Chromosome-level genome assembly and annotation of the degu (Octodon degus)

Chiu, J. H.-C.; Zemke, N. R.; Garduno, M.; Yang, B.; Oakes, M. L.; Wong, K.; Pezo-Valderrama, P.; Xie, Y.; Urra, C.; Macias, J.; Tomlinson, C.; Cogram, P.; Xu, X.; Ren, B.

doi:10.64898/2026.01.22.701162

bioRxiv · 10.64898/2026.01.22.701162

Chromosome-level genome assembly and annotation of the degu (Octodon degus)

Chiu, J. H.-C.·Zemke, N. R.·Garduno, M.·Yang, B.·Oakes, M. L.·Wong, K.·Pezo-Valderrama, P.·Xie, Y.·Urra, C.·Macias, J.·Tomlinson, C.·Cogram, P.·Xu, X.·Ren, B.

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Abstract

High-quality reference genomes are essential for comparative and functional genomics yet remain unavailable for many emerging model organisms. Here, we report OctDeg2.0, a chromosome-level genome assembly and annotation of the degu (Octodon degus), generated using PacBio HiFi long-read sequencing and Hi-C scaffolding from a single male individual. Octodon degus is of growing interest as a natural animal model for aging and Alzheimers disease research. The 3.4 billion base-pair assembly comprises 28 autosomes and both sex chromosomes, with markedly improved contiguity and completeness over the prior short-read assembly while maintaining high base accuracy. The new assembly provides substantially enhanced gene annotation, clearer resolution of chromatin architecture and cis-regulatory element landscapes, with much improved characterization of repetitive and structurally complex regions, including centromeres and segmental duplications. We present a streamlined and reproducible pipeline for high-resolution de novo genome assembly and gene annotation applicable to other emerging model organisms. This work establishes a robust genomic resource for studying molecular and cellular mechanisms in health and disease in Octodon degus.

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Chiu, J. H.-C., Zemke, N. R., Garduno, M., Yang, B., Oakes, M. L., Wong, K., Pezo-Valderrama, P., Xie, Y., Urra, C., Macias, J., Tomlinson, C., Cogram, P., Xu, X., Ren, B.. 2026-01-25. Chromosome-level genome assembly and annotation of the degu (Octodon degus). https://doi.org/10.64898/2026.01.22.701162

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