About Fasciolopsis buski
Fasciolopsis buski (subfamily Fasciolopsinae) is a large fluke (up to 7.5 cm long, 2.5 cm wide) that infects the small intestine of humans and pigs in East and Southeast Asia, causing diarrhea, abdominal pain, fever, ascites, and bowel obstruction. Along with Fasciola gigantica and Fasciola hepatica, Fasciolopsis buski is a liver fluke of the family Fasciolidae that have a substantial impact on both agriculture (3 billion USD per year) and human health (∼90,000 disability-adjusted life years) throughout the world.
Genome Assembly & Annotation
The genome assembly was produced by the Mitreva laboratory of the Division of Infectious Diseases at theWashington University School of Medicine in St. Louis. The assembly uses Illumina HiSeq platform (2X100bp) paired-end sequencing complemented by PacBio RS II P5-C3/P6-C4, 20-kb long-read sequencing. ALLPATHS-LG was used to assemble the Illumina reads. SSPACE-standard v3.0 and SSPACE-longread v1.1 were sequentially run using the Illumina and PacBio reads, respectively, to scaffold the assembled contigs. Gapfiller v1.10 and PBJelly v15.8.24 were used to close gaps, and the resulting assembly was error-corrected using Pilon v1.20 and screened for contaminants using blobtools v0.9.19. Mitochondrial genomes (mtDNA) were assembled with NOVOPlasty v2.6.3 using the Illumina fragment reads.
The gene predictions were made by the Mitreva laboratory of the Division of Infectious Diseases at theWashington University School of Medicine in St. Louis. The nuclear genome was annotated using the MAKER pipeline v2.31.8. Publicly available and in-house RNA-Seq studies, mRNA and EST sequences and protein sequences from closely related species were used by BRAKER and MAKER pipelines as supporting evidence. The best-supported gene models were chosen based on Annotation Edit Distance. PANNZER2 and sma3s v2 were employed to name gene products. Mitochondrial genomes were annotated using MITOS2.
- Choi YJ, Fontenla S, Fischer PU, Le TH, Costábile A, Blair D, Brindley PJ, Tort JF, Cabada MM, Mitreva M. Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species. Mol Biol Evol, 2020;37(1):84-99
|Data Source||McDonnell Genome Institute|
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh