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The genetic diversity and geographical separation study of Oncomelania hupensis populations in mainland China using microsatellite loci.

ABSTRACT: Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which plays a crucial role in the transmission of schistosomiasis. The endemic area of S. japonicum is strictly consistent with the geographical distribution of O. hupensis.A total of 24 populations of O. hupensis from four ecological landscapes were selected for analysis of genetic diversity by screening eight microsatellite DNA polymorphic loci.The number of alleles per locus ranged from 29 to 70 with an average of 45.625 and that of effective alleles were 18.5 to 45.8 with an average of 27.4. The observed (Ho) and expected (He) heterozygosities varied from 0.331 to 0.57 and from 0.888 to 0.974, respectively. The mean of polymorphism information content (PIC) for all populations was 0.940, appearing polymorphic for all loci. For the fixation index of F-Statistics, Fit and Fst were 54.95 and 37.62%, respectively. Variation of O. hupensis chiefly exists among individuals, accounting for 60.58% of the total variation determined by Analysis of Molecular Variation (AMOVA). Variation among individuals within populations, among populations within groups and among groups only accounted for 26.60, 8.04 and 4.78%, respectively. This distribution of variation suggests that genetic differences principally originate from within-populations rather than among-populations. Moreover, UPGMA cluster analysis showed that the populations spreading within middle and lower reaches of the Yangtze River (HBWH, JSYZ, JXNC, HNHS, JXJJ, AHWW, HBJL, JXDC, HNNX, JSYZJZ, ZJJH, AHNG and AHWJ) clustered together first, then gathered with the populations in the high mountains (SCMS, SCYA, SCPJ, YNEY, SCLS, YNWS and SCXC), coastal hills (FJFQ and FJFZ) and Karst landform (GXBS and GXYZ) successively.This study provides novel insight into the theoretical source of genetic differentiation of Oncomelania hupensis in mainland China, which is critical for the epidemiological investigation and surveillance of S. japonicum.

SUBMITTER: Guan W

PROVIDER: S-EPMC4721134 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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The genetic diversity and geographical separation study of Oncomelania hupensis populations in mainland China using microsatellite loci.

Guan Wei W Li Shi-Zhu SZ Abe Eniola Michael EM Webster Bonnie L BL Rollinson David D Zhou Xiao-Nong XN

Parasites & vectors 20160120

<h4>Background</h4>Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which plays a crucial role in the transmission of schistosomiasis. The endemic area of S. japonicum is strictly consistent with the geographical distribution of O. hupensis.<h4>Methods</h4>A total of 24 populations of O. hupensis from four ecological landscapes were selected for analysis of genetic diversity by screening eight microsatellite DNA polymorphic loci.<h4>Results</h4>The number of alleles ...[more]

PMID: 26791938

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Project description:BACKGROUND: Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which causes schistosomiasis endemic in the Far East, and especially in mainland China. O. hupensis largely determines the parasite's geographical range. How O. hupensis's genetic diversity is distributed geographically in mainland China has never been well examined with DNA sequence data. METHODOLOGY/PRINCIPAL FINDINGS: In this study we investigate the genetic variation among O. hupensis from different geographical origins using the combined complete internal transcribed spacer 1 (ITS1) and ITS2 regions of nuclear ribosomal DNA. 165 O. hupensis isolates were obtained in 29 localities from 7 provinces across mainland China: lake/marshland and hill regions in Anhui, Hubei, Hunan, Jiangxi and Jiangsu provinces, located along the middle and lower reaches of Yangtze River, and mountainous regions in Sichuan and Yunnan provinces. Phylogenetic and haplotype network analyses showed distinct genetic diversity and no shared haplotypes between populations from lake/marshland regions of the middle and lower reaches of the Yangtze River and populations from mountainous regions of Sichuan and Yunnan provinces. The genetic distance between these two groups is up to 0.81 based on Fst, and branch time was estimated as 2-6 Ma. As revealed in the phylogenetic tree, snails from Sichuan and Yunnan provinces were also clustered separately. Geographical separation appears to be an important factor accounting for the diversification of the two groups of O. hupensis in mainland China, and probably for the separate clades between snails from Sichuan and Yunnan provinces. In lake/marshland and hill regions along the middle and lower reaches of the Yangtze River, three clades were identified in the phylogenetic tree, but without any obvious clustering of snails from different provinces. CONCLUSIONS: O. hupensis in mainland China may have considerable genetic diversity, and a more complex population structure than expected. It will be of significant importance to consider the genetic diversity of O. hupensis when assessing co-evolutionary interactions with S. japonicum.

Project description:Background:The freshwater snail Oncomelania hupensis is the obligate intermediate host for Schistosoma japonicum in China. Transcriptomic examination of snail-schistosome interactions can provide valuable information of host response at physiological and immune levels. Methods:To investigate S. japonicum-induced changes in O. hupensis gene expression, we utilized high-throughput sequencing to identify transcripts that were differentially expressed between infected snails and their uninfected controls at two key time-point, Day 7 and Day 30 after challenge. Time-series transcriptomic profiles were analyzed using R package DESeq 2, followed by GO, KEGG and (weighted gene correlation network analysis) WGCNA analysis to elucidate and identify important molecular mechanism, and subsequently understand host-parasite relationship. The identified unigenes was verified by bioinformatics and real-time PCR. Possible adaptation molecular mechanisms of O. hupensis to S. japonicum challenge were proposed. Results:Transcriptomic analyses of O. hupensis by S. japonicum invasion yielded billion reads including 92,144 annotated transcripts. Over 5000 differentially expressed genes (DEGs) were identified by pairwise comparisons of infected libraries from two time points to uninfected libraries in O. hupensis. In total, 6032 gene ontology terms and 149 KEGG pathways were enriched. After the snails were infected with S. japonicum on Day 7 and Day 30, DEGs were shown to be involved in many key processes associated with biological regulation and innate immunity pathways. Gene expression patterns differed after exposure to S. japonicum. Using WGCNA, 16 modules were identified. Module-trait analysis identified that a module involved in RNA binding, ribosome, translation, mRNA processing, and structural constituent of ribosome were strongly associated with S. japonicum invasion. Many of the genes from enriched KEGG pathways were involved in lysosome, spliceosome and ribosome, indicating that S. japonicum invasion may activate the regulation of ribosomes and immune response to infection in O. hupensis. Conclusions:Our analysis provided a temporally dynamic gene expression pattern of O. hupensis by S. japonicum invasion. The identification of gene candidates serves as a foundation for future investigations of S. japonicum infection. Additionally, major DEGs expression patterns and putative key regulatory pathways would provide useful information to construct gene regulatory networks between host-parasite crosstalk.

Project description:BackgroundSchistosoma 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.MethodsThe 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.ResultsA 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.ConclusionsIntegrated 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.

Project description:BackgroundSchistosomiasis japonica is a chronic parasitic disease that seriously harms people's health. Oncomelania hupensis is the only intermediate host of Schistosoma japonicum. The micro-environmental factors surrounding the snail have a great impact on the survival, growth and reproduction of O. hupensis, but there are few relevant systematic analyses until the present. This scoping review aims to identify and summarize the micro-environmental factors that greatly affect O. hupensis, and to find gaps in research thus to provide directions for future in-depth studies.Main bodyThis scoping review searched databases with search terms of the combinations of "Micro(-)environment", "Oncomelania" and their expanded aspects. A total of 133 original articles were recruited. Predefined data fields were extracted including research methods, influencing factors, and their effects on O. hupensis. Most studies focused on vegetation factors (54.1%), and other factors noted were soil composition (27.8%), water environmental factors (24.1%), and predator (3.0%), respectively. The factors with positive impacts included water level, pH value, soil temperature, soil humidity, the coverage and height of vegetation at suitable levels. This could provide more detailed information for O. hupensis habitat identification and prediction. The factors with negative impacts included plant extracts, snail control and disease prevention forests, and microorganisms with molluscicidal activities. It revealed a potential application as ecological molluscicides in the future. Factors such as physico-chemical properties of water, soil chemistry showed a gap in scientific studies, thus required further extensive research.ConclusionsMicro-environmental factors including water quality, soil composition as well as the technology and application of biomolluscicides (plant extracts and microorganisms) deserve more attention. Relative study findings on micro-environment have good potentials in snail control applications. Further studies should be implemented to investigate the impact of micro-environmental factors on snails and close the research gaps.

Project description:BackgroundOncomelania snails serve as the sole intermediate host for Schistosoma japonicum, one of the most important neglected tropical diseases in the world. Afforestation suppression of the Oncomelania hupensis snail has been a long-term effective national strategy to decrease snail density in China. Many previous studies have made clear that vegetation (biotic factors) and soil (abiotic factors) were the basic requirements for snail survival on beaches. Moreover, a lot of research on snail control has been focused on the specific influencing environmental factors for snail survival, such as the vegetation community structure, species composition, diversity index, and the physical and chemical properties of the soil. Most of the existing research has studied the influence of a single factor on snail population density. Conversely, there have been only a few studies focused on the food sources and food composition of the snails. The current research situation on snail control has indicated that the mechanisms underlying ecological snail control have not been systematically characterized. The question of whether biotic or abiotic factors were more important in influencing snail survival remains unclear. Afforestation on beaches has significantly suppressed snail density in China so far. In this study, we proposed that the reduction of snail density was not affected by a single factor but by the interactions of multiple related factors introduced by afforestation. Moreover, different biotic and abiotic factors have significantly different effects on snail control. Therefore the goal of this study was to evaluate the relative importance and interactions of related biotic and abiotic factors on snail density. Methods: Four major vegetation communities: Sedge, Reed, Artificial poplar (3 years of age) and Artificial poplar (5 years of age), on the beaches of the Yangtze River in China were selected for vegetation and snail surveys, as well as for soil sampling. Structural Equation Model (SEM) analysis was used to assess the interactions of biotic and abiotic factors in the context of snail ecology. The soil properties were considered as abiotic factors, while algae of Chlorophyta, Cyanophyta and Bacillariophyta phyla were considered to be biotic factors. In the path analysis, the total effect between the variables was the sum of the direct and indirect effects.ResultsThe snail density had significant correlations with soil properties, such as water content, bulk density, capillary porosity and pH value, as well as with all three types of soil algae, Chlorophyta, Cyanophyta, and Bacillariophyta. Snail density had a direct negative relationship with capillary porosity and soil bulk density, an indirect negative relationship with soil pH value and an indirect positive relationship with soil water content via soil algae. Meanwhile, as an important food source for the snail, the Chlorophyta, Cyanophyta and Bacillariophyta algae had a significant positive correlation with snail density. High soil pH had a negative impact on Chlorophyta, Bacillariophyta, while soil water content had a positive impact on Chlorophyta, and soil bulk density had a negative impact on Cyanophyta. In addition, the soil pH value and soil bulk density both had negative correlations with soil water content.ConclusionAfforestation of the beach environment can significantly reduce the snail population density by altering ecological factors. Soil algae (biological factors) might be the key element that drives ecological snail control. As important habitat determinants, the impact of the properties of the soil (non-biological factors) on the snail population was largely mediated through soil algae.

Dataset Information

The genetic diversity and geographical separation study of Oncomelania hupensis populations in mainland China using microsatellite loci.

Publications

The genetic diversity and geographical separation study of Oncomelania hupensis populations in mainland China using microsatellite loci.

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