ArticleG3 (Bethesda, Md.)2022
A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Whole genome sequence analysis supports the genomic mosaicism of the endangered Hawaiian duck (Anas wyvilliana).Scientific reports · 2026Article
- Large Inversion Polymorphisms are Widespread in North American Songbirds.Genome biology and evolution · 2025Article
- Comparative Whole Genome Phylogeography Reveals Genetic Distinctiveness of Appalachian Populations of Boreal Songbirds.Evolutionary applications · 2025Article
- Haemosporidian Infection Risk Variation Across an Urban Gradient in a Songbird.Ecology and evolution · 2025Article
- Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.Molecular ecology resources · 2025Article
- Long-distance seasonal migration to the tropics promotes genetic diversity but not gene flow in boreal birds.Nature ecology & evolution · 2025Article
- Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.Genome biology and evolution · 2024Article
- An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).G3 (Bethesda, Md.) · 2023Article
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4 authors.
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Abstract
The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.
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