Background: Transposable elements (TEs) are the largest component of the genetic material of most eukaryotes and can play roles in shaping genome architecture and regulating phenotypic variation; thus, understanding genome evolution is only possible if we comprehend the contributions of TEs. However, the quantitative and qualitative contributions of TEs can vary, even between closely related lineages. For palm species, in particular, the dynamics of the process through which TEs have differently shaped their genomes remains poorly understood because of a lack of comparative studies. Materials and methods: We conducted a genome-wide comparative analysis of palm TEs, focusing on identifying and classifying TEs using the draft assemblies of four palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, and Elaeis oleifera. Our TE library was generated using both de novo structure-based and homology-based methodologies. Results: The generated libraries revealed the TE component of each assembly, which varied from 41–81%. Class I retrotransposons covered 36–75% of these species’ draft genome sequences and primarily consisted of LTR retroelements, while non-LTR elements covered about 0.56–2.31% of each assembly, mainly as LINEs. The least represented were Class DNA transposons, comprising 1.87–3.37%. Conclusion: The current study contributes to a detailed identification and characterization of transposable elements in Palmae draft genome assemblies.
Cite this article
Genome-wide comparative analysis of transposable elements in Palmae genomes
Mohanad A. Ibrahim1, Badr M. Al-Shomrani1, Sultan N. Alharbi1, Tyler A. Elliott2, Mohammed S. Alsuabeyl3, Fahad H. Alqahtani1,*, Manee M. Manee1,4,*
1 National Centre for Bioinformatics, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
2 Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
3 National Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
4 National Center for Agricultural Technology, King Abdulaziz City for Science and Technology, 11442 Riyadh, Saudi Arabia
*Correspondence: email@example.com (Fahad H. Alqahtani); firstname.lastname@example.org (Manee M. Manee)
Front. Biosci. (Landmark Ed) 2021, 26(11), 1119–1131; https://doi.org/10.52586/5014
Submitted: 15 June 2021 | Revised: 7 November 2021 | Accepted: 11 November 2021 | Published: 30 November 2021
Copyright: © 2021 The Author(s). Published by BRI.
This is an open access article under the CC BY 4.0 license (https://creativecommons.org/licenses/by/4.0/).