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A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

Ben Thompsky·Eric Beraut·Robert D. Cooper·Merly Escalona·Robert E. Espinoza·Robert N. Fisher·Courtney Miller·Oanh Nguyen·Samuel Sacco·Ruta Sahasrabudhe·William E. Seligmann·Erin Tofflemier·Ian J. Wang·H. Bradley Schaffer
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Abstract

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

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Ben Thompsky, Eric Beraut, Robert D. Cooper, Merly Escalona, Robert E. Espinoza, Robert N. Fisher, Courtney Miller, Oanh Nguyen, Samuel Sacco, Ruta Sahasrabudhe, William E. Seligmann, Erin Tofflemier, Ian J. Wang, H. Bradley Schaffer. 2026-04-08. A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii. https://doi.org/10.1093/jhered%2Fesag009

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