Globodera pallida

Genome Assembly & Annotation

Assembly

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).

Annotation

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).

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, Lozano-Torres JL, Putker V, Thorpe P, Goverse A, Sterken MG, Smant G, Helder J. Comparative genomics among cyst nematodes reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs. Mol Ecol, 2023;32(6):1515-1529

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression