Background Schistosoma mekongi is a human blood fluke causing schistosomiasis that threatens approximately 1.5 million humans in the world. Nonetheless, the limited availableS. mekongi genomic resources have hindered ...Background Schistosoma mekongi is a human blood fluke causing schistosomiasis that threatens approximately 1.5 million humans in the world. Nonetheless, the limited availableS. mekongi genomic resources have hindered understanding of its biology and parasite-host interactions for disease management and pathogen control. The aim of our study was to integrate multiple technologies to construct a high-quality chromosome-level assembly of theS. mekongi genome.Methods The reference genome forS. mekongi was generated through integrating Illumina, PacBio sequencing, 10 × Genomics linked-read sequencing, and high-throughput chromosome conformation capture (Hi-C) methods. In this study, we conducted de novo assembly, alignment, and gene prediction to assemble and annotate the genome. Comparative genomics allowed us to compare genomes across different species, shedding light on conserved regions and evolutionary relationships. Additionally, our transcriptomic analysis focused on genes associated with parasite-snail interactions inS. mekongi infection. We employed gene ontology (GO) enrichment analysis for functional annotation of these genes.Results In the present study, theS. mekongi genome was both assembled into 8 pseudochromosomes with a length of 404 Mb, with contig N50 and scaffold N50 lengths of 1168 kb and 46,759 kb, respectively. We detected that 43% of the genome consists of repeat sequences and predicted 9103 protein-coding genes. We also focused on proteases, particularly leishmanolysin-like metalloproteases (M8), which are crucial in the invasion of hosts by 12 flatworm species. Through phylogenetic analysis, it was discovered that the M8 gene exhibits lineage-specific amplification among the genusSchistosoma. Lineage-specific expansion of M8 was observed in blood flukes. Additionally, the results of the RNA-seq revealed that a mass of genes related to metabolic and biosynthetic processes were upregulated, which might be beneficial for cercaria production.Conclusions This study delivers a high-quality, chromosome-scale reference genome ofS. mekongi, enhancing our understanding of the divergence and evolution ofSchistosoma. The molecular research conducted here also plays a pivotal role in drug discovery and vaccine development. Furthermore, our work greatly advances the understanding of host-parasite interactions, providing crucial insights for schistosomiasis intervention strategies.展开更多
基金supported by the National Key Research and Development Program(2021ZFC2300800 and 2021ZFC2300803)the National Natural Science Foundation of China(No.82072303)+4 种基金the Major Science and Technology Program of Hainan Province(No.ZDKJ202003 and No.ZDKJ2021035)the Key Research and Development Program of Hainan Province(No.ZDYF2020120)the Academician Innovation Platform Special Project of Hainan Province(No.YSPTZX202133)the Open project of Key Laboratory of Tropical Disease Prevention and Control of National Health Commission of Hainan Medical College(2022NHCTDCKFKT11003)the National Parasitic Resources Center of China(No.NPRC-2019-194-30).
文摘Background Schistosoma mekongi is a human blood fluke causing schistosomiasis that threatens approximately 1.5 million humans in the world. Nonetheless, the limited availableS. mekongi genomic resources have hindered understanding of its biology and parasite-host interactions for disease management and pathogen control. The aim of our study was to integrate multiple technologies to construct a high-quality chromosome-level assembly of theS. mekongi genome.Methods The reference genome forS. mekongi was generated through integrating Illumina, PacBio sequencing, 10 × Genomics linked-read sequencing, and high-throughput chromosome conformation capture (Hi-C) methods. In this study, we conducted de novo assembly, alignment, and gene prediction to assemble and annotate the genome. Comparative genomics allowed us to compare genomes across different species, shedding light on conserved regions and evolutionary relationships. Additionally, our transcriptomic analysis focused on genes associated with parasite-snail interactions inS. mekongi infection. We employed gene ontology (GO) enrichment analysis for functional annotation of these genes.Results In the present study, theS. mekongi genome was both assembled into 8 pseudochromosomes with a length of 404 Mb, with contig N50 and scaffold N50 lengths of 1168 kb and 46,759 kb, respectively. We detected that 43% of the genome consists of repeat sequences and predicted 9103 protein-coding genes. We also focused on proteases, particularly leishmanolysin-like metalloproteases (M8), which are crucial in the invasion of hosts by 12 flatworm species. Through phylogenetic analysis, it was discovered that the M8 gene exhibits lineage-specific amplification among the genusSchistosoma. Lineage-specific expansion of M8 was observed in blood flukes. Additionally, the results of the RNA-seq revealed that a mass of genes related to metabolic and biosynthetic processes were upregulated, which might be beneficial for cercaria production.Conclusions This study delivers a high-quality, chromosome-scale reference genome ofS. mekongi, enhancing our understanding of the divergence and evolution ofSchistosoma. The molecular research conducted here also plays a pivotal role in drug discovery and vaccine development. Furthermore, our work greatly advances the understanding of host-parasite interactions, providing crucial insights for schistosomiasis intervention strategies.
