Fasciola hepatica

Genome Assembly & Annotation

Assembly

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 first version of this assembly submitted in late 2013 as part of the 50 Helminth Genomes project. The version presented here is an improved version of the assembly (GCA_002763495.2) submitted in 2019. The assembly uses Illumina HiSeq2000 paired-end sequencing. ALLPATHS-LG was used to assemble the Illumina reads. Pygap, an in-house assembly improvement tool, was used to join and extend contigs using unassembled reads when possible.

Annotation

The gene predictions were made by the Mitreva laboratory of the Division of Infectious Diseases at theWashington University School of Medicine in St. Louis. Protein coding genes were predicted from the masked assembly using a combination of Snap, Fgenesh, Augustus, and the MAKER annotation pipeline using evidence from assembled transcripts, ESTs (GenBank EST database), and protein sequences from F. hepatica and related organisms.

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

• McNulty SN, Tort JF, Rinaldi G, Fischer K, Rosa BA, Smircich P, Fontenla S, Choi YJ, Tyagi R, Hallsworth-Pepin K, Mann VH, Kammili L, Latham PS, Dell'Oca N, Dominguez F, Carmona C, Fischer PU, Brindley PJ, Mitreva M. Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers. PLoS Genet, 2017;13(1):e1006537
• International Helminth Genomes Consortium. Comparative genomics of the major parasitic worms. Nat Genet, 2019;51(1):163-174

Resources

• CDC page on Fascioliasis.

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression