Hymenolepis microstoma

Genome Assembly & Annotation

Assembly

The H. microstoma genome was sequenced by the Parasite Genomics group at the Wellcome Trust Sanger Institute, in collaboration with Pete Olson (Natural History Museum, London). The initial version of the genome was described in Tsai et al (2013). ParaSite releases 5-11 (January 2016 to October 2018) presented the November 2015 snapshot from GeneDB, corresponding to INSDC assembly HMIC002. Assembly presented here is the third consecutive version of the assembly. As described in Olson et al (2020), the previous assembly was improved by scaffolding a de novo PacBio assembly using Bionano's hybrid scaffolder (optical mapping). Further improvement was then carried out in gap5 using all the available optical map and sequence data.

Annotation

As described in Olson et al (2020), the annotation was produced by running BRAKER, incorporating de novo gene predictions and RNASeq alignments, predicted on an unmasked assembly. The resulting predictions were then clustered using OrthoMCL and repeated predictions in low-complexity and repeat regions manually removed. A number of gene models were manually curated using Apollo.

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

• Olson PD, Tracey A, Baillie A, James K, Doyle SR, Buddenborg SK, Rodgers FH, Holroyd N, Berriman M. Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection. BMC Biol, 2020;18(1):165
• Olson PD, Zarowiecki M, James K, Baillie A, Bartl G, Burchell P, Chellappoo A, Jarero F, Tan LY, Holroyd N, Berriman M. Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms. Evodevo, 2018;9():21
• Cunningham LJ, Olson PD. Description of Hymenolepis microstoma (Nottingham strain): a classical tapeworm model for research in the genomic era. Parasit Vectors, 2010;3():123
• Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sánchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai X, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernández C, Holland PWH, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, Kiss F, Koziol U, Lambert O, Liu K, Luo X, Luo Y, Macchiaroli N, Nichol S, Paps J, Parkinson J, Pouchkina-Stantcheva N, Riddiford N, Rosenzvit M, Salinas G, Wasmuth JD, Zamanian M, Zheng Y, Taenia solium Genome Consortium, Cai J, Soberón X, Olson PD, Laclette JP, Brehm K, Berriman M. The genomes of four tapeworm species reveal adaptations to parasitism. Nature, 2013;496(7443):57-63

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression