Heterodera schachtii

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by The H. schachtii genome sequencing consortium. As described by Shahid Siddique et al., (2022), the assembly uses a combination of Pacific Biosciences sequencing, and Illumina sequencing. PacBio reads were assembled using wtdbg2. The assembly was submitted to decontamination with BlobTools, upgrade with FinisherSC, scaffolding with SSPACE_longread and gapFinisher, polishing with PacBio's smrttools and Pilon using the raw PacBio reads and the Illumina reads.

Annotation

As described by Shahid Siddique et al., (2022), the gene predictions were made by The H. schachtii genome sequencing consortium. An in-house pipeline was developed to generate gene models using Braker2 supplied with RNAseq data.

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