Work

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

Year: 2025

Type: data-paper

Abstract: 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.

Source: Scientific Data

DOI: 10.1038/s41597-025-06156-5

Authors: Prashant Ghimire, Nan Wang, Yiai Hu, Sangeet Lamichhaney

Institutions: Kent State University, Beijing Forestry University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,490

Funder: Kent State University