Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Oct 26;14(1):25573.
doi: 10.1038/s41598-024-77773-0.

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data

Hussain Bahbahani  1 , Zainab Mohammad  2 , Abdulaziz Al-Ateeqi  3 , Faisal Almathen  4   5
Affiliations

A comprehensive map of copy number variations in dromedary camels based on whole genome sequence data

Hussain Bahbahani et al. Sci Rep. .

Abstract

Copy number variants (CNVs) are structural variants within the eukaryotic genome that vary among individuals of a species. These variants have been associated with different phenotypic traits, making them a valuable consideration as markers for designing breeding programmes. In this study, whole genome sequence data of 60 dromedary camel samples originating from the Arabian Peninsula were analyzed to construct a comprehensive dromedary CNV map. Utilizing four CNV callers employing read-depth, split-read and paired-end mapping approaches, a total of 37,519 CNV events (17,847 deletions and 19,672 duplications) were called on the dromedary autosomes. These CNV events were merged into 2,557 regions, categorized as 1,322 losses, 122 gains, and 1,113 "mixed regions" comprising both types. The cumulative size of the CNV regions amounted to 22.5 Mb, covering roughly 1.16% of the dromedary autosomes. Approximately 32% of the defined CNV regions (comprising 60% losses, 18% gains, and 0.27% mixed regions) were found in ≥ 90% of the dromedary samples, classifying them as prevalent regions. Genes with biological functions related to the different adaptive physiologies of dromedary camels, such as fertility, heat stress, musculoskeletal development, and fat metabolism, were overlapping with or in close proximity to ~ 68% of the defined CNV regions, demonstrating their potential role in dromedaries' physiology. This study presents the first comprehensive CNV map of dromedary camels and builds on the present knowledge in understanding the genetic structure of this species.

Keywords: Copy number variants; Paired-end mapping CNV caller; Read-depth CNV caller; Split-read CNV callers; Structural variants.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The genomic landscape of the CNV regions characterized on the autosomes of dromedary camels. The plot was created using SRplot online platform https://www.bioinformatics.com.cn/en.
Fig. 2
Fig. 2
A bar plot indicating the types and counts of the CNV regions defined on the dromedary autosomes.
Fig. 3
Fig. 3
A circular Manhattan plot indicating the copy number of the CNV regions on the dromedary autosomes. Ring markers indicate copy numbers. The outer bound numbers indicate the dromedary autosomes. The plot was created using CMplot package in R version 4.4.
Fig. 4
Fig. 4
The counts of (A) CNV regions and (B) CNV types for the different size ranges (kb) in the dromedary autosomes.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Burger, P. A., Ciani, E. & Faye, B. Old World camels in a modern world - a balancing act between conservation and genetic improvement. Anim. Genet. 50, 598–612. 10.1111/age.12858 (2019). - PMC - PubMed
    1. Tibary, A. & El Allali, K. Dromedary camel: A model of heat resistant livestock animal. Theriogenology. 154, 203–211. 10.1016/j.theriogenology.2020.05.046 (2020). - PubMed
    1. Musa, H., Shuiep, E. & El-Zubeir, I. Camel Husbandry Among Pastoralists in Darfur, Western Sudan. Nomadic Peoples. 10, 101–105. 10.3167/082279406780246438 (2006).
    1. Almathen, F. et al. Genetic structure of Arabian Peninsula dromedary camels revealed three geographic groups. Saudi J. Biol. Sci. 29, 1422–1427. 10.1016/j.sjbs.2021.11.032 (2022). - PMC - PubMed
    1. Bahbahani, H. & Almathen, F. Homogeneity of Arabian Peninsula dromedary camel populations with signals of geographic distinction based on whole genome sequence data. Sci. Rep. 12, 130. 10.1038/s41598-021-04087-w (2022). - PMC - PubMed

Grants and funding

LinkOut - more resources