Steinernema hermaphroditum

Genome Assembly & Annotation

Assembly

Oxford Nanopore Technologies (ONT) reads, short Illumina reads, and Dovetail Omni-C reads (Illumina for Hi-C chromosomal scaffolding) sequencing data for the wild-type reference strain PS9179 (described by Cao et al. 2022) have been assembled into a chromosomally scaffolded genome (using raven v. 1.7.0 assembler) by Erich Schwarz and collaborators at Cornell University.

Annotation

Four runs of initial prediction of protein-coding genes were done with BRAKER2 in parallel, using four different modes: - ab initio, without softmasking - with input data from RNA-seq only, without softmasking - with input data from Clade IV proteomes, without softmasking - with input data from both RNA-seq and Clade IV proteomes, with softmasking.

The RNA-seq data came from two developmental stages, infectious juveniles (IJs) and mixed-sex adults; these stages were chosen to try getting data from as wide a range of genes as reasonably possible from two biological replicates. The Clade IV protein data came from previously published proteomes of these related nematodes, taken from the WBPS17 release of ParaSite: Bursaphelenchus okinawaensis, Panagrellus redivivus, Rhabditophanes sp. KR3021, Steinernema carpocapsae, Steinernema feltiae (two alternative proteomes), Steinernema glaseri, Steinernema monticolum, Steinernema scapterisci, and Strongyloides ratti. The results of multiple BRAKER2 runs were merged with TSEBRA while enforcing retention of all transcripts. Structurally redundant transcripts (transcripts belonging to a single merged gene, and encoding either exactly the same protein or subsets of exactly the same protein) were then reduced to a single transcript encoding the largest possible protein. The annotation was generated and provided by Erich Schwarz and collaborators at Cornell University.

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

• Cao M, Schwartz HT, Tan CH, Sternberg PW. The entomopathogenic nematode Steinernema hermaphroditum is a self-fertilizing hermaphrodite and a genetically tractable system for the study of parasitic and mutualistic symbiosis. Genetics, 2022;220(1):iyab170

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