Chromosome-scale genome assembly and annotation of Octodon degus
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 Alzheimer's 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 .
Authors
- Xiangmin Xu (ORCID: https://orcid.org/0000-0002-5828-1533)
- Weronika M. Bartosik (ORCID: https://orcid.org/0009-0007-7724-5216)
- Yang Xie (ORCID: https://orcid.org/0000-0002-7453-6786)
- Juan F Macias-Velasco (ORCID: https://orcid.org/0000-0003-2827-4647)
- Nathan R. Zemke (ORCID: https://orcid.org/0000-0002-6326-5925)
- Kristie Wong
- Chad Tomlinson (ORCID: https://orcid.org/0000-0001-9905-6159)
- Patricio Pezo (ORCID: https://orcid.org/0000-0001-5027-7145)
- Bing Yang (ORCID: https://orcid.org/0000-0001-6739-2932)
- Patricia Cogram (ORCID: https://orcid.org/0000-0002-4198-0821)
- Bing Ren (ORCID: https://orcid.org/0000-0002-5435-1127)
- B. Maximiliano Garduño (ORCID: https://orcid.org/0000-0001-8828-0614)
- Melanie Oakes (ORCID: https://orcid.org/0009-0002-2369-4810)
- Urra Claudio (ORCID: https://orcid.org/0009-0009-4210-7758)
- Jeffrey Huey-Chuan Chiu (ORCID: https://orcid.org/0009-0008-2041-9331)
- Xiaomeng Gao (ORCID: https://orcid.org/0009-0003-6165-9634)
Institutions
- University of California, Irvine (US)
- Washington University in St. Louis (US)
- Columbia University Irving Medical Center (US)
- University of California San Diego (US)
- Fundación Ciencia and Vida (CL)
- Institut de Biologia Evolutiva (ES)
- New York Genome Center (US)
- University of Chile (CL)
Publication Details
- Journal
- Genome Research
- Published
- 2026-10-26
- DOI
- https://doi.org/10.1101/gr.281858.126
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- preprint