Globodera rostochiensis

Genome Assembly & Annotation

Assembly

The genome assembly was produced by the Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands. The assembly uses PacBio SMRT sequencing complemented by 2 × 250 bp Illumina NovaSeq short-read sequencing. PacBio reads were assembled with wtdgb2 v2.3. Unmerged haplotigs were filtered from the assembly using Purge Haplotigs v1.0.4. The assembly was then tested for contamination using the blobtools pipeline v.1.0.1, while scaffolding performed with SSPACE-Longread. The Illumina reads were used to polish the assembly with Arrow v2.3.3 and Pilon. All scripts used for the generation of the genome assemblies are available here.

Annotation

Gene models were provided by Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands. Genes were predicted using the BRAKER pipeline. The prediction of gene models was aided by RNAseq datasets of different life stages of G. rostochiensis. All scripts used for the generation of the genome annotation are available here.

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

• van Steenbrugge JJM, van den Elsen S, Holterman M, Sterken MG, Thorpe P, Goverse A, Smant G, Helder J. Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns. BMC Genomics, 2021;22(1):611

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression