Mesocestoides corti

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Estela Castillo (Seccion Bioquimica-Facultad de Ciencias-UDELAR- Montevideo- Uruguay) as part of the 50 Helminth Genomes project. The assembly uses Illumina paired-end sequencing followed by an in-house genome assembly pipeline comprising various steps, including contig assembly, scaffolding, gap-filling and error-correction.

Annotation

The original gene predictions were made by the Parasite Genomics group at the Wellcome Trust Sanger Institute and WormBase, as part of the 50 Helminth Genomes project.

In June 2019 the predictions were improved by Alicia Costábile using MAKER and incorporating additional evidence from RNASeq data, as described in Costábile et al (2018). 8367 original genes were updated and given new identifiers, and remaining 1311 gene models from the original annotation which were no longer predicted given new evidence and methodology were preserved unchanged. The update also contains 5076 new genes not present in the original annotation.

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

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression