Journal Article

Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

Ibrahim, Mohanad A., Al-Shomrani, Badr M., Alharbi, Sultan N., Simenc, Mathew, Manee, Manee M., Alqahtani, Fahad H., Al-Fageeh, Mohamed B.

2021

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Animals / Annotations / Behavior / Biological evolution / Biomedical and Life Sciences / Camelid genomes / Camelidae / Camels / Camelus / Camelus bactrianus / Camelus dromedarius / Camelus ferus / Comparative analysis / De novo TEs annotation / DNA Transposable Elements - genetics / Endogenous retroviruses / Evolution / Evolution, Molecular / Evolutionary genetics / Gene regulation / Genes / Genetic aspects / Genomes / Genomic structural variations / Genomics / Growth / Homology / Life Sciences / Methods / Microarrays / Microbial Genetics and Genomics / Plant Genetics and Genomics / Proteins / Proteomics / Research Article / Retroelements - genetics / Retrotransposons / Short Interspersed Nucleotide Elements / Transposable elements / Transposition / Transposons / Vertebrates / Vicugna pacos