A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni

A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.

A first report of Biomphalaria pfeifferi in the Lower Shire Valley, Southern Malawi, a major intermediate snail host species for intestinal schistosomiasis

The distribution of certain permissive intermediate snail host species in freshwater is a crucial factor shaping transmission of intestinal schistosomiasis, a neglected tropical disease that causes much human suffering in Africa. To shed new light on southern Malawi, where cases of intestinal schistosomiasis have been found, repeated malacological surveys were conducted in Chikwawa and Nsanje Districts in the Lower Shire Valley, to detect and to characterize populations of Biomphalaria, the intermediate host for intestinal schistosomiasis. Sampling took place across a total of 45 freshwater sites, noting water conductivity, pH, temperature, total dissolved salts (TDS) and geographical elevation. The presence or absence of snails was predicted upon physiochemical and environmental conditions in Random Forest modelling. Water conductivity, TDS and geographical elevation were most important in predicting abundance of snails with water temperature and pH of slightly less important roles. This first report of B. pfeifferi in the Lower Shire Valley enhances understanding of the environmental factors that strongly associate and allow prediction of its local distribution. This represents a useful step towards developing appropriate intervention strategies to mitigate intestinal schistosomiasis transmission.

Mating system of Biomphalaria sudanica, a vector of Schistosoma mansoni

Biomphalaria snails are intermediate hosts for schistosome parasites, which cause morbidity and mortality in humans worldwide. We aimed to determine the mating system of Biomphalaria sudanica, a hermaphroditic vector of schistosomiasis in the African Great Lakes, with the goal of informing the design of genetic studies such as linkage mapping to improve genome assembly and genetic association studies to identify snail resistance genes. To determine the relative rates of outcrossing versus selfing, we assayed the progeny of experimental crosses of snails in the laboratory using a PCR and restriction enzyme digest to determine snail genotype and parentage. Out of 7 experimental crosses and 56 total offspring assayed, 100% were derived from outcrossing rather than inbreeding. These results indicate that B. sudanica is primarily an outcrossing species, although previous work has shown that this species retains the capability of self-fertilization.

Immune targets for schistosomiasis control identified by a genome-wide association study of African snail vectors

Schistosomiasis, a neglected tropical disease, is transmitted by freshwater snails. Interruption of transmission will require novel vector-focused interventions. We performed a genome-wide association study of African snails, Biomphalaria sudanica, exposed to Schistosoma mansoni in an endemic area of high transmission in Kenya. Two snail genomic regions, SudRes1 and SudRes2, were significantly associated with snail immunity to schistosomes. SudRes1 includes receptor-like protein tyrosine phosphatases while SudRes2 includes a class of leucine-rich repeat-containing G-protein coupled receptors, both comprising diverse extracellular binding domains suggestive of host-pathogen interaction. Resistant and susceptible haplotypes show numerous coding differences including presence/absence of entire genes. No loci previously tied to schistosome resistance in neotropical snail species showed any association with compatibility suggesting that loci involved in the resistance of African vectors are distinct. Snail ancestry was also strongly correlated with parasite compatibility. These results will inform future efforts to predict and manipulate immunity of a major schistosome vector.

Molecular xenomonitoring of Schistosoma mansoni infections in Biomphalaria choanomphala at Lake Victoria, East Africa: Assessing roles of abiotic and biotic factors

Lake Victoria is a well-known hot spot for intestinal schistosomiasis, caused by infection with the trematode Schistosoma mansoni. The snail intermediate hosts of this parasite are Biomphalaria snails, with Biomphalaria choanomphala being the predominant intermediate host within Lake Victoria. The prevalence of S. mansoni infection within snail populations is influenced by both biotic and abiotic factors, including the physical and chemical characteristics of their environment, the incidence of infection in human populations (and reservoir hosts) and the level of genetic compatibility between the parasite and the host. Using molecular xenomonitoring, we measured the prevalence of S. mansoni infection within B. choanomphala populations along the Kenyan, Tanzanian and Ugandan shorelines of Lake Victoria and related this to the abiotic (habitat type, water depth, turbulence, temperature, conductivity, total dissolved solids, salinity, pH level) and biotic (B. choanomphala abundance, genetic diversity of host snail populations) factors of the lake. The overall mean prevalence of S. mansoni infection at Lake Victoria was 9.3%, with the highest prevalence of infection occurring on the Tanzanian shoreline (13.1%), followed by the Ugandan (8.2%) and Kenyan (4.7%) shorelines. There was a significant difference in B. choanomphala abundance, water temperature, conductivity, salinity, total dissolved solids and major anion/cation concentrations between the Kenyan, Tanzanian and Ugandan shorelines of Lake Victoria. A Spearman's rank analysis found that the prevalence of S. mansoni infection had a significant, positive relationship with higher levels of B. choanomphala abundance, water acidity, and cation (Ca2+, Mg2+) concentrations. Additionally, we observed that sites with S. mansoni infection correlated with B. choanomphala populations with a higher mean haplotype diversity score compared to sites found without infection, though there was no significant relationship between the prevalence of infection and B. choanomphala haplotype diversity scores. Although our analysis is based upon an archival and unique collection of Biomphalaria snails, the abiotic and biotic relationships uncovered are useful for eco-epidemiological comparisons of intestinal schistosomiasis across Lake Victoria in future.

Localization of Cholecystokinin/Sulfakinin Neuropeptides in Biomphalaria glabrata, an Intermediate Host for Schistosomiasis

Snails belonging to the genus Biomphalaria serve as obligatory intermediate hosts for the trematode Schistosoma mansoni, the causative agent for the most widespread form of schistosomiasis. The simpler nervous systems of gastropod molluscs, such as Biomphalaria, provide advantageous models for investigating neural responses to infection at the cellular and network levels. The present study examined neuropeptides related to cholecystokinin (CCK), a major multifunctional regulator of central nervous system (CNS) function in mammals. A neural transcriptome generated from the CNS of Biomphalaria alexandrina included a transcript encoding two CCK-related peptides, designated Balex-CCK1 (pEGEWSYDY(SO 3 H)GLGGGRF-NH2) and Balex-CCK2 (NYGDY(SO 3 H)GIGGGRF-NH2). Peptide expression was examined in Biomphalaria glabrata at the mRNA level using the hybridization chain reaction (HCR) protocol and at the protein level using an antibody against Balex-CCK1. Expression was detected in 60-70 neurons distributed throughout the CNS, as well as in profuse fiber systems connecting the ganglia and projecting to the periphery. CCK-like immunoreactive (CCKli) fibers were also observed on organs associated with the cardiorespiratory (nephridium, mantle, gill) and male reproductive systems. A comparison of mRNA and peptide localization suggested that CCK expression could be regulated at the level of translation. A potential role of these peptides in mediating responses to infection by larval schistosomes is discussed.

Exploring the genome-wide transcriptomic responses of Bulinus truncatus to Schistosoma haematobium infection: An important host-parasite system involved in the transmission of human urogenital schistosomiasis

Freshwater snails of the genus Bulinus are critical hosts for Schistosoma haematobium, the causative agent of urogenital schistosomiasis. Among the 37 recognized Bulinus species, B. truncatus is a key vector. Using RNA sequencing (RNAseq), we investigated the genome-wide transcriptional responses of B. truncatus to S. haematobium infection. Our findings suggest that snails employ a complex defense strategy against the parasites by up-regulating genes involved in immune response, stress reaction, structural integrity, metabolism, and detoxification. In response, schistosome parasites appear to manipulate the snail's defense system, as evidenced by the suppression of immune-related genes such as ficolin, peptidoglycan recognition protein, and C-type lectin domain-containing protein genes. The down-regulation of biomphalysin 9, compared to its function in Biomphalaria glabrata, indicates divergent immune strategies among snail hosts. Additionally, we compared transcriptome profiles between embryos and juveniles, providing insights into developmental processes. This study offers valuable genomic data for Bulinus snails, illuminating the molecular interactions between bulinids and schistosomes, and advancing our understanding of their developmental biology.

Immune targets for schistosomiasis control identified by a genome-wide association study of East African snail vectors

Schistosomiasis, afflicting >260 million people worldwide, could be controlled by preventing infection of freshwater snail vectors. Intestinal schistosomiasis, caused by Schistosoma mansoni, occurs predominantly in Sub-Saharan Africa and is vectored by Biomphalaria sudanica and related Biomphalaria species. Despite their importance in transmission, very little genomic work has been initiated in African snails, thus hindering development of novel control strategies. To identify genetic factors influencing snail resistance to schistosomes, we performed a pooled genome-wide association study (pooled-GWAS) on the offspring of B. sudanica collected from a persistent hotspot of schistosomiasis in Lake Victoria, Kenya, and exposed to sympatric S. mansoni. Results of the pooled-GWAS were used to develop an amplicon panel to validate candidate loci by genotyping individual snails. This validation revealed two previously uncharacterized, evolutionarily dynamic regions, SudRes1 and SudRes2, that were significantly associated with resistance. SudRes1 includes receptor-like protein tyrosine phosphatases and SudRes2 includes a class of leucine-rich repeat-containing G-protein coupled receptors, both comprising diverse extracellular binding domains, suggesting roles in pathogen recognition. No loci previously tied to schistosome resistance in other snail species showed any association with compatibility suggesting that loci involved in the resistance of African vectors differ from those of neotropical vectors. Beyond these two loci, snail ancestry was strongly correlated with schistosome compatibility, indicating the importance of population structure on transmission dynamics and infection risk. These results provide the first detail of the innate immune system of the major schistosome vector, B. sudanica, informing future studies aimed at predicting and manipulating vector competence.

Different metazoan parasites, different transcriptomic responses, with new insights on parasitic castration by digenetic trematodes in the schistosome vector snail Biomphalaria glabrata

BACKGROUND

Gastropods of the genus Biomphalaria (Family Planorbidae) are exploited as vectors by Schistosoma mansoni, the most common causative agent of human intestinal schistosomiasis. Using improved genomic resources, overviews of how Biomphalaria responds to S. mansoni and other metazoan parasites can provide unique insights into the reproductive, immune, and other systems of invertebrate hosts, and their responses to parasite challenges.

RESULTS

Using Illumina-based RNA-Seq, we compared the responses of iM line B. glabrata at 2, 8, and 40 days post-infection (dpi) to single infections with S. mansoni, Echinostoma paraensei (both digenetic trematodes) or Daubaylia potomaca (a nematode parasite of planorbid snails). Responses were compared to unexposed time-matched control snails. We observed: (1) each parasite provoked a distinctive response with a predominance of down-regulated snail genes at all time points following exposure to either trematode, and of up-regulated genes at 8 and especially 40dpi following nematode exposure; (2) At 2 and 8dpi with either trematode, several snail genes associated with gametogenesis (particularly spermatogenesis) were down-regulated. Regarding the phenomenon of trematode-mediated parasitic castration in molluscs, we define for the first time a complement of host genes that are targeted, as early as 2dpi when trematode larvae are still small; (3) Differential gene expression of snails with trematode infection at 40dpi, when snails were shedding cercariae, was unexpectedly modest and revealed down-regulation of genes involved in the production of egg mass proteins and peptide processing; and (4) surprisingly, D. potomaca provoked up-regulation at 40dpi of many of the reproduction-related snail genes noted to be down-regulated at 2 and 8dpi following trematode infection. Happening at a time when B. glabrata began to succumb to D. potomaca, we hypothesize this response represents an unexpected form of fecundity compensation. We also document expression patterns for other Biomphalaria gene families, including fibrinogen domain-containing proteins (FReDs), C-type lectins, G-protein coupled receptors, biomphalysins, and protease and protease inhibitors.

CONCLUSIONS

Our study is relevant in identifying several genes involved in reproduction that are targeted by parasites in the vector snail B. glabrata and that might be amenable to manipulation to minimize their ability to serve as vectors of schistosomes.

Accelerating snail vector genomics

The three most important genera of snails for the transmission of schistosomes are Bulinus, Biomphalaria and Oncomelania. Each of these genera, found in two distantly related families, includes species that act as the intermediate host for one of the three most widespread schistosome species infecting humans, Schistosoma haematobium, S. mansoni and S. japonicum, respectively. An important step in the fight against schistosomiasis in Asia has been taken with the publication of the article "Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum", which means that genomes for all three major genera, including species across three continents, are now available in the public domain. This includes the first genomes of African snail vectors, namely Biomphalaria sudanica, Bi. pfeifferi and Bulinus truncatus, as well as high-quality chromosome level assemblies for South American Bi. glabrata. Most importantly, the wealth of new genomic and transcriptomic data is helping to establish the specific molecular mechanisms that underly compatibility between snails and their schistosomes, which although diverse and complex, may help to identify potential targets dictating host parasite interactions that can be utilised in future transmission control strategies. This new work on Oncomelania hupensis and indeed studies on other snail vectors, which provide deep insights into the genome, will stimulate research that may well lead to new and much needed control interventions.

Transcriptional profiling of Bulinus globosus provides insights into immune gene families in snails supporting the transmission of urogenital schistosomiasis

Schistosomiasis, urogenital and intestinal, afflicts 251 million people worldwide with approximately two-thirds of the patients suffering from the urogenital form of the disease. Freshwater snails of the genus Bulinus (Gastropoda: Planorbidae) serve as obligate intermediate hosts for Schistosoma haematobium, the etiologic agent of human urogenital schistosomiasis. These snails also act as vectors for the transmission of schistosomiasis in livestock and wildlife. Despite their crucial role in human and veterinary medicine, our basic understanding at the molecular level of the entire Bulinus genus, which comprises 37 recognized species, is very limited. In this study, we employed Illumina-based RNA sequencing (RNAseq) to profile the genome-wide transcriptome of Bulinus globosus, one of the most important intermediate hosts for S. haematobium in Africa. A total of 179,221 transcripts (N50 = 1,235) were assembled and the benchmarking universal single-copy orthologs (BUSCO) was estimated to be 97.7%. The analysis revealed a substantial number of transcripts encoding evolutionarily conserved immune-related proteins, particularly C-type lectin (CLECT) domain-containing proteins (n = 316), Toll/Interleukin 1-receptor (TIR)-containing proteins (n = 75), and fibrinogen related domain-containing molecules (FReD) (n = 165). Notably, none of the FReDs are fibrinogen-related proteins (FREPs) (immunoglobulin superfamily (IgSF) + fibrinogen (FBG)). This RNAseq-based transcriptional profile provides new insights into immune capabilities of Bulinus snails, helps provide a framework to explain the complex patterns of compatibility between snails and schistosomes, and improves our overall understanding of comparative immunology.

Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum

BACKGROUND

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum.

METHODS

The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.

RESULTS

A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.

CONCLUSIONS

Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

BACKGROUND

Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs).

RESULTS

De novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ~ 944.2 Mb (6,728 fragments, N50 = 1.067 Mb), comprising 23,598 genes (BUSCO = 93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata, including the polymorphic transmembrane clusters (PTC1 and PTC2), RADres, and other loci. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes was seen in African compared to South American lineages.

CONCLUSIONS

The B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.

A haplotype-like, chromosome-level assembled and annotated genome of Biomphalaria glabrata, an important intermediate host of schistosomiasis and the best studied model of schistosomiasis vector snails

Schistosomiasis is one of the world's most devastating parasitic diseases, afflicting 251 million people globally. The Neotropical snail Biomphalaria glabrata is an important intermediate host of the human blood fluke Schistosoma mansoni and a predominant model for schistosomiasis research. To fully exploit this model snail for biomedical research, here we report a haplotype-like, chromosome-level assembled and annotated genome of the homozygous iM line of B. glabrata that we developed at the University of New Mexico. Using multiple sequencing platforms, including Illumina, PacBio, and Omni-C sequencing, 18 sequence contact matrices representing 18 haploid chromosomes (2n = 36) were generated (337x genome coverage), and 96.5% of the scaffold sequences were anchored to the 18 chromosomes. Protein-coding genes (n = 34,559), non-coding RNAs (n = 2,406), and repetitive elements (42.52% of the genome) were predicted for the whole genome, and detailed annotations for individual chromosomes were also provided. Using this genomic resource, we have investigated the genomic structure and organization of the Toll-like receptor (TLR) and fibrinogen-domain containing protein (FReD) genes, the two important immune-related gene families. Notably, TLR-like genes are scattered on 13 chromosomes. In contrast, almost all (39 of 40) fibrinogen-related genes (FREPs) (immunoglobulin superfamily (IgSF) + fibrinogen (FBG)) are clustered within a 5-million nucleotide region on chromosome 13, yielding insight into mechanisms involved in the diversification of FREPs. This is the first genome of schistosomiasis vector snails that has been assembled at the chromosome level, annotated, and analyzed. It serves as a valuable resource for a deeper understanding of the biology of vector snails, especially Biomphalaria snails.

Immuno-molecular profile for Biomphalaria glabrata/Schistosoma mansoni interaction

The complex innate immune defense of Biomphalaria glabrata, the intermediate host of Schistosoma mansoni, governs the successful development of the intramolluscan stages of the parasite. The interaction between the snail and the parasite involves a complex immune molecular crosstalk between several parasite antigens and the snail immune recognition receptors, evoking different signals and effector molecules. This work seeks to discuss the immune-related molecules that influence compatibility in Biomphalaria glabrata/Schistosoma mansoni interaction and the differential expression of these molecules between resistant and susceptible snails. It also includes the current understanding of the immune molecular determinants that govern the compatibility in sympatric and allopatric interactions, and the expression of these molecules after immune priming and the secondary immune response. Herein, the differences in the immune-related molecules in the interaction of other Biomphalaria species with Schistosoma mansoni compared to the Biomphalaria glabrata model snail are highlighted. Understanding the diverse immune molecular determinants in the snail/schistosome interaction can lead to alternative control strategies for schistosomiasis.

Gut microbiota in parasite-transmitting gastropods

BACKGROUND

Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives.

METHODS

A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria.

RESULTS

Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed.

CONCLUSIONS

This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.

The genome and transcriptome of the snail Biomphalaria sudanica s.l.: Immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

Background

Control and elimination of schistosomiasis is an arduous task, with current strategies proving inadequate to break transmission. Exploration of genetic approaches to interrupt Schistosoma mansoni transmission, the causative agent for human intestinal schistosomiasis in sub-Saharan Africa and South America, has led to genomic research of the snail vector hosts of the genus Biomphalaria. Few complete genomic resources exist, with African Biomphalaria species being particularly underrepresented despite this being where the majority of S. mansoni infections occur. Here we generate and annotate the first genome assembly of Biomphalaria sudanica sensu lato, a species responsible for S. mansoni transmission in lake and marsh habitats of the African Rift Valley. Supported by whole-genome diversity data among five inbred lines, we describe orthologs of immune-relevant gene regions in the South American vector B. glabrata and present a bioinformatic pipeline to identify candidate novel pathogen recognition receptors (PRRs).

Results

De novo genome and transcriptome assembly of inbred B. sudanica originating from the shoreline of Lake Victoria (Kisumu, Kenya) resulted in a haploid genome size of ~944.2 Mb (6732 fragments, N50=1.067 Mb), comprising 23,598 genes (BUSCO=93.6% complete). The B. sudanica genome contains orthologues to all described immune genes/regions tied to protection against S. mansoni in B. glabrata. The B. sudanica PTC2 candidate immune genomic region contained many PRR-like genes across a much wider genomic region than has been shown in B. glabrata, as well as a large inversion between species. High levels of intra-species nucleotide diversity were seen in PTC2, as well as in regions linked to PTC1 and RADres orthologues. Immune related and putative PRR gene families were significantly over-represented in the sub-set of B. sudanica genes determined as hyperdiverse, including high extracellular diversity in transmembrane genes, which could be under pathogen-mediated balancing selection. However, no overall expansion in immunity related genes were seen in African compared to South American lineages.

Conclusions

The B. sudanica genome and analyses presented here will facilitate future research in vector immune defense mechanisms against pathogens. This genomic/transcriptomic resource provides necessary data for the future development of molecular snail vector control/surveillance tools, facilitating schistosome transmission interruption mechanisms in Africa.

Identification and characterization of microRNAs in Biomphalaria tenagophila and comparative analysis of their expression in Schistosoma mansoni-resistant and -susceptible snail populations

BACKGROUND

Schistosomiasis is a neglected tropical disease caused by Schistosoma and affects over 240 million people worldwide. One of the most prominent causative agents is Schistosoma mansoni, which develops inside the intermediate host. Biomphalaria tenagophila is the second most important vector of schistosomiasis in Brazil and the Taim population is completely resistant to infection by S. mansoni.

OBJECTIVE

This study aims to identify and characterize B. tenagophila microRNAs (miRNAs) and evaluate their differential expression in S. mansoni-susceptible and -resistant populations of B. tenagophila.

METHODS

Two populations of B. tenagophila snails, susceptible and resistant to S. mansoni infection, were used to investigate the small RNA response of these snails after being infected with the parasite. Small RNA sequencing and quantitative real-time PCR were employed to identify and validate differentially expressed miRNAs. Bioinformatics analysis were performed to identify miRNA precursors and mature and evaluate their differential expression.

FINDINGS

The study predicted 173 mature miRNAs and 123 precursors. Among them were six Lophotrochozoa-specific miRNAs, three mollusk-specific miRNAs, and six pre-miRNAs in a cluster. The small RNA sequencing and RT-PCR of B. tenagophila samples allowed assessing the expression patterns of miRNAs.

MAIN CONCLUSIONS

The results obtained may support future studies in Biomphalaria spp., generating a global impact on disease control.