Globodera pallida

The Potato Cyst Nematodes (PCN), Globodera pallida and Globodera rostochiensis are the most economically important nematode problems of the U.K. potato industry. They occur in 65% of U.K. potato land with G. pallida present at 92% of these sites. PCN impose an annual cost in excess of £50 million on U.K. potato growers and threaten the future of the crop for many growers. Breeding for resistance since 1950s has produced a few commercially acceptable varieties with resistance to G. pallida. Effective control of G. pallida is an essential requirement to maintain the competitiveness of U.K. potato production. The aim of this project is to obtain the full genome sequence of G. pallida to aide in defining new control measures and pest management strategies.

Data Downloads

[Genome Research Limited]

This is a BBSRC funded project to sequence and and analyse the nuclear and mitochondrial genomes of G. pallida with the goal of producing a reference quality genome sequence. The sequencing is being done using a combination of capillary sequencing, Roche (454) and Illumina (Solexa) sequencing technology platforms. As part of the project we are profiling the transcriptome of the parasite across its life cycle using RNA-seq.

We are collaborating with John Jones and Vivian Blok and Peter Cock (The James Hutton Institute), Brian Kerry (Rothamsted Research), Catherine Lilley and Peter Urwin (University of Leeds).

Studies

Globodera pallida transcriptomics

Sample

Strain

Run Accession

GPal_J2_dscDNAStandard Pa2/3 pathotype isolate LindleyERR406996
GPal_21dpi_dscDNAStandard Pa2/3 pathotype isolate LindleyERR406997
GPal_28dpi_dscDNAStandard Pa2/3 pathotype isolate LindleyERR406995
GPal_35dpi_dscDNAStandard Pa2/3 pathotype isolate LindleyERR406998
GPal_male_dscDNAStandard Pa2/3 pathotype isolate LindleyERR406999
Gpal_E_Egg_dscDNAStandard Pa2/3 pathotype isolate Lindley ERR407000
Gpal_Male_172616LindleyERR202422
Gpal_14dpi_172616LindleyERR202423
GPal_J2_RNASeq1Standard Pa2/3 pathotype isolate LindleyERR202424
Gpal7dpi_206183Standard Pa2/3 pathotype isolate LindleyERR202425
Gpal21dpi_3_206183Standard Pa2/3 pathotype isolate LindleyERR202426
Gpal28dpi_2_206183Standard Pa2/3 pathotype isolate LindleyERR202427
Gpal35dpi_4_206183Standard Pa2/3 pathotype isolate LindleyERR202428
ELindley09J2_216539Standard Pa2/3 pathotype isolate LindleyERR202429
ELindley09Egg_216539Standard Pa2/3 pathotype isolate LindleyERR202430
Bedale97J2_216539UnknownERR202431
Newton97J2_216539UnknownERR202432
Luffness98J2_216539UnknownERR202433
Bedale12674_97J2_216539UnknownERR202434
GpalMaleP15_224626UnknownERR202435
Gpal7dpi_224626UnknownERR202436
222467Gpal14dpiP6P7UnknownERR407001
245944GpalDMSO24hr_1LindleyERR202437
245944GpalDMSO24hr_2LindleyERR202438
245944GpalDMSO24hr_3LindleyERR202439
245944GpalCHL24hr_1LindleyERR202440
245944GpalCHL24hr_2LindleyERR202441
245944GpalIMI24hr_1LindleyERR202442
245944GpalIMI24hr_2LindleyERR202443
245944GpalDZM24hr_1LindleyERR202444
245944GpalDMSO4hr_1LindleyERR202445
245944GpalDMSO4hr_2LindleyERR202446
245944GpalTHI4hr_1LindleyERR202447
245944GpalTHI4hr_2LindleyERR202448
24h43CHL_Gpal250061LindleyERR202449
24h43CHL_Gpal250061LindleyERR202464
24hr3IMI_Gpal250061LindleyERR202450
24hr3IMI_Gpal250061LindleyERR202465
24hr1_012DZM_Gpal250061LindleyERR202451
24hr1_012DZM_Gpal250061LindleyERR202466
24hr1_006DZM_Gpal250061LindleyERR202452
24hr1_006DZM_Gpal250061LindleyERR202467
24hr2_006DZM_Gpal250061LindleyERR202468
24hr2_006DZM_Gpal250061LindleyERR202453
4hr3DMSO_Gpal250061LindleyERR202454
4hr3DMSO_Gpal250061LindleyERR202469
4hr3THI_Gpal250061LindleyERR202470
4hr3THI_Gpal250061LindleyERR202455
2hr1DMSO_Gpal250061LindleyERR202456
2hr1DMSO_Gpal250061LindleyERR202471
2hr2DMSO_Gpal250061LindleyERR202457
2hr2DMSO_Gpal250061LindleyERR202472
2hr1FLU_Gpal250061LindleyERR202458
2hr1FLU_Gpal250061LindleyERR202473
2hr2FLU_Gpal250061LindleyERR202474
2hr2FLU_Gpal250061LindleyERR202459
2hr1IVM_Gpal250061LindleyERR202475
2hr1IVM_Gpal250061LindleyERR202460
2hr2IVM_Gpal250061LindleyERR202461
2hr2IVM_Gpal250061LindleyERR202476
2hr1LEV_Gpal250061LindleyERR202462
2hr1LEV_Gpal250061LindleyERR202477
2hr2LEV_Gpal250061LindleyERR202463
2hr2LEV_Gpal250061LindleyERR202478
GpRD3Eggs_E2010_253573E2010ERR202486
GpRD2Eggs_E2010_253573E2010ERR202485
Gp1RD1Eggs_E2010_253573E2010ERR202484
GpHEggs_E2010_253573E2010ERR202483
Gp1DEggs_E2010_253573E2010ERR202482
Gp1RD3Eggs_E2010_253573UnknownERR202492
Gp1RD2Eggs_E2010_253573UnknownERR202491
GpRD1Eggs_E2010_253573UnknownERR202490
Gp1HEggs_E2010_253573UnknownERR202489
GpDEggs_E2010_253573UnknownERR202488

Data Use Statement

This sequencing centre plans on publishing the completed and annotated sequences in a peer-reviewed journal as soon as possible. Permission of the principal investigator should be obtained before publishing analyses of the sequence/open reading frames/genes on a chromosome or genome scale. See our data sharing policy.

Sequencing enquiries

Please address all sequencing enquiries to: pathinfo@sanger.ac.uk

* quick link - http://q.sanger.ac.uk/clolxp7i