Whole genome analysis of a schistosomiasis-transmitting freshwater snail

The evolution of the metazoan Toll receptor family and its expression during protostome development

BACKGROUND

Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa.

RESULTS

We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development.

CONCLUSIONS

Our findings suggest that a clade α TLR gene (TLR-Ca) and a clade β/γ TLR gene (TLR-Cβ/γ) were already present in the cnidarian-bilaterian common ancestor. However, although TLR-Ca was conserved in cnidarians, TLR-Cβ/γ was lost during the early evolution of these taxa. Moreover, TLR-Cβ/γ duplicated to generate TLR-Cβ and TLR-Cγ in the lineage to the last common protostome-deuterostome ancestor. TLR-Ca, TLR-Cβ and TLR-Cγ further expanded generating the three major TLR clades. While all three clades radiated in several spiralian lineages, specific TLRs clades have been presumably lost in other lineages. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests a likely role in development.

Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya

Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world's most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.

The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor

BACKGROUND

5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species.

RESULTS

Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression.

CONCLUSIONS

Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.

Draft genome of Semisulcospira libertina, a species of freshwater snail

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.

PIWI silencing mechanism involving the retrotransposon nimbus orchestrates resistance to infection with Schistosoma mansoni in the snail vector, Biomphalaria glabrata

Background

Schistosomiasis remains widespread in many regions despite efforts at its elimination. By examining changes in the transcriptome at the host-pathogen interface in the snail Biomphalaria glabrata and the blood fluke Schistosoma mansoni, we previously demonstrated that an early stress response in juvenile snails, manifested by induction of heat shock protein 70 (Hsp 70) and Hsp 90 and of the reverse transcriptase (RT) domain of the B. glabrata non-LTR- retrotransposon, nimbus, were critical for B. glabrata susceptibility to S. mansoni. Subsequently, juvenile B. glabrata BS-90 snails, resistant to S. mansoni at 25°C become susceptible by the F2 generation when maintained at 32°C, indicating an epigenetic response.

Methodology/Principal findings

To better understand this plasticity in susceptibility of the BS-90 snail, mRNA sequences were examined from S. mansoni exposed juvenile BS-90 snails cultured either at 25°C (non-permissive temperature) or 32°C (permissive). Comparative analysis of transcriptomes from snails cultured at the non-permissive and permissive temperatures revealed that whereas stress related transcripts dominated the transcriptome of susceptible BS-90 juvenile snails at 32°C, transcripts encoding proteins with a role in epigenetics, such as PIWI (BgPiwi), chromobox protein homolog 1 (BgCBx1), histone acetyltransferase (BgHAT), histone deacetylase (BgHDAC) and metallotransferase (BgMT) were highly expressed in those cultured at 25°C. To identify robust candidate transcripts that will underscore the anti-schistosome phenotype in B. glabrata, further validation of the differential expression of the above transcripts was performed by using the resistant BS-90 (25°C) and the BBO2 susceptible snail stock whose genome has now been sequenced and represents an invaluable resource for molecular studies in B. glabrata. A role for BgPiwi in B. glabrata susceptibility to S. mansoni, was further examined by using siRNA corresponding to the BgPiwi encoding transcript to suppress expression of BgPiwi, rendering the resistant BS-90 juvenile snail susceptible to infection at 25°C. Given transposon silencing activity of PIWI as a facet of its role as guardian of the integrity of the genome, we examined the expression of the nimbus RT encoding transcript at 120 min after infection of resistant BS90 piwi-siRNA treated snails. We observed that nimbus RT was upregulated, indicating that modulation of the transcription of the nimbus RT was associated with susceptibility to S. mansoni in BgPiwi-siRNA treated BS-90 snails. Furthermore, treatment of susceptible BBO2 snails with the RT inhibitor lamivudine, before exposure to S. mansoni, blocked S. mansoni infection concurrent with downregulation of the nimbus RT transcript and upregulation of the BgPiwi encoding transcript in the lamivudine-treated, schistosome-exposed susceptible snails.

Conclusions and significance

These findings support a role for the interplay of BgPiwi and nimbus in the epigenetic modulation of plasticity of resistance/susceptibility in the snail-schistosome relationship.

Progress is being made to eliminate schistosomiasis, a tropical disease that remains endemic in the tropics and neotropics. In 2020, WHO proposed controlling the snail population as part of a strategy toward reducing schistosomiasis, a vector borne disease, by 2025. The life cycle of the causative parasite is, however, complex and in the absence of vaccines, new drugs, and access to clean water and sanitation, reduction of schistosomiasis will remain elusive. To break the parasite’s life cycle during the snail stage of its development, a better understanding of the molecular basis of how schistosomes survive, or not, in the snail is required. By examining changes in the transcriptome at the host-pathogen interface in the snail Biomphalaria glabrata and Schistosoma mansoni, we showed that early stress response, manifested by the induction of Heat Shock Proteins (Hsps) and the RT domain of the non-LTR retrotransposon, nimbus, were critical for snail susceptibility. Subsequently, juvenile B. glabrata BS-90 snails, resistant to S. mansoni at 25°C were observed to become susceptible by the F2 generation when maintained at 32°C, indicating an epigenetic response. This study confirms these earlier results and shows an interplay between PIWI and nimbus in the anti-schistosome response in the snail host.

FMRF-NH2 -related neuropeptides in Biomphalaria spp., intermediate hosts for schistosomiasis: Precursor organization and immunohistochemical localization

Freshwater snails of the genus Biomphalaria serve as intermediate hosts for the digenetic trematode Schistosoma mansoni, the etiological agent for the most widespread form of intestinal schistosomiasis. As neuropeptide signaling in host snails can be altered by trematode infection, a neural transcriptomics approach was undertaken to identify peptide precursors in Biomphalaria glabrata, the major intermediate host for S. mansoni in the Western Hemisphere. Three transcripts that encode peptides belonging to the FMRF-NH2 -related peptide (FaRP) family were identified in B. glabrata. One transcript encoded a precursor polypeptide (Bgl-FaRP1; 292 amino acids) that included eight copies of the tetrapeptide FMRF-NH2 and single copies of FIRF-NH2 , FLRF-NH2 , and pQFYRI-NH2 . The second transcript encoded a precursor (Bgl-FaRP2; 347 amino acids) that comprised 14 copies of the heptapeptide GDPFLRF-NH2 and 1 copy of SKPYMRF-NH2 . The precursor encoded by the third transcript (Bgl-FaRP3; 287 amino acids) recapitulated Bgl-FaRP2 but lacked the full SKPYMRF-NH2 peptide. The three precursors shared a common signal peptide, suggesting a genomic organization described previously in gastropods. Immunohistochemical studies were performed on the nervous systems of B. glabrata and B. alexandrina, a major intermediate host for S. mansoni in Egypt. FMRF-NH2 -like immunoreactive (FMRF-NH2 -li) neurons were located in regions of the central nervous system associated with reproduction, feeding, and cardiorespiration. Antisera raised against non-FMRF-NH2 peptides present in the tetrapeptide and heptapeptide precursors labeled independent subsets of the FMRF-NH2 -li neurons. This study supports the participation of FMRF-NH2 -related neuropeptides in the regulation of vital physiological and behavioral systems that are altered by parasitism in Biomphalaria.

Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis

DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.

Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam

Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate coevolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 Gb, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene families, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 Mb but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host–symbiont genomes show not only tight metabolic complementarity but also distinct signatures of coevolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.

Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving "living fossil"

The nautilus, commonly known as a "living fossil," is endangered and may be at risk of extinction. The lack of genomic information hinders a thorough understanding of its biology and evolution, which can shed light on the conservation of this endangered species. Here, we report the first high-quality chromosome-level genome assembly of Nautilus pompilius. The assembled genome size comprised 785.15 Mb. Comparative genomic analyses indicated that transposable elements (TEs) and large-scale genome reorganizations may have driven lineage-specific evolution in the cephalopods. Remarkably, evolving conserved genes and recent TE insertion activities were identified in N. pompilius, and we speculate that these findings reflect the strong adaptability and long-term survival of the nautilus. We also identified gene families that are potentially responsible for specific adaptation and evolution events. Our study provides unprecedented insights into the specialized biology and evolution of N. pompilius, and the results serve as an important resource for future conservation genomics of the nautilus and closely related species.

Development and Interrogation of a Transcriptomic Resource for the Giant Triton Snail (Charonia tritonis)

Gastropod molluscs are among the most abundant species that inhabit coral reef ecosystems. Many are specialist predators, along with the giant triton snail Charonia tritonis (Linnaeus, 1758) whose diet consists of Acanthaster planci (crown-of-thorns starfish), a corallivore known to consume enormous quantities of reef-building coral. C. tritonis are considered vulnerable due to overexploitation, and a decline in their populations is believed to have contributed to recurring A. planci population outbreaks. Aquaculture is considered one approach that could help restore natural populations of C. tritonis and mitigate coral loss; however, numerous questions remain unanswered regarding their life cycle, including the molecular factors that regulate their reproduction and development. In this study, we have established a reference C. tritonis transcriptome derived from developmental stages (embryo and veliger) and adult tissues. This was used to identify genes associated with cell signalling, such as neuropeptides and G protein-coupled receptors (GPCRs), involved in endocrine and olfactory signalling. A comparison of developmental stages showed that several neuropeptide precursors are exclusively expressed in post-hatch veligers and functional analysis found that FFamide stimulated a significant (20.3%) increase in larval heart rate. GPCRs unique to veligers, and a diversity of rhodopsin-like GPCRs located within adult cephalic tentacles, all represent candidate olfactory receptors. In addition, the cytochrome P450 superfamily, which participates in the biosynthesis and degradation of steroid hormones and lipids, was also found to be expanded with at least 91 genes annotated, mostly in gill tissue. These findings further progress our understanding of C. tritonis with possible application in developing aquaculture methods.

Mobilizing molluscan models and genomes in biology

Molluscs are among the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and their genomes to address important questions in animal biology, and the state of the field when it comes to the availability of resources such as genome assemblies, cell lines, and other key elements necessary to mobilising the development of molluscan model systems. We conclude by contending that a cohesive research community that works together to elevate multiple molluscan systems to 'model' status will create new opportunities in addressing basic and applied biological problems, including general features of animal evolution. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Experimental Infection of the Biomphalaria glabrata Vector Snail by Schistosoma mansoni Parasites Drives Snail Microbiota Dysbiosis

Host-parasite interaction can result in a strong alteration of the host-associated microbiota. This dysbiosis can affect the fitness of the host; can modify pathogen interaction and the outcome of diseases. Biomphalaria glabrata is the snail intermediate host of the trematode Schistosoma mansoni, the agent of human schistosomiasis, causing hundreds of thousands of deaths every year. Here, we present the first study of the snail bacterial microbiota in response to Schistosoma infection. We examined the interplay between B. glabrata, S. mansoni and host microbiota. Snails were infected and the microbiota composition was analysed by 16S rDNA amplicon sequencing approach. We demonstrated that the microbial composition of water did not affect the microbiota composition. Then, we characterised the Biomphalaria bacterial microbiota at the individual scale in both naive and infected snails. Sympatric and allopatric strains of parasites were used for infections and re-infections to analyse the modification or dysbiosis of snail microbiota in different host-parasite co-evolutionary contexts. Concomitantly, using RNAseq, we investigated the link between bacterial microbiota dysbiosis and snail anti-microbial peptide immune response. This work paves the way for a better understanding of snail/schistosome interaction and should have critical consequences in terms of snail control strategies for fighting schistosomiasis disease in the field.

Characterization of a novel toll-like receptor and activation NF-κB signal pathway in triangle sail mussel Hyriopsis cumingii

Toll-like receptor (TLR) family plays an important role in innate immunity for detection of and defense against microbial pathogens. In this study, a novel toll-like receptor (HcTLRn) was characterized from freshwater pearl mussel H. cumingii. The complete sequence of HcTLRn was 3725 bp, and the open reading frame (ORF) encoded 718 amino acid residues. Predicted HcTLRn protein possessed seven atypical leucine-rich repeat (LRR) domains, two typical LRR subfamily domains, a C-terminal domain LRR, a transmembrane domain and an intracellular Toll/interleukin-1 (IL-1) receptor domain. Transcripts of HcTLRn were constitutive expressed in the tissues of healthy mussels and were markedly induced in hepatopancreas and gills after lipopolysaccharide (LPS), peptidoglycan (PGN) and polyinosinic polycytidylic acid (ploy I: C) stimulation. Knockdown of HcTLRn in vivo significantly decreased the mRNA levels of TLR pathway transcription factors p65 and p105 as well as antimicrobial peptides (AMPs) including lysozyme (HcLys), theromacin (HcTher), whey acidic protein (HcWAP), LPS-binding protein/bactericidal permeability increasing protein (HcLBP/BPI) 1 and 2 after mussels challenged by LPS. In situ hybridization results showed that HcTLRn mRNA was significantly increased in hemocytes after LPS, PGN and poly I:C stimulation. HcTLRn protein was mainly expressed in hepatopancreas and gills and was significantly increased after LPS stimulation. Moreover, recombinant extracellular domain of HcTLRn (HcTLRn-ECD) proteins could bind to a variety of bacterial and pathogen-associated molecular patterns such as LPS, PGN, and poly I:C in vitro. Subcellular localization results showed that HcTLRn was mainly distributed near the cell membrane and in cytoplasm. Over-expression of HcTLRn activated the NF-κB luciferase reporter in HEK293T cells. Collectively, these results suggested that HcTLRn was a TLR family member that might play an important role in activation of NF-κB signal pathway in Mollusca.

MolluscDB: a genome and transcriptome database for molluscs

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'.

Sticky problems: extraction of nucleic acids from molluscs

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'.

Examining adaptive evolution of immune activity: opportunities provided by gastropods in the age of 'omics'

Parasites threaten all free-living organisms, including molluscs. Understanding the evolution of immune defence traits in natural host populations is crucial for predicting their long-term performance under continuous infection risk. Adaptive trait evolution requires that traits are subject to selection (i.e. contribute to organismal fitness) and that they are heritable. Despite broad interest in the evolutionary ecology of immune activity in animals, the understanding of selection on and evolutionary potential of immune defence traits is far from comprehensive. For instance, empirical observations are only rarely in line with theoretical predictions of immune activity being subject to stabilizing selection. This discrepancy may be because ecoimmunological studies can typically cover only a fraction of the complexity of an animal immune system. Similarly, molecular immunology/immunogenetics studies provide a mechanistic understanding of immunity, but neglect variation that arises from natural genetic differences among individuals and from environmental conditions. Here, we review the current literature on natural selection on and evolutionary potential of immune traits in animals, signal how merging ecological immunology and genomics will strengthen evolutionary ecological research on immunity, and indicate research opportunities for molluscan gastropods for which well-established ecological understanding and/or 'immune-omics' resources are already available. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Inference of DNA methylation patterns in molluscs

Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Given the evolutionary age and morphological diversity of molluscs, we expected to find evidence for diverse methylation patterns. Our inferences suggest that molluscs possess substantial levels of DNA methylation in gene bodies as a rule. Yet, we found deviations from this general picture with regard to (i) the CpG observed/expected distributions indicating a reduction in DNA methylation in certain groups and (ii) the completeness of the DNMT toolkit. Reductions were evident in Caudofoveata, Solenogastres, Polyplacophora, Monoplacophora, as well as Scaphopoda. Heterobranchia and Oegopsida were remarkable as they lacked DNMT3, usually responsible for de novo methylation, yet showed signs of DNA methylation. Our survey may serve as guidance for direct empirical analyses of DNA methylation in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata

Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.

Environmentally Driven Color Variation in the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus, 1758) Is Associated With Differential Methylation of CpGs in Pigment- and Biomineralization-Related Genes

Today, it is common knowledge that environmental factors can change the color of many animals. Studies have shown that the molecular mechanisms underlying such modifications could involve epigenetic factors. Since 2013, the pearl oyster Pinctada margaritifera var. cumingii has become a biological model for questions on color expression and variation in Mollusca. A previous study reported color plasticity in response to water depth variation, specifically a general darkening of the nacre color at greater depth. However, the molecular mechanisms behind this plasticity are still unknown. In this paper, we investigate the possible implication of epigenetic factors controlling shell color variation through a depth variation experiment associated with a DNA methylation study performed at the whole genome level with a constant genetic background. Our results revealed six genes presenting differentially methylated CpGs in response to the environmental change, among which four are linked to pigmentation processes or regulations (GART, ABCC1, MAPKAP1, and GRL101), especially those leading to darker phenotypes. Interestingly, the genes perlucin and MGAT1, both involved in the biomineralization process (deposition of aragonite and calcite crystals), also showed differential methylation, suggesting that a possible difference in the physical/spatial organization of the crystals could cause darkening (iridescence or transparency modification of the biomineral). These findings are of great interest for the pearl production industry, since wholly black pearls and their opposite, the palest pearls, command a higher value on several markets. They also open the route of epigenetic improvement as a new means for pearl production improvement.

Transcriptome profiling of Lymnaea stagnalis (Gastropoda) for ecoimmunological research

BACKGROUND

Host immune function can contribute to numerous ecological/evolutionary processes. Ecoimmunological studies, however, typically use one/few phenotypic immune assays and thus do not consider the complexity of the immune system. Therefore, "omics" resources that allow quantifying immune activity across multiple pathways are needed for ecoimmunological models. We applied short-read based RNAseq (Illumina NextSeq 500, PE-81) to characterise transcriptome profiles of Lymnaea stagnalis (Gastropoda), a multipurpose model snail species. We used a genetically diverse snail stock and exposed individuals to immune elicitors (injury, bacterial/trematode pathogens) and changes in environmental conditions that can alter immune activity (temperature, food availability).

RESULTS

Immune defence factors identified in the de novo assembly covered elements broadly described in other gastropods. For instance, pathogen-recognition receptors (PRR) and lectins activate Toll-like receptor (TLR) pathway and cytokines that regulate cellular and humoral defences. Surprisingly, only modest diversity of antimicrobial peptides and fibrinogen related proteins were detected when compared with other taxa. Additionally, multiple defence factors that may contribute to the phenotypic immune assays used to quantify antibacterial activity and phenoloxidase (PO)/melanisation-type reaction in this species were found. Experimental treatments revealed factors from non-self recognition (lectins) and signalling (TLR pathway, cytokines) to effectors (e.g., antibacterial proteins, PO enzymes) whose transcription depended on immune stimuli and environmental conditions, as well as components of snail physiology/metabolism that may drive these effects. Interestingly, the transcription of many factors (e.g., PRR, lectins, cytokines, PO enzymes, antibacterial proteins) showed high among-individual variation.

CONCLUSIONS

Our results indicate several uniform aspects of gastropod immunity, but also apparent differences between L. stagnalis and some previously examined taxa. Interestingly, in addition to immune defence factors that responded to immune elicitors and changes in environmental conditions, many factors showed high among-individual variation across experimental snails. We propose that such factors are highly important to be included in future ecoimmunological studies because they may be the key determinants of differences in parasite resistance among individuals both within and between natural snail populations.

Evolutionary dynamics of transposable elements in bdelloid rotifers

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.

Identification and localization of a gonadotropin-releasing hormone-related neuropeptide in Biomphalaria, an intermediate host for schistosomiasis

Freshwater snails of the genus Biomphalaria serve as obligatory hosts for the digenetic trematode Schistosoma mansoni, the causative agent for the most widespread form of intestinal schistosomiasis. Within Biomphalaria, S. mansoni larvae multiply and transform into the cercariae form that can infect humans. Trematode development and proliferation is thought to be facilitated by modifications of host behavior and physiological processes, including a reduction of reproduction known as "parasitic castration." As neuropeptides participate in the control of reproduction across phylogeny, a neural transcriptomics approach was undertaken to identify peptides that could regulate Biomphalaria reproductive physiology. The present study identified a transcript in Biomphalaria alexandrina that encodes a peptide belonging to the gonadotropin-releasing hormone (GnRH) superfamily. The precursor and the predicted mature peptide, pQIHFTPDWGNN-NH₂ (designated Biom-GnRH), share features with peptides identified in other molluscan species, including panpulmonates, opisthobranchs, and cephalopods. An antibody generated against Biom-GnRH labeled neurons in the cerebral, pedal, and visceral ganglia of Biomphalaria glabrata. GnRH-like immunoreactive fiber systems projected to all central ganglia. In the periphery, immunoreactive material was detected in the ovotestis, oviduct, albumen gland, and nidamental gland. As these structures serve crucial roles in the production, transport, nourishment, and encapsulation of eggs, disruption of the GnRH system of Biomphalaria could contribute to reduced reproductive activity in infected snails.

Sequencing of Transcriptome and Small RNA Revealed the Xenobiotic Metabolism-Related Genes and Potential Regulatory miRNA in Asian Tramp Snail

The Asian tramp snail, Bradybaena similaris (Ferusssac), is an invasive land snail species and has been a rising agricultural pest in south of China. As a pest, it also plays a role in transmission of Angiostrongylus cantonensis. However, present studies on this species are rare and the molecular information is limited. For this purpose, we sequenced the transcriptome and small RNA of B. similaris collected from citrus orchards. In total, 89,747 unigenes with an N50 size of 1287 bp and an average length of 817 bp were generated from ∼8.9 Gb transcriptome and 31 Mb clean reads were generated from ∼36 Mb small RNA library. To demonstrate the usefulness of these two datasets, we analyzed a series of genes associated with xenobiotic metabolism and core RNAi machinery. Analysis of the transcripts resulted in annotation of 126 putative genes encoding cytochrome P450 monooxygenases (CYP, 45), carboxyl/cholinesterases (CCE, 13), glutathione-S-transferases (GST, 24), and ATP-binding cassette transporters (ABC, 44). Analysis of the small RNA detected 42 miRNAs. In addition, four genes involved in small RNA pathways (miRNA, piRNA, and siRNA) were identified, and a total of 430 genes that can be targeted by miRNAs were predicted. Moreover, we found that a few miRNAs could target certain genes involved in xenobiotic metabolism. Therefore, we believe that these two datasets and the characterization of the identified/predicted genes will facilitate the molecular study of this species as well as other land snails with agricultural importance.

The Iron-Responsive Genome of the Chiton Acanthopleura granulata

Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.

Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis

BACKGROUND

The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST libraries and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome.

RESULTS

In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved.

CONCLUSIONS

Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.

Bulinus truncatus transcriptome – a resource to enable molecular studies of snail and schistosome biology

Despite advances in high-throughput sequencing and bioinformatics, molecular investigations of snail intermediate hosts that transmit parasitic trematodes are scant. Here, we report the first transcriptome for Bulinus truncatus – a key intermediate host of Schistosoma haematobium – a blood fluke that causes urogenital schistosomiasis in humans. We assembled this transcriptome from short- and long-read RNA-sequence data. From this transcriptome, we predicted 12,998 proteins, 58% of which had orthologs in Biomphalaria glabrata – an intermediate host of Schistosoma mansoni – a blood fluke that causes hepato-intestinal schistosomiasis. We predicted that select protein groups are involved in signal transduction, cell growth and death, the immune system, environmental adaptation and/or the excretory/secretory system, suggesting roles in immune responses, pathogen defence and/or parasite-host interactions. The transcriptome of Bu. truncatus provides a useful resource to underpin future molecular investigations of this and related snail species, and its interactions with pathogens including S. haematobium. The present resource should enable comparative investigations of other molluscan hosts of socioeconomically important parasites in the future.

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First transcriptome to represent Bulinus truncatus – a snail intermediate host of Schistosoma haematobium.

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Select protein groups of Bu. truncatus are inferred to associate with innate immune responses against pathogens.

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Transcriptome provides a resource for future studies of parasite-host interactions and snail-host resistance to pathogens.

Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments

BACKGROUND

The scaly-foot snail (Chrysomallon squamiferum) is highly adapted to deep-sea hydrothermal vents and has drawn much interest since its discovery. However, the limited information on its genome has impeded further related research and understanding of its adaptation to deep-sea hydrothermal vents.

FINDINGS

Here, we report the whole-genome sequencing and assembly of the scaly-foot snail and another snail (Gigantopelta aegis), which inhabits similar environments. Using Oxford Nanopore Technology, 10X Genomics, and Hi-C technologies, we obtained a chromosome-level genome of C. squamiferum with an N50 size of 20.71 Mb. By constructing a phylogenetic tree, we found that these 2 deep-sea snails evolved independently of other snails. Their divergence from each other occurred ∼66.3 million years ago. Comparative genomic analysis showed that different snails have diverse genome sizes and repeat contents. Deep-sea snails have more DNA transposons and long terminal repeats but fewer long interspersed nuclear elements than other snails. Gene family analysis revealed that deep-sea snails experienced stronger selective pressures than freshwater snails, and gene families related to the nervous system, immune system, metabolism, DNA stability, antioxidation, and biomineralization were significantly expanded in scaly-foot snails. We also found 251 H-2 Class II histocompatibility antigen, A-U α chain-like (H2-Aal) genes, which exist uniquely in the Gigantopelta aegis genome. This finding is important for investigating the evolution of major histocompatibility complex (MHC) genes.

CONCLUSION

Our study provides new insights into deep-sea snail genomes and valuable resources for further studies.

Evolutionary novelty in the apoptotic pathway of aphids

Apoptotic processes play an important role in the development and physiology of almost all metazoan clades. In the highly diverse group of insects, apoptotic pathways have been characterized in only a few dipteran and lepidopteran species, which may not be representative of all insect species. Here, we report the first complete annotation of the apoptotic pathway in a hemipteran insect, the pea aphid Acyrthosiphon pisum. We showed that its apoptotic pathway is rewired compared to other insects, with a significant increase in the number of inhibitors of apoptosis (IAPs) and evidence for functional diversification and structural modularity of this protein family. These novelties are widespread in the aphid lineage, suggesting a yet not understood novel aphid-specific function of IAPs.

Apoptosis, a conserved form of programmed cell death, shows interspecies differences that may reflect evolutionary diversification and adaptation, a notion that remains largely untested. Among insects, the most speciose animal group, the apoptotic pathway has only been fully characterized in Drosophila melanogaster, and apoptosis-related proteins have been studied in a few other dipteran and lepidopteran species. Here, we studied the apoptotic pathway in the aphid Acyrthosiphon pisum, an insect pest belonging to the Hemiptera, an earlier-diverging and distantly related order. We combined phylogenetic analyses and conserved domain identification to annotate the apoptotic pathway in A. pisum and found low caspase diversity and a large expansion of its inhibitory part, with 28 inhibitors of apoptosis (IAPs). We analyzed the spatiotemporal expression of a selected set of pea aphid IAPs and showed that they are differentially expressed in different life stages and tissues, suggesting functional diversification. Five IAPs are specifically induced in bacteriocytes, the specialized cells housing symbiotic bacteria, during their cell death. We demonstrated the antiapoptotic role of these five IAPs using heterologous expression in a tractable in vivo model, the Drosophila melanogaster developing eye. Interestingly, IAPs with the strongest antiapoptotic potential contain two BIR and two RING domains, a domain association that has not been observed in any other species. We finally analyzed all available aphid genomes and found that they all show large IAP expansion, with new combinations of protein domains, suggestive of evolutionarily novel aphid-specific functions.

The pond snail Lymnaea stagnalis

The freshwater snail Lymnaea stagnalis has a long research history, but only relatively recently has it emerged as an attractive model organism to study molecular mechanisms in the areas of developmental biology and translational medicine such as learning/memory and neurodegenerative diseases. The species has the advantage of being a hermaphrodite and can both cross- and self-mate, which greatly facilitates genetic approaches. The establishment of body-handedness, or chiromorphogenesis, is a major topic of study, since chirality is evident in the shell coiling. Chirality is maternally inherited, and only recently a gene-editing approach identified the actin-related gene Lsdia1 as the key handedness determinant. This short article reviews the natural habitat, life cycle, major research questions and interests, and experimental approaches.

Toxicity of engineered nanomaterials to aquatic and land snails: A scientometric and systematic review

The emerging growth of nanotechnology has attracted great attention due to its application in the parasite and intermediate host control. However, the knowledge concerning the mechanism of action (MoA) and toxicity of nanomaterials (NMs) to snails remain unclear. In this context, the present study revised the historical use of snails as experimental models in nanotoxicological studies and summarized the MoA and toxicity of NMs in aquatic and land snails. The data concerning the bioaccumulation, reproductive and transgenerational toxicity, embryotoxicity, genotoxicity and potential molluscicidal activity of NMs were revised. Furthermore, the data about the experimental conditions, such as exposure time, concentrations, cell and tissue-specific responses, snail species and nanoparticle types are discussed. Revised data showed that the toxic effects of NMs were reported for 21 snail species with medical, veterinary and ecological importance. The NM toxicity to snails is dependent on the physical and chemical properties of NMs, as well as their environmental transformation and experimental design. The NM bioaccumulation on snails was related to several toxic effects, such as reactive oxygen species (ROS) production, oxidative stress, following by oxidative damage to DNA, lipids and proteins. The NM metabolism in snails remains unknown. Results showed the potential use of NMs in the snail control program. Also, significant research gaps and recommendations for future researches are indicated. The present study confirms that snails are suitable invertebrate model system to assess the nanotoxicity.

CRISPR/Cas9: A new tool for the study and control of helminth parasites

Recent reports of CRISPR/Cas9 genome editing in parasitic helminths open up new avenues for research on these dangerous pathogens. However, the complex morphology and life cycles inherent to these parasites present obstacles for the efficient application of CRISPR/Cas9-targeted mutagenesis. This is especially true with the trematode flukes where only modest levels of gene mutation efficiency have been achieved. Current major challenges in the application of CRISPR/Cas9 for study of parasitic worms thus lie in enhancing gene mutation efficiency and overcoming issues involved in host passage so that mutated parasites survive. Strategies developed for CRISPR/Cas9 studies on Caenorhabditis elegans, protozoa and mammalian cells, including novel delivery methods, the choice of selectable markers, and refining mutation precision represent novel tactics whereby these impediments can be overcome. Furthermore, employing CRISPR/Cas9-mediated gene drive to interfere with vector transmission represents a novel approach for the control of parasitic worms that is worthy of further exploration.

Toll-like signaling pathway in the transcriptome of Littorina littorea

The transcriptome of the caenogastropod mollusk Littorina littorea was scanned for the presence of sequences encoding Toll-like receptors (TLRs) and corresponding proteins involved in downstream TLR signaling pathway. In the transcriptomic snapshots of hemocytes and kidney tissues, 45 complete TLRs encoded by 35 genes were identified. Out of the 59 non-TLR molecules involved in a canonical TLR signaling pathway, 35 genes were classified as homologous and could be placed within the TLR-mediated MyD88-and MAPK-dependent circuitries. No reference vertebrate adapters TIRAP, TRIF and TRAM were identified in the transcriptome. The results of RNA-seq experiments with an immune challenge (rediae of the digenean Himasthla elongata) indicate that four TLRs (LlTLR1, 3, 5 and 8) and a set of upregulated genes involved in signal transduction (LlMyd88, LlTNFα, LlCASP8, LlFADD, LlNFKBIA (IkBα), LlIRAK1, LlSTAT1, LlMAPK14 (P38), LlMAP2K1 (MEK1/2), LlIRF3 and LlIRF5) may participate in the anti-digenean immune response of L. littorea.

Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

Whole-genome duplication (WGD), contributing to evolutionary diversity and environmental adaptability, has been observed across a wide variety of eukaryotic groups, but not in molluscs. Molluscs are the second largest animal phylum in terms of species numbers, and among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition. We assembled a chromosome-level reference genome for Achatina immaculata, a globally invasive species, and compared the genomes of two giant African snails (A. immaculata and Achatina fulica) to other available mollusc genomes. Macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested a WGD event in the two snails. The estimated WGD timing (~70 million years ago) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD may have been a common event shared by all Sigmurethra-Orthurethra species and conferred ecological adaptability allowing survival after the K-T extinction event. Furthermore, the adaptive mechanism of WGD in terrestrial ecosystems was confirmed by the presence of gene families related to the respiration, aestivation and immune defence. Several mucus-related gene families expanded early in the Stylommatophora lineage, and the haemocyanin and phosphoenolpyruvate carboxykinase families doubled during WGD, and zinc metalloproteinase genes were highly tandemly duplicated after WGD. This evidence suggests that although WGD may not have been the direct driver of the A-T transition, it played an important part in the terrestrial adaptation of giant African snails.

Diminished adherence of Biomphalaria glabrata embryonic cell line to sporocysts of Schistosoma mansoni following programmed knockout of the allograft inflammatory factor

BACKGROUND

Larval development in an intermediate host gastropod snail of the genus Biomphalaria is an obligatory component of the life-cycle of Schistosoma mansoni. Understanding of the mechanism(s) of host defense may hasten the development of tools that block transmission of schistosomiasis. The allograft inflammatory factor 1, AIF, which is evolutionarily conserved and expressed in phagocytes, is a marker of macrophage activation in both mammals and invertebrates. AIF enhances cell proliferation and migration. The embryonic cell line, termed Bge, from Biomphalaria glabrata is a versatile resource for investigation of the snail-schistosome relationship since Bge exhibits a hemocyte-like phenotype. Hemocytes perform central roles in innate and cellular immunity in gastropods and in some cases can kill the parasite. However, the Bge cells do not kill the parasite in vitro.

METHODS

Bge cells were transfected by electroporation with plasmid pCas-BgAIFx4, encoding the Cas9 nuclease and a guide RNA specific for exon 4 of the B. glabrata AIF (BgAIF) gene. Transcript levels for Cas9 and for BgAIF were monitored by reverse-transcription-PCR and, in parallel, adhesion of gene-edited Bge cells during co-culture with of schistosome sporocysts was assessed.

RESULTS

Gene knockout manipulation induced gene-disrupting indels, frequently 1-2 bp insertions and/or 8-30 bp deletions, at the programmed target site; a range from 9 to 17% of the copies of the BgAIF gene in the Bge population of cells were mutated. Transcript levels for BgAIF were reduced by up to 73% (49.5 ± 20.2% SD, P ≤ 0.05, n = 12). Adherence by BgAIF gene-edited (ΔBgAIF) Bge to sporocysts diminished in comparison to wild type cells, although cell morphology did not change. Specifically, as scored by a semi-quantitative cell adherence index (CAI), fewer ΔBgAIF than control wild type cells adhered to sporocysts; control CAI, 2.66 ± 0.10, ΔBgAIF, 2.30 ± 0.22 (P ≤ 0.01).

CONCLUSIONS

The findings supported the hypothesis that BgAIF plays a role in the adherence of B. glabrata hemocytes to sporocysts during schistosome infection in vitro. This demonstration of the activity of programmed gene editing will enable functional genomics approaches using CRISPR/Cas9 to investigate additional components of the snail-schistosome host-parasite relationship.

A critical evaluation of some of the recent so-called 'evidence' for the involvement of vertebrate-type sex steroids in the reproduction of mollusks

Many studies on the control of reproduction in mollusks have focused on hormones (and proteins associated with the production and signaling of those hormones) which were originally discovered in humans, in the belief that if they are also present in mollusks, they must have the same role. However, although human sex steroids can be found in mollusks, they are so readily absorbed that their presence is not necessarily evidence of endogenous synthesis. A homolog of the vertebrate nuclear estrogen receptor has been found in mollusks, but it does not bind to estrogens or indeed to any steroid at all. Antibodies against human aromatase show positive immunostaining in mollusks, yet the aromatase gene has not been found in the genome of any invertebrates (let alone mollusks). This review will deal with these and other examples of contradictory evidence for a role of human hormones in invertebrate reproduction.

Molluscicidal and parasiticidal activities of Eryngium triquetrum essential oil on Schistosoma mansoni and its intermediate snail host Biomphalaria glabrata, a double impact

Background

Freshwater snails are the intermediate hosts of a large variety of trematode flukes such as Schistosoma mansoni responsible for one of the most important parasitic diseases caused by helminths, affecting 67 million people worldwide. Recently, the WHO Global Vector Control Response 2017–2030 (GVCR) programme reinforced its message for safer molluscicides as part of required strategies to strengthen vector control worldwide. Here, we present the essential oil from Eryngium triquetrum as a powerful product with molluscicide and parasiticide effect against S. mansoni and the snail intermediate host Biomphalaria glabrata.

Methods

In the present study, we describe using several experimental approaches, the chemical composition of E. triquetrum essential oil extract and its biological effects against the snail B. glabrata and its parasite S. mansoni. Vector and the free-swimming larval stages of the parasite were exposed to different oil concentrations to determine the lethal concentration required to produce a mortality of 50% (LC₅₀) and 90% (LC₉₀). In addition, toxic activity of this essential oil was analyzed against embryos of B. glabrata snails by monitoring egg hatching and snail development. Also, short-time exposure to sublethal molluscicide concentrations on S. mansoni miracidia was performed to test a potential effect on parasite infectivity on snails. Mortality of miracidia and cercariae of S. mansoni is complete for 5, 1 and 0.5 ppm of oil extract after 1 and 4 h exposure.

Results

The major chemical component found in E. triquetrum oil determined by GC-FID and GC/MS analyses is an aliphatic polyacetylene molecule, the falcarinol with 86.9–93.1% of the total composition. The LC₅₀ and LC₉₀ values for uninfected snails were 0.61 and 1.02 ppm respectively for 24 h exposure. At 0.5 ppm, the essential oil was two times more toxic to parasitized snails with a mortality rate of 88.8 ± 4.8%. Moderate embryonic lethal effects were observed at the concentration of 1 ppm. Severe surface damage in miracidia was observed with a general loss of cilia that probably cause their immobility. Miracidia exposed 30 min to low concentration of plant extract (0.1 ppm) were less infective with 3.3% of prevalence compare to untreated with a prevalence of 44%.

Conclusions

Essential oil extracted from E. triquetrum and falcarinol must be considered as a promising product for the development of new interventions for schistosomiasis control and could proceed to be tested on Phase II according to the WHO requirements.

Clusters of polymorphic transmembrane genes control resistance to schistosomes in snail vectors

Schistosomiasis is a debilitating parasitic disease infecting hundreds of millions of people. Schistosomes use aquatic snails as intermediate hosts. A promising avenue for disease control involves leveraging innate host mechanisms to reduce snail vectorial capacity. In a genome-wide association study of Biomphalaria glabrata snails, we identify genomic region PTC2 which exhibits the largest known correlation with susceptibility to parasite infection (>15 fold effect). Using new genome assemblies with substantially higher contiguity than the Biomphalaria reference genome, we show that PTC2 haplotypes are exceptionally divergent in structure and sequence. This variation includes multi-kilobase indels containing entire genes, and orthologs for which most amino acid residues are polymorphic. RNA-Seq annotation reveals that most of these genes encode single-pass transmembrane proteins, as seen in another resistance region in the same species. Such groups of hyperdiverse snail proteins may mediate host-parasite interaction at the cell surface, offering promising targets for blocking the transmission of schistosomiasis.

The Members of the Highly Diverse Crassostrea gigas Integrin Family Cooperate for the Generation of Various Immune Responses

Studies on invertebrate immune receptors can provide insights into characteristics specific to innate immune system. Here, eight α and three β integrins are identified from an invertebrate, the Pacific oyster Crassostrea gigas, and their possible immune functions are studied. Oyster α/β integrins exhibit a higher degree of sequence and structural variability than the members from Homo sapiens and Drosophila melanogaster. The analysis reveals that oyster RGD- and laminin-binding receptor homologs are present in the phylogenetic tree of α integrins, but the other six oyster α integrins mainly form a species-specific branch; meanwhile, oyster β integrins are clustered with insect β integrins but distinct from a member from the mollusk Biomphalaria glabrata. Although phylogenetically lacking the important α integrin branches of LDV-binding, PS3-type, and αI-containing integrins, oyster integrins can bind to most ECM ligands, including RGDCP, LDVCP, GFOGERCP, and laminin protein in a distinct binding pattern. Besides, oyster integrins are distributed in different hemocyte subpopulations, while only specific integrins are selectively involved in hemocyte phagocytosis, migration, and encapsulation, and some of them participate in more than one immune response in a sophisticated pattern. Especially, oyster β integrins are arranged in the core to mediate complex immune responses, unlike the counterparts in humans that mainly depend on αI-containing integrins to incite immune reactions. This study represents the first comprehensive attempt to reveal the structural and evolutionary features of the integrin family and their involvement in cellular immune responses in the non-model invertebrate C. gigas and sheds light on the characteristics specific to the innate immune system in the integrin family.

Genome-wide identification and transcriptome-based expression profiling of Wnt gene family in Ruditapes philippinarum

The Wnt genes encode a set of conserved glycoproteins regulating early development, cell proliferation and differentiation, and tissue regeneration in metazoans. In some mollusks, the knowledge of Wnt gene family has been limited because of the short of the genomic and transcriptomic resources. Ruditapes philippinarum is an economically important bivalve with a variety of shell coloration patterns and ability to regenerate its siphon. To gain a greater understanding of the evolutionary dynamics of Wnt gene family, we carried out a genome-wide identification and phylogenetic analysis of Wnt gene family in R. philippinarum and other four mollusks. A total of 12 Wnt genes were identified in the genome of R. philippinarum, and the dynamic patterns of gene conservation, loss and duplication of Wnt genes were analyzed in mollusks and model organisms. Furthermore, the transcriptome analyses demonstrated the expression profiles of the Wnt genes at different developmental stage, in adult tissues, during siphon regeneration, in four different shell color strains, and at uncolored and colored developmental stages in two different shell color strains. These findings suggest that the expansion of Wnt genes may play vital roles in the larval development, the formation of shell color pattern and siphon regeneration in R. philippinarum. This study provides a valuable insight into Wnt function and evolution in mollusks.

Deep sequencing of small RNAs reveals the repertoire of miRNAs and piRNAs in Biomphalaria glabrata

BACKGROUND

Biomphalaria glabrata snails are widely distributed in schistosomiasis endemic areas like America and Caribe, displaying high susceptibility to infection by Schistosoma mansoni. After the availability of B. glabrata genome and transcriptome data, studies focusing on genetic markers and small non-coding RNAs have become more relevant. The small RNAs have been considered important through their ability to finely regulate the gene expression in several organisms, thus controlling the functions like cell growth, metabolism, and susceptibility/resistance to infection.

OBJECTIVE

The present study aims on identification and characterisation of the repertoire of small non-coding RNAs in B. glabrata (Bgl-small RNAs).

METHODS

By using small RNA sequencing, bioinformatics tools and quantitative reverse transcription polymerase chain reaction (RT-qPCR), we identified, characterised, and validated the presence of small RNAs in B. glabrata.

FINDINGS

89 mature miRNAs were identified and five of them were classified as Mollusk-specific. When compared to model organisms, sequences of B. glabrata miRNAs showed a high degree of conservation. In addition, several target genes were predicted for all the mature miRNAs identified. Furthermore, piRNAs were identified in the genome of B. glabrata for the first time. The B. glabrata piRNAs showed strong conservation of uridine as first nucleotide at 5’ end, besides adenine at 10th position. Our results showed that B. glabrata has diverse repertoire of circulating ncRNAs, several which might be involved in mollusk susceptibility to infection, due to their potential roles in the regulation of S. mansoni development.

MAIN CONCLUSIONS

Further studies are necessary in order to confirm the role of the Bgl-small RNAs in the parasite/host relationship thus opening new perspectives on interference of small RNAs in the organism development and susceptibility to infection.

Snail-Related Contributions from the Schistosomiasis Consortium for Operational Research and Evaluation Program Including Xenomonitoring, Focal Mollusciciding, Biological Control, and Modeling

The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) was created in 2008 to answer questions of importance to program managers working to reduce the burden of schistosomiasis in Africa. In the past, intermediate host snail monitoring and control was an important part of integrated schistosomiasis control. However, in Africa, efforts to control snails have declined dramatically over the last 30 years. A resurgence of interest in the control of snails has been prompted by the realization, backed by a World Health Assembly resolution (WHA65.21), that mass drug administration alone may be insufficient to achieve schistosomiasis elimination. SCORE has supported work on snail identification and mapping and investigated how xenomonitoring techniques can aid in the identification of infected snails and thereby identify potential transmission areas. Focal mollusciciding with niclosamide was undertaken in Zanzibar and Côte d'Ivoire as a part of elimination studies. Two studies involving biological control of snails were conducted: one explored the association of freshwater riverine prawns and snail hosts in Côte d'Ivoire and the other assessed the current distribution of Procambarus clarkii, the invasive Louisiana red swamp crayfish, in Kenya and its association with snail hosts and schistosomiasis transmission. SCORE also supported modeling studies on the importance of snail control in achieving elimination and a meta-analysis of the impact of molluscicide-based snail control programs on human schistosomiasis prevalence and incidence. SCORE's snail control studies contributed to increased investment in building capacity, and specimens collected during SCORE research deposited in the Schistosomiasis Collections at the Natural History Museum (SCAN) will provide a valuable resource for the years to come.

Endophytic Fungi in the Fight Against Neglected Tropical Diseases

Neglected tropical diseases are a serious global public health problem and they are one of the main causes of mortality and morbidity, especially in underdeveloped countries. These diseases have several implications for health and they are considered a priority in global eradication programs for disease control. The aim of this mini-review is to report recent studies on the fight against neglected diseases, namely dengue fever, chikungunya, zika, malaria protozoa, Chagas disease, leishmaniasis, schistosomiasis helminths, filariasis, and tuberculosis bacteria using extracts and isolated substances of endophytic fungi based on their bioactivity profiles in relation to these diseases.

Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies

Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium

BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium. OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome. METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.

Spiralian Genomes Reveal Gene Family Expansions Associated with Adaptation to Freshwater

The colonization of freshwater habitats by marine-adapted organisms represents a major transition that has only occurred a few times in the evolution of animals. Only around half of the extant animal phyla have representatives in both marine and freshwater environments and even within those phyla some major clades are restricted to marine environments. Moving from marine to freshwater environments can create severe osmotic and ionic stresses and the mechanisms that animals have used to adapt to those stresses are still not well understood. In this study, we downloaded amino acid sequence data from 11 spiralian animal genomes (four freshwater taxa representing four different phyla as well as 7 marine taxa) and identified a number of gene family expansions that have occurred exclusively in the freshwater lineages. Further investigation of these gene families and the timing and nature of their expansions will illuminate one of the major evolutionary transitions in the history of life on Earth.

Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves

Crassostrea hongkongensis is a popular and important native oyster species that is cultured mainly along the coast of the South China Sea. However, the absence of a reference genome has restricted genetic studies and the development of molecular breeding schemes for this species. Here, we combined PacBio and 10 × Genomics technologies to create a C. hongkongensis genome assembly, which has a size of 610 Mb, and is close to that estimated by flow cytometry (~650 Mb). Contig and scaffold N50 are 2.57 and 4.99 Mb, respectively, and BUSCO analysis indicates that 95.8% of metazoan conserved genes are completely represented. Using a high-density linkage map of its closest related species, C. gigas, a total of 521 Mb (85.4%) was anchored to 10 haploid chromosomes. Comparative genomic analyses with other molluscs reveal that several immune- or stress response-related genes extensively expanded in bivalves by tandem duplication, including C1q, Toll-like receptors and Hsp70, which are associated with their adaptation to filter-feeding and sessile lifestyles in shallow sea and/or deep-sea ecosystems. Through transcriptome sequencing, potential genes and pathways related to sex determination and gonad development were identified. The genome and transcriptome of C. hongkongensis provide valuable resources for future molecular studies, genetic improvement and genome-assisted breeding of oysters.

The evo-devo of molluscs: Insights from a genomic perspective

Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.

Physiology and immunity of the invasive giant African snail, Achatina (Lissachatina) fulica, intermediate host of Angiostrongylus cantonensis

As one of the most successful invasive land snail species, Achatina (Lissachatina) fulica Bowdich, 1822 has achieved wide global distribution, particularly in (sub)tropical regions, with further dispersal likely due to climate change. This species of giant African snails (up to 17 cm shell length) is a pest that has extensive negative impact on agriculture and can serve as vector for several parasites, including Angiostrongylus cantonensis, a nematode parasite that causes (human) eosinophilic meningitis, an emergent disease. Investigation showed that A. cantonensis infection negatively impacts the metabolism of A. fulica by depleting polysaccharide stores of the intermediate host, compromising the energy balance of the snail. A review of the literature indicates that A. fulica possesses potent innate type immune defenses to counter infection, including phagocytic hemocytes capable of deploying reactive oxygen species and lectins for non-self recognition, a serine protease-dependent coagulation response (not observed in other taxa of gastropods), as well as antimicrobial proteins including achacin, an antimicrobial protein. A recent chromosome level genome assembly will facilitate progressively detailed characterization of these immune features of A. fulica. We strongly encourage further immunological studies of A. fulica, ranging from organismal level to molecular biology to gain better understanding of the A. fulica internal defense response to nematode pathogens like A. cantonensis and the contribution of immune function to the invasiveness of (snail) species. Characterization of immunity of A. fulica, representing the understudied Stylommatophora (panpulmonate landsnails) will also broaden the comparative immunology of Gastropoda.