Angiostrongylus vasorum

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the Institute of Parasitology of the Vetsuisse-Faculty at the University of Zurich. The assembly uses GridION X5 Oxford Nanopore sequencing followed by further polishing with Illumina RNA-seq short reads (Novaseq 6000 pair end at 2 × 150 bp) using 4 rounds of Pilon v1.23 with – fix all parameter.

Annotation

The gene predictions were made by the Institute of Parasitology of the Vetsuisse-Faculty at the University of Zurich. A custom repeat library along with the Dfam (3.0) database of repetitive DNA families was used for masking on the draft genome using RepeatMasker v4.0.9. An in-house pipeline was developed that used MAKER to generate high-quality annotations by integrating evidence from multiple sources: ab initio gene predictions from AUGUSTUS, SNAP and mRNAs and proteins from 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

• Tayyrov A, Gillis-Germitsch N, Tritten L, Schnyder M. Genome sequence of the cardiopulmonary canid nematode Angiostrongylus vasorum reveals species-specific genes with potential involvement in coagulopathy. Genomics, 2021;113(4):2695-2701

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree