Schmidtea mediterranea

Genome Assembly & Annotation

Assembly

This genome was produced by the Department Rink at the Max Planck Institute for Multidisciplinary Sciences and PlanMine.

Unpublished data

This is an unpublished genome project (publication pending). Before working with these data, please read our Policy for using unpublished data.

Circular consensus sequences from ~30x coverage PacBio reads were called using pbccs v(6.0.0) and reads with quality > 0.99 (Q20) were taken forward as "HiFi" reads. Additionally 1,000 Million Hi-C reads were generated from extracted nuclei of whole animals using the Arima-HiC+ Kit. PacBio HiFi and Hi-C reads were used to assemble phased contigs with hifiasm v0.7. Next, Hi-C reads whose mapping quality no less than 10 (-q 10) were further utilized to scaffold the contigs from each haplotype by SALSA v2 following the hic-pipeline, which includes filtering procedures such as removal of experimental artifacts from Hi-C alignments, fixation of Hi-C pair mates, and removal of PCR duplicates, etc. Four chromosome-level scaffolds could be observed in both haplotypes after scaffolding. However, Hi-C heatmap revealed evidence of misplacement of contigs in terms of positions and orientations. These errors were then manually curated based on the interaction frequency indicated by the intensity of Hi-C signals.

This genome page corresponds to the Haplotype 2 of this phased assembly. For Haplotype 1 click here.

Annotation

The gene predictions were made by the Department Rink at the Max Planck Institute for Multidisciplinary Sciences.

This annotation is unpublished (publication pending). To work with this data you must follow our Unpublished data Usage Policy.

The transcript annotation was generated by a hybrid genome-guided approach relying on dedicated long-read Oxford Nanopore cDNA/dRNA sequencing runs and Illumina short-read and poly-adenylation data obtained by publically available datasets. After read quality trimming, deduplication, filtering, and mapping (using HISAT and minimap2 for short and long reads, respectively), a draft transcriptome was generated using Stringtie2, then it was further refined using FLAIR and a collection of custom scripts to filter high confidence isoforms.

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

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree