Fine-scale map reveals highly variable recombination rates associated with genomic features in the European blackcap

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