University of Oulu

Sven Winter, René Meißner, Carola Greve, Alexander Ben Hamadou, Petr Horin, Stefan Prost, Pamela A Burger, A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus), Journal of Heredity, Volume 114, Issue 3, May 2023, Pages 271–278,

A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus)

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Author: Winter, Sven1; Meißner, René1; Greve, Carola2;
Organizations: 1Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
2LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
3Department of Animal Genetics, University of Veterinary Sciences, Brno, Czech Republic
4Central European Institute of Technology, University of Veterinary Sciences Brno (CEITEC Vetuni), Brno, Czech Republic
5Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
6Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna, Austria
7Natural History Museum Vienna, Central Research Laboratories, Vienna, Austria
8South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 3.5 MB)
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Language: English
Published: Oxford University Press, 2023
Publish Date: 2023-09-22


The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.

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Series: Journal of heredity
ISSN: 0022-1503
ISSN-E: 1471-8505
ISSN-L: 0022-1503
Volume: 114
Issue: 3
Pages: 271 - 278
DOI: 10.1093/jhered/esad015
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Funding: This study was funded by the Central European Science Partnership (CEUS) project Austrian Science Fund (FWF) I5081-B/ GACRCzech Republic 21-28637L (to P.H. and P.B.).
Dataset Reference: All underlying read data and the assembly are available at GenBank under BioProject PRJNA854353. A detailed list of commands used to generate the presented assembly and related analyses are available as Supplementary Material 2. The annotation, assembly, repeat masked assemblies, and all commands are also available at Dryad (
Copyright information: © The Author(s) 2023. The American Genetic Association 2023. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact