Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern

Dustin A. Wood; Jonathan Q. Richmond; Merly Escalona; Mohan P. A. Marimuthu; Oanh Nguyen; Samuel Sacco; Eric Beraut; Michael F. Westphal; Robert N. Fisher; A. G. Vandergast; Erin Toffelmier; Ian J Wang; H. Bradley Shaffer

doi:10.1093/jhered/esac040

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern

Journal of Heredity

By: Dustin A. Wood, Jonathan Q. Richmond, Merly Escalona, Mohan P. A. Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Michael F. Westphal, Robert N. Fisher, A. G. Vandergast, Erin Toffelmier, Ian J Wang, and H. Bradley Shaffer

https://doi.org/10.1093/jhered/esac040

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Abstract

The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.

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Additional publication details
Publication type	Article
Publication Subtype	Journal Article
Title	Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern
Series title	Journal of Heredity
DOI	10.1093/jhered/esac040
Volume	113
Issue	6
Year Published	2022
Language	English
Publisher	Oxford University Press
Contributing office(s)	Western Ecological Research Center
Description	9 p.
First page	632
Last page	640
Country	United States
State	California
Google Analytic Metrics	Metrics page