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An Atlas of Plant Transposable Elements

Advances in genomic sequencing have recently offered vast opportunities for biological exploration, unraveling the evolution and improving our understanding of Earth biodiversity. Due to distinct plant species characteristics in terms of genome size, ploidy and heterozygosity, transposable elements...

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Detalles Bibliográficos
Autores principales: Pedro, Daniel Longhi Fernandes, Amorim, Tharcisio Soares, Varani, Alessandro, Guyot, Romain, Domingues, Douglas Silva, Paschoal, Alexandre Rossi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8729191/
https://www.ncbi.nlm.nih.gov/pubmed/35035898
http://dx.doi.org/10.12688/f1000research.74524.1
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author Pedro, Daniel Longhi Fernandes
Amorim, Tharcisio Soares
Varani, Alessandro
Guyot, Romain
Domingues, Douglas Silva
Paschoal, Alexandre Rossi
author_facet Pedro, Daniel Longhi Fernandes
Amorim, Tharcisio Soares
Varani, Alessandro
Guyot, Romain
Domingues, Douglas Silva
Paschoal, Alexandre Rossi
author_sort Pedro, Daniel Longhi Fernandes
collection PubMed
description Advances in genomic sequencing have recently offered vast opportunities for biological exploration, unraveling the evolution and improving our understanding of Earth biodiversity. Due to distinct plant species characteristics in terms of genome size, ploidy and heterozygosity, transposable elements (TEs) are common characteristics of many genomes. TEs are ubiquitous and dispersed repetitive DNA sequences that frequently impact the evolution and composition of the genome, mainly due to their redundancy and rearrangements. For this study, we provided an atlas of TE data by employing an easy-to-use portal ( APTE website ). To our knowledge, this is the most extensive and standardized analysis of TEs in plant genomes. We evaluated 67 plant genomes assembled at chromosome scale, recovering a total of 49,802,023 TE records, representing a total of 47,992,091,043 (~47,62%) base pairs (bp) of the total genomic space. We observed that new types of TEs were identified and annotated compared to other data repositories. By establishing a standardized catalog of TE annotation on 67 genomes, new hypotheses, exploration of TE data and their influences on the genomes may allow a better understanding of their function and processes. All original code and an example of how we developed the TE annotation strategy is available on GitHub ( Extended data).
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spelling pubmed-87291912022-01-14 An Atlas of Plant Transposable Elements Pedro, Daniel Longhi Fernandes Amorim, Tharcisio Soares Varani, Alessandro Guyot, Romain Domingues, Douglas Silva Paschoal, Alexandre Rossi F1000Res Brief Report Advances in genomic sequencing have recently offered vast opportunities for biological exploration, unraveling the evolution and improving our understanding of Earth biodiversity. Due to distinct plant species characteristics in terms of genome size, ploidy and heterozygosity, transposable elements (TEs) are common characteristics of many genomes. TEs are ubiquitous and dispersed repetitive DNA sequences that frequently impact the evolution and composition of the genome, mainly due to their redundancy and rearrangements. For this study, we provided an atlas of TE data by employing an easy-to-use portal ( APTE website ). To our knowledge, this is the most extensive and standardized analysis of TEs in plant genomes. We evaluated 67 plant genomes assembled at chromosome scale, recovering a total of 49,802,023 TE records, representing a total of 47,992,091,043 (~47,62%) base pairs (bp) of the total genomic space. We observed that new types of TEs were identified and annotated compared to other data repositories. By establishing a standardized catalog of TE annotation on 67 genomes, new hypotheses, exploration of TE data and their influences on the genomes may allow a better understanding of their function and processes. All original code and an example of how we developed the TE annotation strategy is available on GitHub ( Extended data). F1000 Research Limited 2021-11-24 /pmc/articles/PMC8729191/ /pubmed/35035898 http://dx.doi.org/10.12688/f1000research.74524.1 Text en Copyright: © 2021 Pedro DLF et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Brief Report
Pedro, Daniel Longhi Fernandes
Amorim, Tharcisio Soares
Varani, Alessandro
Guyot, Romain
Domingues, Douglas Silva
Paschoal, Alexandre Rossi
An Atlas of Plant Transposable Elements
title An Atlas of Plant Transposable Elements
title_full An Atlas of Plant Transposable Elements
title_fullStr An Atlas of Plant Transposable Elements
title_full_unstemmed An Atlas of Plant Transposable Elements
title_short An Atlas of Plant Transposable Elements
title_sort atlas of plant transposable elements
topic Brief Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8729191/
https://www.ncbi.nlm.nih.gov/pubmed/35035898
http://dx.doi.org/10.12688/f1000research.74524.1
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