Schmidtea mediterranea

Genome Assembly & Annotation

Assembly

The assembly was produced using long-read sequencing and a de novo assembler (MARVEL) enhanced for low-complexity reads, as described by Grohme et al. (2018).

Annotation

The annotation is a set of Augustus predictions filtered for overlap with known repeats and coverage, as described by Rozanski et al. (2019). WormBase retrieved it from PlanMine 3.0.

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

• Grohme MA, Schloissnig S, Rozanski A, Pippel M, Young GR, Winkler S, Brandl H, Henry I, Dahl A, Powell S, Hiller M, Myers E, Rink JC. The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms. Nature, 2018;554(7690):56-61
• Rozanski A, Moon H, Brandl H, Martín-Durán JM, Grohme MA, Hüttner K, Bartscherer K, Henry I, Rink JC. PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity. Nucleic Acids Res, 2019;47(d1):D812-D820

Resources

PlanMine

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression