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 altitudinal migration (0-3700 m), 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 contigs with a contig N₅₀ 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 resources for evolutionary genomics studies of passerines and genetic studies of high-altitude adaptation.