An improved genome assembly of the fluke Schistosoma japonicum

PLoS Negl Trop Dis. 2019 Aug 7;13(8):e0007612. doi: 10.1371/journal.pntd.0007612. eCollection 2019 Aug.


Background: Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery.

Findings: In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation.

Conclusions: Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • China
  • Evolution, Molecular
  • Female
  • Genome Size
  • Genome, Helminth*
  • Genomics
  • High-Throughput Nucleotide Sequencing
  • Male
  • Philippines
  • Phylogeny
  • Proteins / genetics
  • Schistosoma japonicum / genetics*
  • Schistosoma japonicum / physiology*
  • Schistosomiasis japonica / parasitology
  • Trematoda / parasitology*
  • Whole Genome Sequencing


  • Proteins

Grants and funding

This research was funded by the National Natural Science Foundation of China (No. 31725025 and 91431104) to Wei Hu. The website of the funder " the National Natural Science Foundation of China (NSFC)" is "". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.