Meloidogyne chitwoodi

Genome Assembly & Annotation

Assembly

For this assembly, M. chitwoodi race 1 population, extracted from 3-month-old infected tomato plants, was used. This population did not reproduce on alfalfa (used as a rotation crop to control M. chitwoodi populations).

According to Bali S, et al., (2021), PacBio long sequencing reads were assembled using the SMRT analysis pipeline. Short Illumina reads were used to error correct PacBio data contigs using pilon v.1.22.

Annotation

According to Bali S, et al., (2021), genome annotation was performed using the M. hapla protein dataset as Protein Homology Evidence and the SNAP training file prepared from the first round of annotation. EST evidence was used.

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

• Bali S, Hu S, Vining K, Brown C, Mojtahedi H, Zhang L, Gleason C, Sathuvalli V. Nematode Genome Announcement: Draft Genome of <i>Meloidogyne chitwoodi</i>, an Economically Important Pest of Potato in the Pacific Northwest. Mol Plant Microbe Interact, 2021;34(8):981-986

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree