Strongyloides stercoralis

Genome Assembly & Annotation

Assembly

The genome assembly was produced by the Thomas Nutman Lab at the Laboratory of Parasitic Diseases of the National Institute of Allergy and Infectious Diseases (NIAID), using Oxford Nanopore reads followed by a genome assembly pipeline including Flye 2.8.1 with a minimum overlap allowance of 2500bp, Necat v. December-2021; Smart Denovo v. December-2021; Canu v. December-2021. Following assembly, no polishing occurred as this is built into Flye.

This genome replaced the previous S. stercoralis GCA_000947215 genome as of WormBase ParaSite release 19.

Annotation

The genes were annotated using an in-house pipeline using both the MAKER pipeline and the FunAnnotate pipeline by the Thomas Nutman Lab at the Laboratory of Parasitic Diseases of the National Institute of Allergy and Infectious Diseases (NIAID).

Three iterations of annotation were run with MAKER. In the first iteration, a gene model was generated using proteins and transcripts taken from the previous S. stercoralis GCA_000947215 genome. The gene model used in the second iteration was taken from the first iteration, and the gene model used in the final iteration was from the second iteration.

For FunAnnotate, gene models were first predicted using the Augustus c_elegans_trsk database, the BUSCO nematoda_odb10 database, and the proteins and transcripts for S. strongyloides taken from the previous S. stercoralis GCA_000947215 genome. After gene prediction, the genome was annotated using the gene model.

Once both annotations were generated, the overlap between the two was then found, and a combined annotation was generated, which used high-quality genes found in either GFF.

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

• Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet, 2016;48(3):299-307

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression