Globodera pallida

Genome Assembly & Annotation

Assembly

The G. pallida genome was sequenced by the Parasite Genomics group at the Wellcome Trust Sanger Institute, as described in Cotton et al (2014). The assembly version represented here is that used in the analysis for publication, and corresponds to INSDC assembly GPAL001.

Annotation

The gene predictions were made by the Parasite Genomics group at the Wellcome Trust Sanger Institute, as described in Cotton et al (2014).

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

• Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ, Eves-van den Akker S, Holroyd N, Hunt M, Mantelin S, Naghra H, Pain A, Palomares-Rius JE, Zarowiecki M, Berriman M, Jones JT, Urwin PE. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol, 2014;15(3):R43

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression