An improved genome assembly of the fluke Schistosoma japonicum

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.

Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

“…These authors used only two RNA-Seq libraries from S. japonicum, one from males and one from females [10]. Here we used a much higher number of RNA-Seq libraries from cercariae, sporocysts, schistosomula, and early-development or adult males and females, including the two libraries used by Liao et al [10], along with the newest version of the genome and transcriptome of S. japonicum, which were recently released with significant improvement in assembly contiguity [13]. Our group has recently developed an improved pipeline for identification of lncRNAs [12] and we showed that a large set of the S. mansoni transcripts that we previously annotated as lncRNAs with a different pipeline [14] and also that by Liao et al [10], now seem to represent partially processed pre-mRNAs arising from novel protein-coding genes annotated in the newest version of the S. mansoni genome and transcriptome [12].…”

“…For this work, we used 66 S. japonicum RNA-Seq libraries that are publicly available at SRA from the following stages-cercariae, sporocysts, schistosomula, early-development, and adult males and females ( Supplementary File 10). The most recent SKCS01000000 version of the S. japonicum genome and transcriptome [13] were used as references.…”

“…When any transcript isoform was classified as a protein-coding mRNA at any step, all transcripts mapping to the same genomic locus were removed to avoid eventual pre-mRNAs. After this final step, a new GTF file was created containing the lncRNAs identified here, plus the protein-coding genes previously annotated by Luo et al [13].…”

Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasiteSchistosoma mansoni

“…Understanding the basic biology of schistosomes at the cellular and molecular levels is critical to identifying exploitable vulnerabilities of the parasite. High-throughput datasets, including high quality reference genomes for the three main species of schistosomes [5][6][7], have been generated. More recently, a thorough transcriptome analysis during the parasite's intra-mammalian development [8], and the identification of different cell types by single-cell RNA sequencing of various life cycle stages [9,10] represent significant steps towards deciphering cell fate and pathways involved in parasite development and host-parasite interactions.…”

Oncomelania hupensis retains its ability to transmit Schistosoma japonicum 13 years after migration from permissive to non-permissive areas

“…All of the downstream analysis was based on clean reads with high quality. The improved genome of S. japonicum [30] was used as the reference genome. An index of the reference genome was constructed and paired-end clean reads were aligned to the S. japonicum reference genome using HISAT v2.1.0 [31].…”