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

Abstract

Abstract Background Schistosomiasis is a zoonotic parasitic disease that is estimated to affect almost 300 million people worldwide. As one of the three major human parasites, Schistosoma japonicum is endemic in Southeast Asia, including China, Philippines and Indonesia. Transmission relies only on one snail host Oncomelania hupensis (Gastropoda: Pomatiopsidae). However, no genomic information for this important intermediate host is available. Methods Contig-level of O. hupensis assembly of an individual male O. hupensis snail was performed with full PacBio long reads using Next Denovo. The completeness and continuity of the assembly were assessed with Benchmarking Universal Single-Copy Orthologs (BUSCO). CAFÉ 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 using single copy protein-coding genes revealed that O. hupensis was separated from a common ancestors 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 gene families (p < 0.05) 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, transposase activity and hyalurononglucosaminidase activity. Additionally, a total of 281 protein-coding genes related to protein kinase activity, protein phosphorylation, catalytic activity and metabolic process under positive selection were identified in O. hupensis (FDR < 0.05). Conclusion A complete genome sequence of O. hupensis would enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite causing schistosomiasis in humans. Using a single molecular DNA sequencing technology, we have successfully constructed the genome at the chromosomal-level. These data will not only provide the compressive genomic information for the sole intermediated host of S. japonicum, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.