An Atlas of Plant Transposable Elements
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.12688/f1000research.74524.1 http://hdl.handle.net/11449/223343 |
Resumo: | 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). |
id |
UNSP_e92e69bc170918d89cbc8294fb128dce |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/223343 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
An Atlas of Plant Transposable Elementsatlasgenome-widelarge-scalemobile elementsplantsstandardizedAdvances 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).Department of Computer Science; Bioinformatics and Pattern Recognition Group, Graduation Program in Bioinformatics, Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Paraná, 86300000, BrazilDepartament of Agricultural and Environmental Biotechnology School of Agricultural and Veterinary Sciences São Paulo State University (UNESP)Institut de Recherche pour le Développement IRD University of MontpellierDepartment of Electronics and Automatization Universidad Autónoma de ManizalesGroup of Genomics and Transcriptomes in Plants Institute of Biosciences São Paulo State University (UNESP)Departament of Agricultural and Environmental Biotechnology School of Agricultural and Veterinary Sciences São Paulo State University (UNESP)Group of Genomics and Transcriptomes in Plants Institute of Biosciences São Paulo State University (UNESP)Universidade Estadual Paulista (UNESP)University of MontpellierUniversidad Autónoma de ManizalesPedro, Daniel Longhi FernandesAmorim, Tharcisio SoaresVarani, Alessandro [UNESP]Guyot, RomainDomingues, Douglas Silva [UNESP]Paschoal, Alexandre Rossi2022-04-28T19:50:06Z2022-04-28T19:50:06Z2021-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1194http://dx.doi.org/10.12688/f1000research.74524.1F1000Research, v. 10, p. 1194-.2046-1402http://hdl.handle.net/11449/22334310.12688/f1000research.74524.12-s2.0-85123567291Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengF1000Researchinfo:eu-repo/semantics/openAccess2022-04-28T19:50:06Zoai:repositorio.unesp.br:11449/223343Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:51:51.335002Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
An Atlas of Plant Transposable Elements |
title |
An Atlas of Plant Transposable Elements |
spellingShingle |
An Atlas of Plant Transposable Elements Pedro, Daniel Longhi Fernandes atlas genome-wide large-scale mobile elements plants standardized |
title_short |
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_sort |
An Atlas of Plant Transposable Elements |
author |
Pedro, Daniel Longhi Fernandes |
author_facet |
Pedro, Daniel Longhi Fernandes Amorim, Tharcisio Soares Varani, Alessandro [UNESP] Guyot, Romain Domingues, Douglas Silva [UNESP] Paschoal, Alexandre Rossi |
author_role |
author |
author2 |
Amorim, Tharcisio Soares Varani, Alessandro [UNESP] Guyot, Romain Domingues, Douglas Silva [UNESP] Paschoal, Alexandre Rossi |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) University of Montpellier Universidad Autónoma de Manizales |
dc.contributor.author.fl_str_mv |
Pedro, Daniel Longhi Fernandes Amorim, Tharcisio Soares Varani, Alessandro [UNESP] Guyot, Romain Domingues, Douglas Silva [UNESP] Paschoal, Alexandre Rossi |
dc.subject.por.fl_str_mv |
atlas genome-wide large-scale mobile elements plants standardized |
topic |
atlas genome-wide large-scale mobile elements plants standardized |
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). |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-01-01 2022-04-28T19:50:06Z 2022-04-28T19:50:06Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.12688/f1000research.74524.1 F1000Research, v. 10, p. 1194-. 2046-1402 http://hdl.handle.net/11449/223343 10.12688/f1000research.74524.1 2-s2.0-85123567291 |
url |
http://dx.doi.org/10.12688/f1000research.74524.1 http://hdl.handle.net/11449/223343 |
identifier_str_mv |
F1000Research, v. 10, p. 1194-. 2046-1402 10.12688/f1000research.74524.1 2-s2.0-85123567291 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
F1000Research |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1194 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129259259035648 |