Heterodera schachtii

Genome Assembly & Annotation

Assembly

Genome assembly was conducted as described in Siddique et al., (2022). Error corrected reads were assembled using wtdbg2 Version: 2.1 − 2018100730. Analysis using BlobTools version 1.0 was conducted, in order to find and remove contaminated contigs.

Annotation

Genome annotation was conducted as described in Siddique et al., (2022).

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

• Siddique S, Radakovic ZS, Hiltl C, Pellegrin C, Baum TJ, Beasley H, Bent AF, Chitambo O, Chopra D, Danchin EGJ, Grenier E, Habash SS, Hasan MS, Helder J, Hewezi T, Holbein J, Holterman M, Janakowski S, Koutsovoulos GD, Kranse OP, Lozano-Torres JL, Maier TR, Masonbrink RE, Mendy B, Riemer E, Sobczak M, Sonawala U, Sterken MG, Thorpe P, van Steenbrugge JJM, Zahid N, Grundler F, Eves-van den Akker S. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nat Commun, 2022;13(1):6190

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree