to the evolutionary diversification of molluscs. We propose that dorsoventral decoupling of Hox expression allowed lineage-specific dorsal and ventral patterning, which may have facilitated the evolution of diverse body plans in different molluscan lineages.
Topics: Animals; Biodiversity; Biological Evolution; Gastropoda; Gene Expression Profiling; Gene Expression Regulation, Developmental; Genes, Homeobox; Larva; Phylogeny; Polyplacophora
PubMed: 31871200
DOI: 10.1073/pnas.1907328117 -
Anais Da Academia Brasileira de Ciencias 2022Due to the competition for food, space, oxygen and due to their role as diseases vector, epibionts can negatively affect oyster farming. We assessed the efficacy of six...
Due to the competition for food, space, oxygen and due to their role as diseases vector, epibionts can negatively affect oyster farming. We assessed the efficacy of six methods commonly used for the removal of epibionts from oyster shells during farming. The experiment was conducted at an oyster farm on the Paraná coast - South Brazil. Oysters (Crassostrea gasar) were acclimated for 90 d in the cultivation system and later exposed to cleaning treatments: i) freshwater; ii) hypersaline water; iii) sodium hypochlorite solution; iv) quaternary ammonia solution; v) exposure to air; vi) hydroblasting; and vii) no cleaning procedure (control). After treatment, oysters were kept in the cultivation system for 15 and 30 d - when the total incrustation and mortality were measured. Epibionts from nine phyla were identified. The most abundant were Arthropoda (Crustacea) (62.5%), Mollusca (33.8%) and Annelida (3.1%). Freshwater [15 (n = 2263 epibionts) and 30 days (n = 2822 epibionts)] and hydroblasting [15 (n = 1850 epibionts) and 30 days (n = 2389 epibionts)] treatments were the most efficient to reduce epibionts and caused lower rates of oyster mortality [15 (5.0 and 3.33%, respectively) and 30 days (1.67 and 6.67%, respectively)].
Topics: Animals; Crassostrea; Ammonia; Sodium Hypochlorite; Agriculture; Water; Oxygen
PubMed: 36287482
DOI: 10.1590/0001-3765202220190975