WormBase ParaSite HomeVersion: WBPS17 (WS282)

Heterodera glycines

BioProject PRJNA381081 | Data Source Iowa State University | Taxonomy ID 51029

About Heterodera glycines

The soybean cyst nematode (SCN), Heterodera glycines, is a plant-parasitic nematode infecting soybean roots. SCN has threatened the U.S. crop since the 1950s, and is also a problem in soybean growing areas of Latin America and Asia.

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.

Key Publications

Resources

http://scnbase.org/

Assembly Statistics

AssemblyASM414822v2, GCA_004148225.2
StrainTN10
Database VersionWBPS17
Genome Size157,978,452
Data SourceIowa State University
Annotation Version2021-12-WormBase

Gene counts

Coding genes22,465
Gene transcripts23,933

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