Gyrodactylus bullatarudis

Genome Assembly & Annotation

Assembly

The genome assembly was produced by the Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University. The assembly uses Illumina HiSeq4000 paired-end sequencing. The reads were assembled with shovil pipeline 1.0-pre1. Decontamination was performed using BLAST against UniRef90. Scaffolding was performed with BESST. Gaps were filled with the GAPCLOSER software. The mitochondrial genome was assembled with mitobim.

Annotation

Gene models were provided by the Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University. Different ab initio/evidence-based gene prediction were combined to obtain gene models: Geneid, glimmerHMM, GeneMarkES, geneMarkET and SNAP, using a combination of external RNASeq data, training gene models produced by PASA pipeline and PASA-derived transcript evidence. A very thorough procedure had been followed to combine the output of the above methods and produce the final gene models. More details can be found here.

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

• Konczal M, Przesmycka KJ, Mohammed RS, Phillips KP, Camara F, Chmielewski S, Hahn C, Guigo R, Cable J, Radwan J. Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis. Mol Ecol, 2020;29(8):1494-1507

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree