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

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...

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Autores principales: Ibrahim, Mohanad A., Al-Shomrani, Badr M., Simenc, Mathew, Alharbi, Sultan N., Alqahtani, Fahad H., Al-Fageeh, Mohamed B., Manee, Manee M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8605555/
https://www.ncbi.nlm.nih.gov/pubmed/34800971
http://dx.doi.org/10.1186/s12864-021-08117-9
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author Ibrahim, Mohanad A.
Al-Shomrani, Badr M.
Simenc, Mathew
Alharbi, Sultan N.
Alqahtani, Fahad H.
Al-Fageeh, Mohamed B.
Manee, Manee M.
author_facet Ibrahim, Mohanad A.
Al-Shomrani, Badr M.
Simenc, Mathew
Alharbi, Sultan N.
Alqahtani, Fahad H.
Al-Fageeh, Mohamed B.
Manee, Manee M.
author_sort Ibrahim, Mohanad A.
collection PubMed
description 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.
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spelling pubmed-86055552021-11-22 Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus Ibrahim, Mohanad A. Al-Shomrani, Badr M. Simenc, Mathew Alharbi, Sultan N. Alqahtani, Fahad H. Al-Fageeh, Mohamed B. Manee, Manee M. BMC Genomics Research Article 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. BioMed Central 2021-11-20 /pmc/articles/PMC8605555/ /pubmed/34800971 http://dx.doi.org/10.1186/s12864-021-08117-9 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Ibrahim, Mohanad A.
Al-Shomrani, Badr M.
Simenc, Mathew
Alharbi, Sultan N.
Alqahtani, Fahad H.
Al-Fageeh, Mohamed B.
Manee, Manee M.
Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
title Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
title_full Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
title_fullStr Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
title_full_unstemmed Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
title_short Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
title_sort comparative analysis of transposable elements provides insights into genome evolution in the genus camelus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8605555/
https://www.ncbi.nlm.nih.gov/pubmed/34800971
http://dx.doi.org/10.1186/s12864-021-08117-9
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