PDF(Pubmed)
Abstract：
BACKGROUND: Schistosoma mekongi is a human blood fluke causing schistosomiasis that threatens approximately 1.5 million humans in the world. Nonetheless, the limited available S. 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 the S. mekongi genome.
METHODS: The reference genome for S. 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 in S. mekongi infection. We employed gene ontology (GO) enrichment analysis for functional annotation of these genes.
RESULTS: In the present study, the S. 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 genus Schistosoma. 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 up-regulated, which might be beneficial for cercaria production.
CONCLUSIONS: This study delivers a high-quality, chromosome-scale reference genome of S. mekongi, enhancing our understanding of the divergence and evolution of Schistosoma. 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.
METHODS: The reference genome for S. 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 in S. mekongi infection. We employed gene ontology (GO) enrichment analysis for functional annotation of these genes.
RESULTS: In the present study, the S. 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 genus Schistosoma. 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 up-regulated, which might be beneficial for cercaria production.
CONCLUSIONS: This study delivers a high-quality, chromosome-scale reference genome of S. mekongi, enhancing our understanding of the divergence and evolution of Schistosoma. 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.
摘要：
背景：mkongi血吸虫是一种引起血吸虫病的人类血吸虫，威胁着世界上大约150万人。尽管如此，有限的可用S.mekongi基因组资源阻碍了对疾病管理和病原体控制的生物学和寄生虫-宿主相互作用的理解。我们研究的目的是整合多种技术以构建S.mekongi基因组的高质量染色体水平组装。
方法：通过整合Illumina产生了S.mekongi的参考基因组，PacBio测序，10倍基因组学连锁阅读测序，和高通量染色体构象捕获(Hi-C)方法。在这项研究中,我们进行了从头组装，对齐,和基因预测来组装和注释基因组。比较基因组学允许我们比较不同物种的基因组，揭示保守区域和进化关系。此外,我们的转录组学分析集中于与梅孔伊氏链球菌感染中寄生虫-蜗牛相互作用相关的基因。我们采用基因本体论（GO）富集分析对这些基因进行功能注释。
结果：在本研究中，S.mekongi基因组都组装成8个假染色体，长度为404Mb，重叠群N50和支架N50长度为1168kb和46,759kb，分别。我们检测到43％的基因组由重复序列组成，并预测了9103个蛋白质编码基因。我们还专注于蛋白酶，特别是利什曼溶血素样金属蛋白酶（M8），这对12种扁虫入侵宿主至关重要。通过系统发育分析,发现M8基因在血吸虫属中表现出谱系特异性扩增。在血吸虫中观察到M8的谱系特异性扩增。此外,RNA-seq的结果表明，大量与代谢和生物合成过程相关的基因被上调，这可能有利于尾蚴的生产。
结论：这项研究提供了高质量的，MekongiS.的染色体尺度参考基因组，增强我们对血吸虫的分歧和进化的理解。这里进行的分子研究在药物发现和疫苗开发中也起着关键作用。此外，我们的工作大大推进了对宿主-寄生虫相互作用的理解，为血吸虫病干预策略提供重要见解。
方法：通过整合Illumina产生了S.mekongi的参考基因组，PacBio测序，10倍基因组学连锁阅读测序，和高通量染色体构象捕获(Hi-C)方法。在这项研究中,我们进行了从头组装，对齐,和基因预测来组装和注释基因组。比较基因组学允许我们比较不同物种的基因组，揭示保守区域和进化关系。此外,我们的转录组学分析集中于与梅孔伊氏链球菌感染中寄生虫-蜗牛相互作用相关的基因。我们采用基因本体论（GO）富集分析对这些基因进行功能注释。
结果：在本研究中，S.mekongi基因组都组装成8个假染色体，长度为404Mb，重叠群N50和支架N50长度为1168kb和46,759kb，分别。我们检测到43％的基因组由重复序列组成，并预测了9103个蛋白质编码基因。我们还专注于蛋白酶，特别是利什曼溶血素样金属蛋白酶（M8），这对12种扁虫入侵宿主至关重要。通过系统发育分析,发现M8基因在血吸虫属中表现出谱系特异性扩增。在血吸虫中观察到M8的谱系特异性扩增。此外,RNA-seq的结果表明，大量与代谢和生物合成过程相关的基因被上调，这可能有利于尾蚴的生产。
结论：这项研究提供了高质量的，MekongiS.的染色体尺度参考基因组，增强我们对血吸虫的分歧和进化的理解。这里进行的分子研究在药物发现和疫苗开发中也起着关键作用。此外，我们的工作大大推进了对宿主-寄生虫相互作用的理解，为血吸虫病干预策略提供重要见解。
