Heterodera schachtii
BioProject PRJNA767548 | Data Source Wageningen University and Research | Taxonomy ID 97005
About Heterodera schachtii
Heterodera schachtii, also known as the beet cyst nematode or sugarbeet nematode, is a plant pathogenic parasite which can infect more than 200 plants including the model plant Arabidopsis thaliana. H. schachtii is an important agricultural pest on sugar beet and brassicaceous crops in its own right and is closely related to the soybean cyst nematode, H. glycines, which is one of the severely economically damaging plant-parasitic nematodes worldwide.
There is 1 alternative genome project for Heterodera schachtii available in WormBase ParaSite: PRJNA522950
Genome Assembly & Annotation
Assembly
For this assembly, a Heterodera schachtii IRS (a Dutch beet cyst nematode population) was used.
According to Joris J. M. van Steenbrugge et. al. (2022), raw long Oxford Nanopore 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 ONT reads using MEDAKA v1.4.1, followed by five iterations of polishing with pilon version 1.23 using Illumina short reads.
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 PRJNA767548). 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).
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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
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Assembly Statistics
| Assembly | WUR_Hsch_IRS_1.0, GCA_020449115.1 |
| Strain | IRS |
| Database Version | WBPS19 |
| Genome Size | 190,153,211 |
| Data Source | Wageningen University and Research |
| Annotation Version | 2022-09-WormBase |
Gene counts
| Coding genes | 29,851 |
| Gene transcripts | 31,564 |
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