Heterodera glycines

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the Genome Informatics Facility, Office of Biotechnology, Iowa State University. This is an updated version of the GCA_004148225 assembly which uses PacBio long-read sequencing polished with Illumina HiSeq X short-read sequencing reads. Previously deposited Pacbio sequencing (SRX2692203 - SRX2692222) long reads were used with Falcon to generate a new draft assembly which was scaffolded using SNAP read mapper, HiRise and SSPACE-LONGREAD. PILON was used to polish the assembly using the Illumina reads and CCS reads.

Annotation

The gene predictions were made by the Genome Informatics Facility, Office of Biotechnology, Iowa State University. Gene models were predicted using a MIKADO pipeline. Consensus transcripts from 7 transcriptom assemblies and gene predictions, previously published ESTs, previously published effectors and IsoSeq data were supplied with BRAKER to the pipeline as external evidence.

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

• Masonbrink RE, Maier TR, Hudson M, Severin A, Baum T. A chromosomal assembly of the soybean cyst nematode genome. Mol Ecol Resour, 2021;21(7):2407-2422

Resources

http://scnbase.org/

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression