A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia) - PubMed (original) (raw)

. 2024 May 9;115(3):317-325.

doi: 10.1093/jhered/esae008.

Merly Escalona 3, Kimball L Garrett 4, Ryan S Terrill 2, Ruta Sahasrabudhe 5, Oanh Nguyen 5, Eric Beraut 6, William Seligmann 6, Colin W Fairbairn 6, Ryan J Harrigan 1, John E McCormack 2, Michael E Alfaro 1, Thomas B Smith 1, Rachael A Bay 7

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

Whitney L E Tsai et al. J Hered. 2024.

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.

© The American Genetic Association. 2024.

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Figures

Fig. 1.

Fig. 1.

Geographic variation and distribution of Yellow Warblers (Setophaga petechia). A) The Northern (aestiva) group includes migratory subspecies with chestnut streaking on the breast. Northern subspecies breed in North America and winter in Central and northern South America. Photo taken by R. S. Terrill at Piute Ponds, Los Angeles, CA, USA. B) The Mangrove (erithachorides) group includes resident subspecies with a characteristic chestnut head. Mangrove subspecies inhabit mangroves along the coasts of Central and northern South America year-round. Photo taken by R. S. Terrill on Isla Holbox, Quintana Roo, MX. C) The Galapagos (aureola) and Golden (petechia) subspecies groups include resident subspecies with a chestnut cap and thick breast streaking except for S. p. ruficapilla from Martinique which exhibits the Mangrove phenotype. Populations of the Galapagos subspecies are found on the Galapagos Islands and Cocos Island off Costa Rica and Golden subspecies are found on the islands of the Caribbean. Photo taken by W. L. E. Tsai on Isla Cozumel, Quintana Roo, MX. D) Map of species distributional abundance (Fink et al. 2022). Shaded colors indicate seasonal shifts in distributions: year-round (purple), breeding (red), migrating (yellow), and non-breeding (blue).

Fig. 2.

Fig. 2.

Visual overview of genome assembly metrics. A) K-mer spectra output generated from PacBio HiFi data without adapters using GenomScope2.0. The bimodal pattern observed corresponds to a diploid genome. K-mers covered at lower coverage and lower frequency correspond to differences between haplotypes, whereas the higher coverage and higher frequency k-mers correspond to the similarities between haplotypes. B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the Setophaga petechia primary assembly (bSetPet1.0.p). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers scaffold and length-related metrics. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The outer light and dark blue ring show the mean, maximum, and minimum GC vs. AT content at 0.1% intervals (Challis et al. 2020). C) Omni-C contact map for the primary genome assembly generated with PretextSnapshot. Omni-C contact maps translate proximity of genomic regions in 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two such regions. Scaffolds are separated by black lines and higher density corresponds to higher levels of fragmentation.

References

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