Abstract
The spotted flycatcher (Muscicapa striata) forms with the Mediterranean flycatcher (Muscicapa tyrrhenica) a newly recognized species pair of trans-Saharan migratory passerines. These flycatchers present a nested peripatric distribution, a pattern especially unusual among high dispersal species that questions the eco-evolutionary factors involved during the speciation process. Here, we present a genome assembly for M. striata assembled using a combination of Nanopore and Illumina sequences. The final assembly is 1.08 Gb long and consists of 4,779 contigs with an N50 of 3.2 Mb. The completeness of our M. striata genome assembly is supported by the number of BUSCO (95%) and ultraconserved element (UCE) (4889/5041; 97.0%) loci retrieved. This assembly showed high synteny with the Ficedula albicollis reference genome, the closest species for which a chromosome-scale reference genome is available. Several inversions were identified and will need to be investigated at the family level.