An improved genome assembly of the fluke Schistosoma japonicum

PLoS Neglected Tropical Diseases
Fang LuoWei Hu

Abstract

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. 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 primar...Continue Reading

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Citations

Feb 23, 2020·Seminars in Immunopathology·Donald P McManusHong You
Apr 10, 2021·Wellcome Open Research·Geetha SankaranarayananGabriel Rinaldi
Nov 5, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Xiaofeng DuHong You
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Jun 18, 2021·Frontiers in Immunology·José T Moreira-FilhoCarolina H Andrade
Aug 30, 2021·Parasites & Vectors·Chloé Suzanne BergerNadia Aubin-Horth
Jan 21, 2020·Molecular and Biochemical Parasitology·Danielle E SkinnerPaul J Brindley

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Datasets Mentioned

BETA
PRJNA515567
SKCS00000000

Methods Mentioned

BETA
Illumina sequencing
electrophoresis
RNA-seq
PCR
homology-based prediction

Software Mentioned

INFERNAL
minimap
GenomicFeatures ”
PASA
BLAST2GO
RepeatMasker
tRNAscan
GeneMark
SAMTOOLS
EvidenceModeler (

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