Echinococcus granulosus

Genome Assembly & Annotation

Assembly

The full assembly process is described in Korhonen et al., (2022). PacBio sequence data was assembled using Canu v1.8. The assembly was polished with PacBio raw-reads using Arrow and also with BGISEQ-500 PE reads using Pilon v1.22.

Annotation

The full annotation process is described in Korhonen et al., (2022). Annotation was achieved using InterPro and sequence homology to proteins in the Swiss-Prot, KEGG58 and NCBI NR59 databases using BLASTp (threshold E-value: ≤10−8).

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

• Korhonen PK, Kinkar L, Young ND, Cai H, Lightowlers MW, Gauci C, Jabbar A, Chang BCH, Wang T, Hofmann A, Koehler AV, Li J, Li J, Wang D, Yin J, Yang H, Jenkins DJ, Saarma U, Laurimäe T, Rostami-Nejad M, Irshadullah M, Mirhendi H, Sharbatkhori M, Ponce-Gordo F, Simsek S, Casulli A, Zait H, Atoyan H, de la Rue ML, Romig T, Wassermann M, Aghayan SA, Gevorgyan H, Yang B, Gasser RB. Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule. Commun Biol, 2022;5(1):199

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression