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

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

doi:10.1186/s12864-021-08117-9

Mohanad A Ibrahim, Fahad H Alqahtani + Show 5 more

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https://doi.org/10.1186/s12864-021-08117-9

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Abstract

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.

Highlights

Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation
Class I elements: Long terminal repeat (LTR) retrotransposons Candidate LTR-reverse transcriptase (RT) loci were identified by employing the program LTRharvest [29], a component of GenomeTools [37], which searches the input sequence for direct repeats (LTRs) that are separated by a given distance and outside of which are apparent target site duplications (TSDs)
LTRdigest searches for homologs in the putative long terminal repeat REs (LTR-RTs) using HMMER3 [101] and a set of TE-related Profile hidden Markov models (pHMMs) we provided from Pfam and Gypsy database (GyDB) [31, 63]

Summary

Introduction

Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. TEs are DNA sequences found in most eukaryotes which encode various proteins which carry out the molecular mechanisms which facilitate their relocation and duplication within a host genome [103]. They can comprise substantial proportions of eukaryotic genomes, for example, 50% of the human. An increasing number of studies support a link between TE activity and species responsiveness to environmental conditions [35, 64] In this context, mobile elements contribute to increasing genetic diversity, allowing organisms to better adapt to new conditions [91]. TE activity may have contributed to the high diversity of vertebrate species that colonized many habitats, from water to land and temperate to extreme environments [19]

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