A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)

Whitney L E Tsai; Merly Escalona; Kimball L Garrett; Ryan S Terrill; Ruta Sahasrabudhe; Oanh Nguyen; Eric Beraut; William Seligmann; Colin W Fairbairn; Ryan J Harrigan; John E McCormack; Michael E Alfaro; Thomas B Smith; Rachael A Bay

doi:10.1093/jhered/esae008

A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)

J Hered. 2024 May 9;115(3):317-325. doi: 10.1093/jhered/esae008.

Authors

Affiliations

¹ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States.
² Moore Laboratory of Zoology, Biology Department, Occidental College, Los Angeles, CA 90041, United States.
³ Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States.
⁴ Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, United States.
⁵ DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States.
⁶ Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, United States.
⁷ Department of Evolution and Ecology, University of California, Davis, CA 95616, United States.

Abstract

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

Keywords: California Conservation Genomics Project; Parulidae.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
California
Female
Gene Flow
Genome*
Songbirds* / genetics

Abstract

Publication types

MeSH terms

Grants and funding