WormBase ParaSite HomeVersion: WBPS17 (WS282)

Globodera rostochiensis

BioProject PRJNA695196 | Data Source Wageningen University and Research | Taxonomy ID 31243

About Globodera rostochiensis

Globodera rostochiensis, commonly known as the golden nematode, is a plant pathogenic nematode. It infects plants of the Solanaceae family, such as potatoes and tomatoes.

There is 1 alternative strain from this genome project for Globodera rostochiensis available in WormBase ParaSite: L22

There is 1 alternative genome project for Globodera rostochiensis available in WormBase ParaSite: PRJEB13504

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.

Key Publications

Assembly Statistics

AssemblyWUR_GloGros_L19, GCA_018350325.1
StrainL19
Database VersionWBPS17
Genome Size92,682,755
Data SourceWageningen University and Research
Annotation Version2021-11-WormBase

Gene counts

Coding genes17,856
Gene transcripts21,398

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