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: PRJNA767548
Genome Assembly & Annotation
The draft genome assembly was produced by The H. schachtii genome sequencing consortium. As described by Shahid Siddique et al., (2022), the assembly uses a combination of Pacific Biosciences sequencing, and Illumina sequencing. PacBio reads were assembled using wtdbg2. The assembly was submitted to decontamination with BlobTools, upgrade with FinisherSC, scaffolding with SSPACE_longread and gapFinisher, polishing with PacBio's smrttools and Pilon using the raw PacBio reads and the Illumina reads.
As described by Shahid Siddique et al., (2022), the gene predictions were made by The H. schachtii genome sequencing consortium. An in-house pipeline was developed to generate gene models using Braker2 supplied with RNAseq data.
- Siddique S, Radakovic ZS, Hiltl C, Pellegrin C, Baum TJ, Beasley H, Bent AF, Chitambo O, Chopra D, Danchin EGJ, Grenier E, Habash SS, Hasan MS, Helder J, Hewezi T, Holbein J, Holterman M, Janakowski S, Koutsovoulos GD, Kranse OP, Lozano-Torres JL, Maier TR, Masonbrink RE, Mendy B, Riemer E, Sobczak M, Sonawala U, Sterken MG, Thorpe P, van Steenbrugge JJM, Zahid N, Grundler F, Eves-van den Akker S. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nat Commun, 2022;13(1):6190
|Data Source||The H. schachtii genome sequencing consortium|
This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh