biostudies-arrayexpressMark SterkenMeloidogyne haplahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17107In this experiment we sequence the whole genome DNA of 28 unique populations of the root-knot nematode Meloidogyne hapla to investigate their genetic diversity using illumina sequencing. The hapla populations came from various locations, mostly in the Netherlands and Europe. The nematodes were maintained on tomato cv. Money Maker in the greenhouse of Wageningen University. After DNA extraction, DNA was sent for sequencing. The resulting sequence was used for calling variants and genetic analysis.biostudies-arrayexpressSample Collection - The nematodes were propagated on tomato cv. Money Maker. Fresh eggs were harvested 10 weeks after the nematodes were inoculated. Eggs were obtained by treating roots with 0.05% (v/v) NaOCl for three minutes, following by rinsing with tap water. After further rinsing, eggs were hatched on a 25 µm sieve. Hatched J2 were collected by centrifugation on a 70% sucrose column.Sequencing - Sequencing was done on the Illumina NextSeq500 platform, 100bp paired-end sequencing.Nucleic Acid Extraction - The purified J2s were lysed with nematode lysis buffer with proteinase-K and beta-mercaptoethanol. This was done in a ThermoCycler at 60 ºC for 1 h with continuous shaking at 650 RPM. The lysate was then mixed with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8.0) following a standard DNA purification procedure, followed by precipitation with isopropanol. Afterwards, the DNA pellet was washed with 70% ethanol for two times, before finally resuspended with 10 mM Tris-HCL (pH 8.0).Library Construction - DNA library preparation and sequencing was done in Utrecht sequencing facility (USEQ). Library preparation was done using the Illumina TruSeq protocol.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The variants were mapped to the M. hapla reference genome using bwa_mem2 and variants were called using bcftools. Next, variants were filtered for quality, coverage and, being a SNP. The remaining variants were converted to an alternative allele frequency where 0 is equal to the reference sequence and 1 is a fixed alternative allele. Note that these samples are derived from populations of thousands of individuals.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500DNA-seqMeloidogyne haplaStefan van de RuitenbeekMark SterkenMuhammed Iqbal MaulanafalseDNA-seq of 28 populations of Meloidogyne haplaIn this experiment we sequence the whole genome DNA of 28 unique populations of the root-knot nematode Meloidogyne hapla to investigate their genetic diversity using illumina sequencing. The hapla populations came from various locations, mostly in the Netherlands and Europe. The nematodes were maintained on tomato cv. Money Maker in the greenhouse of Wageningen University. After DNA extraction, DNA was sent for sequencing. The resulting sequence was used for calling variants and genetic analysis.2026-07-31T00:00:00Z2026-07-31T13:26:32.142Z2026-05-28T11:41:54.017ZE-MTAB-17107ERP194108EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0003816EFO_0004184