WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Globodera pallida

BioProject PRJNA764088 | Data Source Wageningen University and Research | Taxonomy ID 36090

About Globodera pallida

The nematode Globodera pallida, or golden nematode or potato cyst nematode (PCN), is one of the most economically important nematode problems of the U.K. potato industry. PCN imposes an annual cost in excess of 50 million on U.K. potato growers and threaten the future of the crop for many growers. Effective control of G. pallida is an essential requirement to maintain the competitiveness of U.K. potato production.

There are 2 alternative genome projects for Globodera pallida available in WormBase ParaSite: PRJEB123 PRJNA702104

Genome Assembly & Annotation


This assembly was generated from collection of preparasitic second-stage juveniles (J2) from Pa2-D383 Globodera pallida line. Pa2-D383 is a relatively avirulent population from The Netherlands.

For the assembly, raw long PacBio reads were corrected to, in essence, merge haplotypes using the correction mode in CANU. Using wtdgb2 version 2.3, multiple initial genome assemblies were generated. The contigs from the assemblies were then improved using finishersc version 2.1. Gaps in the assemblies were then filled using gapfiller version 1.0. The resulting assembly was polished with PacBio reads by three iterations of arrow version 2.3.3, followed by five iterations of polishing with pilon version 1.23 using PacBio and Illumina NovaSeq short reads. Read more at Joris J. M. van Steenbrugge et. al. (2022).


Using braker version 2.1.2, gene annotations were predicted for both assemblies at default settings outputting gff3 annotations and aided by RNAseq data of different life stages (NCBI Bioproject PRJEB2896). Full details on the generation of the genome assemblies and prediction of genes are available here. Read more at Joris J. M. van Steenbrugge et. al. (2022).

Key Publications

Assembly Statistics

AssemblyD383_Gpal_1.0, GCA_020449905.1
Database VersionWBPS19
Genome Size113,220,295
Data SourceWageningen University and Research
Annotation Version2022-08-WormBase

Gene counts

Coding genes18,071
Gene transcripts22,828

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