Schistosoma haematobium

Genome Assembly & Annotation

Assembly

As described by Stroehlein, et al., 2022, the S. haematobium reference genome (designated Shae.V3 – representing the Egyptian reference strain) was assembled from data produced by Oxford Nanopore long-read and Hi-C sequencing and from previous long-read and short-read data sets produced using PacBio, Illumina or Dovetail technology.

Annotation

Gene models were generated using a pipeline incorporating MAKER2, EVM, and transfer from the previous "Shae.V1" gene set using liftOver and RATT. The annotation is described in full by Stroehlein et al., 2019. The gene-set presented here for the Shae. V3, was generated transferring 6277 high-confidence gene models (i.e. 67.4%) from Shae.V2 to Shae.V3, and inferred 3154 more genes based on evidence from mapped long and short RNA sequence reads from all key developmental stages and both sexes of S. haematobium, as described in full by Stroehlein et al., 2022.

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

• Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience, 2019;8(9):giz108
• Young ND, Jex AR, Li B, Liu S, Yang L, Xiong Z, Li Y, Cantacessi C, Hall RS, Xu X, Chen F, Wu X, Zerlotini A, Oliveira G, Hofmann A, Zhang G, Fang X, Kang Y, Campbell BE, Loukas A, Ranganathan S, Rollinson D, Rinaldi G, Brindley PJ, Yang H, Wang J, Wang J, Gasser RB. Whole-genome sequence of Schistosoma haematobium. Nat Genet, 2012;44(2):221-225
• Stroehlein AJ, Korhonen PK, Lee VV, Ralph SA, Mentink-Kane M, You H, McManus DP, Tchuenté LT, Stothard JR, Kaur P, Dudchenko O, Aiden EL, Yang B, Yang H, Emery AM, Webster BL, Brindley PJ, Rollinson D, Chang BCH, Gasser RB, Young ND. Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PLoS Pathog, 2022;18(2):e1010288

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression