A high-quality reference genome for the ornate shrew (Sorex ornatus) - PubMed (original) (raw)

A high-quality reference genome for the ornate shrew (Sorex ornatus)

Isaac J Linn et al. J Hered. 2026.

Abstract

The ornate shrew (Sorex ornatus) is a small predatory mammal with a broad distribution in northern, central, and southern California as well as in Baja California, Mexico. The ornate shrew is a highly productive consumer in wetland environments and is known to hybridize with the closely related vagrant shrew, Sorex vagrans. Here we present a high-quality de novo genome assembly for S. ornatus generated as a part of the California Conservation Genomics Project. The S. ornatus genome was generated using PacBio HiFi long reads and Omni-C chromatin interaction sequencing. The primary assembly is highly contiguous, with a contig N50 of 15.9 Mb, a scaffold N50 of 115.2 Mb, and a BUSCO completeness score of 95.10%. The ornate shrew genome will serve as a valuable resource for future North American Sorex conservation genomics as well as for research into shrew biology more generally.

Keywords: CCGP; California Conservation Genomics Project; Soricidae; conservation; metabolic rate; salt marshes.

© The Author(s) 2025. Published by Oxford University Press on behalf of The American Genetic Association.

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Figures

Fig. 1

Fig. 1

(A) The ornate shrew (Sorex ornatus) is distributed across northern, central, and southern California west of the Sierra Nevada, and into Baja California, Mexico. Dot indicates the collection location for the S. ornatus individual from which the genome in this assembly was generated. Range data retrieved from IUCN. (B) an image of an endangered Buena Vista Lake shrew (S. o. Relictus) (photo by CSU Stanislaus, published by U.S. Fish and Wildlife Service, Pacific southwest region).

Fig. 2

Fig. 2

Graphical representation of genome assembly and quality. (A) GenomeScope2.0 K-mer spectrum from Omni-C reads. (B) BlobToolKit Snailplot showing N50 metrics for S. ornatus assembly (mSorOrn1.0.p) and BUSCO scores for the mammalian set of orthologues. The outer circle displays the base pair composition across individual scaffolds, while the inner circle displays scaffold lengths. Scaffolds are shown clockwise from largest to smallest, with shading to indicate relevant lengths and counts. This indicates that the majority of the genome is in long scaffolds exceeding 34 mb and is highly contiguous. (C, D) Omni-C contact maps of primary and alternate assemblies respectively. Shaded values on the dot plot indicate physical contact between genomic sequences, so that shaded squares designate whole chromosomes. The 27 squares along the diagonal suggest a haploid genomic organization of 27.

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