A complete reference genome assembly and annotation of the Black Redstart Phoenicurus ochruros

The Black Redstart ( Phoenicurus ochruros ) is one of the most widely distributed species, occupying diverse habitats and exhibiting remarkable altitudinal migration, making it suitable model for studying altitudinal migration and high-altitude adaptation. In this study, we present the first reference genome of Phoenicurus ochruros , generated using PacBio HiFi long-read sequencing. The nuclear genome is 1.37 Gb in length, assembled into 296 scaffolds with a scaffold N ₅₀ of 29.9 Mb. Multiple complementary genome validation approaches - including BUSCO analysis, mapping of raw PacBio HiFi reads, and comparative genomics analysis - confirmed the high contiguity and gene-space completeness of the genome. The Black Redstart genome contains one of the highest proportions of transposable elements among passerines (30.58%), second only to Bell’s Sparrow ( Artemisiospiza belli) , 31.2%. We further integrated RNA-seq data, protein homology evidence, and ab initio gene prediction to build high-quality genome annotation of 18,609 genes in the P. ochruros genome. This genomic resource provides invaluable resource for evolutionary genomics studies of passerines and explore genetic basis of high-altitude adaptation.