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

This project estimates historical recombination rates of the Eurasian blackcap (Sylvia atricapilla) and the garden warbler (Sylvia borin) using a linkage disequilibrium-based approach. The population-scaled recombination rates were inferred using 'pyrho' considering the population's demographic information and mutation rates. The mutation rate was taken from a closely related 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 blackcap genome to evaluate the association between recombination rates and 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.本研究基于连锁不平衡（linkage disequilibrium）方法，估算欧亚黑顶林莺（Sylvia atricapilla）与园林莺（Sylvia borin）的历史重组率。研究借助pyrho工具，结合种群的历史动态信息与突变率，推断得到种群尺度的重组率。其中突变率取自近缘物种姬鹟（Ficedula albicollis）。 本研究报道了两个物种全基因组所有染色体的单位点每世代重组率（r，即pyrho的输出结果）。 黑顶林莺数据集文件为：WholeGenome_chromosomes_blackap_n38_Pen20_W50.gz 园林莺数据集文件为：WholeGenome_chromosomes_SylBor_n10_Pen20W50.gz 此外，我们对黑顶林莺基因组进行功能注释，以评估重组率与特定注释特征（如基因、转录起始位点、启动子、5'非翻译区（5'UTR）、3'非翻译区（3'UTR）区域）之间的关联。该基因组注释基于RNA-seq与Iso-Seq数据，对应的注释文件名为bSylAtr1.1.gff。