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

An improved genome assembly of the fluke Schistosoma japonicum

Fang Luo  1 , Mingbo Yin  1   2 , Xiaojin Mo  2 , Chengsong Sun  1 , Qunfeng Wu  1 , Bingkuan Zhu  1 , Manyu Xiang  1 , Jipeng Wang  1 , Yi Wang  1 , Jian Li  1 , Ting Zhang  2 , Bin Xu  2 , Huajun Zheng  3 , Zheng Feng  2 , Wei Hu  1   2
Affiliations

An improved genome assembly of the fluke Schistosoma japonicum

Fang Luo et al. PLoS Negl Trop Dis. .

Abstract

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Genome assembly of Schistosoma japonicum.
(A) Comparison of contiguity between the two versions of S. japonicum genome assembly. N(x)% graph shows the contig and scaffold sizes (y-axis), where x% of the genome assembly consists of contigs and scaffolds of at least that size. (B) comparison between two version of S. japonicum genome assembly, showing the portions of the genomes that are complete (blue), fragmented (yellow) or missing (red), as determined by benchmarking universal single-copy orthologs (BUSCO) analysis with metazoan_odb9 database. (C) Circle plot of synteny between the second version of S. japonicum genome and S. mansoni genome V7 made using SyMAP. It shows a high degree of synteny, with many long S. japonicum scaffolds covering significant portions of S. mansoni chromosome. (D) Circle plot of synteny between the first version of S. japonicum genome and S. mansoni genome. V1 indicated conventional capillary sequenced genome and V2 indicated our improved genome.
Fig 2
Fig 2. Length distribution comparison on total gene, CDS, exon, and intron of annotated gene models of the S. japonicum with other closely related Trematoda species.
Length distribution of total genes (A), CDS (B), exon (C), and intron (D) were compared to those of S. mansoni, S. haematobium, C. sinensis, O. viverrini, and F. hepatica.
Fig 3
Fig 3. Comparative genome analysis between S. japonicum and other six flatworms.
(A) Phylogenetic tree and expansion and contraction of gene families. The phylogenetic tree and divergence time were generated from 2,322 single-copy orthologous genes using BEAST2. The branch lengths of the phylogenetic tree are scaled to estimated divergence time. Tree topology is supported by posterior probability of 1.0 for all nodes. The blue bars on the nodes indicate the 95% credibility intervals of the estimated posterior distributions of the divergence times. The number of expanded (orange) and contracted (blue) gene families is designated on each branch. Bar charts indicates the orthologous and paralogous gene families in S. japonicum and other six flatworm species. (B) Comparison of the number of gene families in 7 Platyhelminthes species.
Fig 4
Fig 4. Gene Ontology enrichment analysis of significantly expanded gene families.
(A) biological processes, (B) molecular function and (C) cellular component.
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Publication types

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 " https://isisn.nsfc.gov.cn". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.