Steinernema carpocapsae

Genome Assembly & Annotation

Assembly

The genome assembly was produced by the University of California, Irvine using PacBio long reads, with BioNano optical mapping, as described in Serra et al. (2019). It is an update to an earlier assembly from the same institute.

Annotation

The gene predictions were made using AUGUSTUS incorporating evidence from open reading frames, RNASeq data across multiple developmental stages and conditions, and alignments from C. elegans. The gene models were updated in release 15 to incorporate UTRs.

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

• Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A. Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. Genome Biol, 2015;16():200
• Serra L, Macchietto M, Macias-Muñoz A, McGill CJ, Rodriguez IM, Rodriguez B, Murad R, Mortazavi A. Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome. G3 (Bethesda), 2019;9(8):2687-2697

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression