Fine-scale map reveals highly variable recombination rates associated with genomic features in the European blackcap
Authors/Creators
- 1. Max Planck Institute for Evolutionary Biology
- 2. Max Planck Institute for Evolutionary Biology, Plön, Germany
- 3. Institute of Avian Research, Wilhelmshaven, Germany
- 4. Department of Ecology and Genetics, Uppsala University
Description
In this project, we estimated historical recombination rates for the European blackcap (Sylvia atricapilla) and the garden warbler (Sylvia borin) using a linkage disequilibrium-based approach. The population-scaled recombination rates were inferred using a program called pyrho, which considers the population's demographic information and mutation rates. The mutation rate was taken from a close species (flycatcher, Ficedula albicollis).
Here we report the recombination rate per site per generation (r, output of pyrho) for all the chromosomes along the genome for both species.
Blackcap dataset file: WholeGenome_chromosomes_blackap_n38_Pen20_W50.gz
Garden warbler dataset file: WholeGenome_chromosomes_SylBor_n10_Pen20W50.gz
Additionally, we annotated the genome of the blackcap to evaluate the association of recombination rates with specific annotation features (e.g., genes, transcription start sites, promoters, 5'UTR, and 3'UTR regions). The annotation of the genome was based on RNA-seq and Iso-Seq data. It can be found with the name: bSylAtr1.1.gff
Files
Restricted
The record is publicly accessible, but files are restricted to users with access.
Request access
If you would like to request access to these files, please fill out the form below.
You need to satisfy these conditions in order for this request to be accepted:
The access is restricted to co-authors and reviewers of the article. Upon acceptance, the dataset will be public.
You are currently not logged in. Do you have an account? Log in here