Comparative Analysis of Transposable Elements Provides Insights into Genome Evolution in the Genus Camelus

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2021 Nov 21

PMID 34800971

Citations 5

Authors

Mohanad A Ibrahim

Badr M Al-Shomrani

Mathew Simenc

Sultan N Alharbi

Fahad H Alqahtani

Mohamed B Al-Fageeh

Manee M Manee

Affiliations

Soon will be listed here.

Abstract

Background: Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available.

Results: We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies ( https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline ). Annotation results indicated a similar proportion of each genomes comprising TEs (35-36%). Class I LTR retrotransposons comprised 16-20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1-2% of each genome.

Conclusions: The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

Citing Articles

Mitochondrial DNA of the Arabian Camel .

Manee M, Al-Shomrani B, Alqahtani F Animals (Basel). 2024; 14(17).

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High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of .

Wang B, Saleh A, Yang N, Asare E, Chen H, Wang Q Animals (Basel). 2024; 14(10).

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Taming transposable elements in livestock and poultry: a review of their roles and applications.

Zhao P, Peng C, Fang L, Wang Z, Liu G Genet Sel Evol. 2023; 55(1):50.

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Zuo B, Micah Nneji L, Sun Y BMC Genomics. 2023; 24(1):379.

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LTR Retroelements and Bird Adaptation to Arid Environments.

Carotti E, Tittarelli E, Canapa A, Biscotti M, Carducci F, Barucca M Int J Mol Sci. 2023; 24(7).

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