Schistosoma margrebowiei

Genome Assembly & Annotation

Assembly

This annotated genome assembly was produced as part of the doctoral thesis of Duncan Berger (Berger, D. (2021). Comparative and population genomic analyses of the parasitic blood flukes (Doctoral thesis)) and, from release 18, replaces an older draft assembly GCA_900618395.1.

The assembly was generated from PacBio long-read sequencing data and scaffolded using Hi-C.

The source material for genome sequencing was a single female adult worm, originally obtained from the Zambia in 2002, archived as part of the SCAN collection at the Natural History Museum, London, and provided by Fiona Allan, Aidan Emery and Muriel Rabone. Additional worms from the same collection were used for gene finding.

Annotation

Gene finding employed a customized pipeline that integrated RNA-Seq, Iso-Seq and homology data. Berger, D. (2021). Comparative and population genomic analyses of the parasitic blood flukes (Doctoral thesis).

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• International Helminth Genomes Consortium. Comparative genomics of the major parasitic worms. Nat Genet, 2019;51(1):163-174

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree