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

BMC Genomics

Mathew Simenc¹  Mohamed B. Al-Fageeh²  Sultan N. Alharbi³  Mohanad A. Ibrahim³  Badr M. Al-Shomrani³  Manee M. Manee³  Fahad H. Alqahtani³ 

[1] Department of Biological Sciences, California State University, Fullerton, USA;Life Sciences and Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia;National Center for Bioinformatics, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia;

关键词: Camelid genomes;    Transposable elements;    De novo TEs annotation;    Transposons;    Retrotransposons;   

DOI  :  10.1186/s12864-021-08117-9

来源: Springer

【 摘 要 】

BackgroundTransposable 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.ResultsWe 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.ConclusionsThe 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.

【 授权许可】

CC BY