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

Abstract 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 re...

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Autores principales:	Mohanad A. Ibrahim, Badr M. Al-Shomrani, Mathew Simenc, Sultan N. Alharbi, Fahad H. Alqahtani, Mohamed B. Al-Fageeh, Manee M. Manee
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Camelid genomes Transposable elements De novo TEs annotation Transposons Retrotransposons Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/135ec9578457440ebaa4752917114c68
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spelling	oai:doaj.org-article:135ec9578457440ebaa4752917114c682021-11-21T12:26:34ZComparative analysis of transposable elements provides insights into genome evolution in the genus Camelus10.1186/s12864-021-08117-91471-2164https://doaj.org/article/135ec9578457440ebaa4752917114c682021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08117-9https://doaj.org/toc/1471-2164Abstract 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.Mohanad A. IbrahimBadr M. Al-ShomraniMathew SimencSultan N. AlharbiFahad H. AlqahtaniMohamed B. Al-FageehManee M. ManeeBMCarticleCamelid genomesTransposable elementsDe novo TEs annotationTransposonsRetrotransposonsBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Camelid genomes Transposable elements De novo TEs annotation Transposons Retrotransposons Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Camelid genomes Transposable elements De novo TEs annotation Transposons Retrotransposons Biotechnology TP248.13-248.65 Genetics QH426-470 Mohanad A. Ibrahim Badr M. Al-Shomrani Mathew Simenc Sultan N. Alharbi Fahad H. Alqahtani Mohamed B. Al-Fageeh Manee M. Manee Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus
description	Abstract 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.
format	article
author	Mohanad A. Ibrahim Badr M. Al-Shomrani Mathew Simenc Sultan N. Alharbi Fahad H. Alqahtani Mohamed B. Al-Fageeh Manee M. Manee
author_facet	Mohanad A. Ibrahim Badr M. Al-Shomrani Mathew Simenc Sultan N. Alharbi Fahad H. Alqahtani Mohamed B. Al-Fageeh Manee M. Manee
author_sort	Mohanad A. Ibrahim
title	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_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_sort	comparative analysis of transposable elements provides insights into genome evolution in the genus camelus
publisher	BMC
publishDate	2021
url	https://doaj.org/article/135ec9578457440ebaa4752917114c68
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Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

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