Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families
Autor(a) principal: | |
---|---|
Data de Publicação: | 2017 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1007/s00438-017-1291-7 http://hdl.handle.net/11449/169458 |
Resumo: | The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron). We propose the existence of novel families: Hypo, belonging to the LTR Gypsy superfamily; Hamp, belonging to non-LTRs; and rosa, belonging to Class II or DNA transposons. Although the rosa clade has been previously described, it was considered to be a basal subfamily of the mariner family. Based on our phylogenetic analysis, including Tc1, mariner, pogo, rosa and Lsra elements from other insects, we propose that rosa and Lsra elements are subfamilies of an independent family of Class II elements termed rosa. The annotations obtained indicate that a low percentage of the assembled CBB genome (approximately 8.2%) consists of TEs. Although these TEs display high diversity, most sequences are degenerate, with few full-length copies of LTR and DNA transposons and several complete and putatively active copies of non-LTR elements. MITEs constitute approximately 50% of the total TEs content, with a high proportion associated with DNA transposons in the Tc1-mariner superfamily. |
id |
UNSP_4001600911ffd8925d00cd23a8079de1 |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/169458 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel familiesCoffee berry borerDe novo TEs annotationHypothenemus hampeiTransposable element libraryThe coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron). We propose the existence of novel families: Hypo, belonging to the LTR Gypsy superfamily; Hamp, belonging to non-LTRs; and rosa, belonging to Class II or DNA transposons. Although the rosa clade has been previously described, it was considered to be a basal subfamily of the mariner family. Based on our phylogenetic analysis, including Tc1, mariner, pogo, rosa and Lsra elements from other insects, we propose that rosa and Lsra elements are subfamilies of an independent family of Class II elements termed rosa. The annotations obtained indicate that a low percentage of the assembled CBB genome (approximately 8.2%) consists of TEs. Although these TEs display high diversity, most sequences are degenerate, with few full-length copies of LTR and DNA transposons and several complete and putatively active copies of non-LTR elements. MITEs constitute approximately 50% of the total TEs content, with a high proportion associated with DNA transposons in the Tc1-mariner superfamily.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Ministerio de Agricultura y Desarrollo RuralUNESP-Univ. Estadual PaulistaEscola Nacional de Saúde Pública Fundação Oswaldo CruzNational Coffee Research Center-CENICAFÉPurdue UniversityCIAT-International Center for Tropical AgricultureUNESP-Univ. Estadual PaulistaFAPESP: 12/24813-8FAPESP: 2013/15070-4CNPq: 306493/2013-6Universidade Estadual Paulista (Unesp)Fundação Oswaldo CruzNational Coffee Research Center-CENICAFÉPurdue UniversityCIAT-International Center for Tropical AgricultureHernandez-Hernandez, Eric M. [UNESP]Fernández-Medina, Rita DanielaNavarro-Escalante, LucioNuñez, JonathanBenavides-Machado, PabloCarareto, Claudia M. A. [UNESP]2018-12-11T16:45:59Z2018-12-11T16:45:59Z2017-06-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article565-583application/pdfhttp://dx.doi.org/10.1007/s00438-017-1291-7Molecular Genetics and Genomics, v. 292, n. 3, p. 565-583, 2017.1617-46231617-4615http://hdl.handle.net/11449/16945810.1007/s00438-017-1291-72-s2.0-850129219802-s2.0-85012921980.pdf34257729983192160000-0002-0298-1354Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Genetics and Genomics1,1681,168info:eu-repo/semantics/openAccess2024-01-06T06:27:10Zoai:repositorio.unesp.br:11449/169458Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-01-06T06:27:10Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
title |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
spellingShingle |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families Hernandez-Hernandez, Eric M. [UNESP] Coffee berry borer De novo TEs annotation Hypothenemus hampei Transposable element library |
title_short |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
title_full |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
title_fullStr |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
title_full_unstemmed |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
title_sort |
Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families |
author |
Hernandez-Hernandez, Eric M. [UNESP] |
author_facet |
Hernandez-Hernandez, Eric M. [UNESP] Fernández-Medina, Rita Daniela Navarro-Escalante, Lucio Nuñez, Jonathan Benavides-Machado, Pablo Carareto, Claudia M. A. [UNESP] |
author_role |
author |
author2 |
Fernández-Medina, Rita Daniela Navarro-Escalante, Lucio Nuñez, Jonathan Benavides-Machado, Pablo Carareto, Claudia M. A. [UNESP] |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Fundação Oswaldo Cruz National Coffee Research Center-CENICAFÉ Purdue University CIAT-International Center for Tropical Agriculture |
dc.contributor.author.fl_str_mv |
Hernandez-Hernandez, Eric M. [UNESP] Fernández-Medina, Rita Daniela Navarro-Escalante, Lucio Nuñez, Jonathan Benavides-Machado, Pablo Carareto, Claudia M. A. [UNESP] |
dc.subject.por.fl_str_mv |
Coffee berry borer De novo TEs annotation Hypothenemus hampei Transposable element library |
topic |
Coffee berry borer De novo TEs annotation Hypothenemus hampei Transposable element library |
description |
The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron). We propose the existence of novel families: Hypo, belonging to the LTR Gypsy superfamily; Hamp, belonging to non-LTRs; and rosa, belonging to Class II or DNA transposons. Although the rosa clade has been previously described, it was considered to be a basal subfamily of the mariner family. Based on our phylogenetic analysis, including Tc1, mariner, pogo, rosa and Lsra elements from other insects, we propose that rosa and Lsra elements are subfamilies of an independent family of Class II elements termed rosa. The annotations obtained indicate that a low percentage of the assembled CBB genome (approximately 8.2%) consists of TEs. Although these TEs display high diversity, most sequences are degenerate, with few full-length copies of LTR and DNA transposons and several complete and putatively active copies of non-LTR elements. MITEs constitute approximately 50% of the total TEs content, with a high proportion associated with DNA transposons in the Tc1-mariner superfamily. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017-06-01 2018-12-11T16:45:59Z 2018-12-11T16:45:59Z |
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/10.1007/s00438-017-1291-7 Molecular Genetics and Genomics, v. 292, n. 3, p. 565-583, 2017. 1617-4623 1617-4615 http://hdl.handle.net/11449/169458 10.1007/s00438-017-1291-7 2-s2.0-85012921980 2-s2.0-85012921980.pdf 3425772998319216 0000-0002-0298-1354 |
url |
http://dx.doi.org/10.1007/s00438-017-1291-7 http://hdl.handle.net/11449/169458 |
identifier_str_mv |
Molecular Genetics and Genomics, v. 292, n. 3, p. 565-583, 2017. 1617-4623 1617-4615 10.1007/s00438-017-1291-7 2-s2.0-85012921980 2-s2.0-85012921980.pdf 3425772998319216 0000-0002-0298-1354 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Molecular Genetics and Genomics 1,168 1,168 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
565-583 application/pdf |
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_ |
1797790218658512896 |