Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1007/s11033-019-05047-4 http://hdl.handle.net/11449/196423 |
Resumo: | A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis, a tropical fruit species. A total of 250 different TE sequences were identified (96% Class I, and 4% Class II), corresponding to similar to 19% of the P. edulis draft genome. TEs were found preferentially in intergenic spaces (70.4%), but also overlapping genes (30.6%). LTR-RTs accounted for 181 single elements corresponding to similar to 13% of the draft genome. A phylogenetic inference of the reverse transcriptase domain of the LTR-RT revealed association of 37 elements with the Copia superfamily (Angela, Ale, Tork, and Sire) and 128 with the Gypsy (Del, Athila, Reina, CRM, and Galadriel) superfamily, and Del elements were the most frequent. Interestingly, according to insertion time analysis, the majority (95.9%) of the LTR-RTs were recently inserted into the P. edulis genome (<2.0 Mya), and with the exception of the Athila lineage, all LTR-RTs are transcriptionally active. Moreover, functional analyses disclosed that the Angela, Del, CRM and Tork lineages are conserved in wild Passiflora species, supporting the idea of a common expansion of Copia and Gypsy superfamilies. Overall, this is the first study describing the P. edulis TE repertoire, and it also lends weight to the suggestion that LTR-RTs had a recent expansion into the analyzed gene-rich region of the P. edulis genome, possibly along WGD (Whole genome duplication) events, but are under negative selection due to their potential deleterious impact on gene regions. |
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Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulisPassifloraPassion fruitGenome evolutionMobile genetic elementsReverse transcriptaseA significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis, a tropical fruit species. A total of 250 different TE sequences were identified (96% Class I, and 4% Class II), corresponding to similar to 19% of the P. edulis draft genome. TEs were found preferentially in intergenic spaces (70.4%), but also overlapping genes (30.6%). LTR-RTs accounted for 181 single elements corresponding to similar to 13% of the draft genome. A phylogenetic inference of the reverse transcriptase domain of the LTR-RT revealed association of 37 elements with the Copia superfamily (Angela, Ale, Tork, and Sire) and 128 with the Gypsy (Del, Athila, Reina, CRM, and Galadriel) superfamily, and Del elements were the most frequent. Interestingly, according to insertion time analysis, the majority (95.9%) of the LTR-RTs were recently inserted into the P. edulis genome (<2.0 Mya), and with the exception of the Athila lineage, all LTR-RTs are transcriptionally active. Moreover, functional analyses disclosed that the Angela, Del, CRM and Tork lineages are conserved in wild Passiflora species, supporting the idea of a common expansion of Copia and Gypsy superfamilies. Overall, this is the first study describing the P. edulis TE repertoire, and it also lends weight to the suggestion that LTR-RTs had a recent expansion into the analyzed gene-rich region of the P. edulis genome, possibly along WGD (Whole genome duplication) events, but are under negative selection due to their potential deleterious impact on gene regions.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, BR-13418900 Piracicaba, BrazilUniv Sao Paulo, Inst Biociencias, Dept Bot, BR-05508090 Sao Paulo, SP, BrazilUniv Estadual Campinas, Inst Biol, Dept Biol Vegetal, BR-13083862 Campinas, SP, BrazilINRA, Ctr Natl Ressources Genom Vegetales, F-31326 Castanet Tolosan, FranceUniv Estadual Paulista, Fac Ciencias Agr & Vet, Dept Tecnol, BR-14884900 Jaboticabal, BrazilUniv Estadual Paulista, Fac Ciencias Agr & Vet, Dept Tecnol, BR-14884900 Jaboticabal, BrazilFAPESP: 2014/25215-2SpringerUniversidade de São Paulo (USP)Universidade Estadual de Campinas (UNICAMP)INRAUniversidade Estadual Paulista (Unesp)Costa, Zirlane Portugal daCauz-Santos, Luiz AugustoRagagnin, Geovani TolfoVan Sluys, Marie-AnneDornelas, Marcelo CarnierBerges, HeleneVarani, Alessandro de Mello [UNESP]Carneiro Vieira, Maria Lucia2020-12-10T19:44:26Z2020-12-10T19:44:26Z2019-12-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article6117-6133http://dx.doi.org/10.1007/s11033-019-05047-4Molecular Biology Reports. Dordrecht: Springer, v. 46, n. 6, p. 6117-6133, 2019.0301-4851http://hdl.handle.net/11449/19642310.1007/s11033-019-05047-4WOS:000503243500043Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMolecular Biology Reportsinfo:eu-repo/semantics/openAccess2024-06-07T15:31:47Zoai:repositorio.unesp.br:11449/196423Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:39:33.389579Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
title |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
spellingShingle |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis Costa, Zirlane Portugal da Passiflora Passion fruit Genome evolution Mobile genetic elements Reverse transcriptase |
title_short |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
title_full |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
title_fullStr |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
title_full_unstemmed |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
title_sort |
Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis |
author |
Costa, Zirlane Portugal da |
author_facet |
Costa, Zirlane Portugal da Cauz-Santos, Luiz Augusto Ragagnin, Geovani Tolfo Van Sluys, Marie-Anne Dornelas, Marcelo Carnier Berges, Helene Varani, Alessandro de Mello [UNESP] Carneiro Vieira, Maria Lucia |
author_role |
author |
author2 |
Cauz-Santos, Luiz Augusto Ragagnin, Geovani Tolfo Van Sluys, Marie-Anne Dornelas, Marcelo Carnier Berges, Helene Varani, Alessandro de Mello [UNESP] Carneiro Vieira, Maria Lucia |
author2_role |
author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade de São Paulo (USP) Universidade Estadual de Campinas (UNICAMP) INRA Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Costa, Zirlane Portugal da Cauz-Santos, Luiz Augusto Ragagnin, Geovani Tolfo Van Sluys, Marie-Anne Dornelas, Marcelo Carnier Berges, Helene Varani, Alessandro de Mello [UNESP] Carneiro Vieira, Maria Lucia |
dc.subject.por.fl_str_mv |
Passiflora Passion fruit Genome evolution Mobile genetic elements Reverse transcriptase |
topic |
Passiflora Passion fruit Genome evolution Mobile genetic elements Reverse transcriptase |
description |
A significant proportion of plant genomes is consists of transposable elements (TEs), especially LTR retrotransposons (LTR-RTs) which are known to drive genome evolution. However, not much information is available on the structure and evolutionary role of TEs in the Passifloraceae family (Malpighiales order). Against this backdrop, we identified, characterized, and inferred the potential genomic impact of the TE repertoire found in the available genomic resources for Passiflora edulis, a tropical fruit species. A total of 250 different TE sequences were identified (96% Class I, and 4% Class II), corresponding to similar to 19% of the P. edulis draft genome. TEs were found preferentially in intergenic spaces (70.4%), but also overlapping genes (30.6%). LTR-RTs accounted for 181 single elements corresponding to similar to 13% of the draft genome. A phylogenetic inference of the reverse transcriptase domain of the LTR-RT revealed association of 37 elements with the Copia superfamily (Angela, Ale, Tork, and Sire) and 128 with the Gypsy (Del, Athila, Reina, CRM, and Galadriel) superfamily, and Del elements were the most frequent. Interestingly, according to insertion time analysis, the majority (95.9%) of the LTR-RTs were recently inserted into the P. edulis genome (<2.0 Mya), and with the exception of the Athila lineage, all LTR-RTs are transcriptionally active. Moreover, functional analyses disclosed that the Angela, Del, CRM and Tork lineages are conserved in wild Passiflora species, supporting the idea of a common expansion of Copia and Gypsy superfamilies. Overall, this is the first study describing the P. edulis TE repertoire, and it also lends weight to the suggestion that LTR-RTs had a recent expansion into the analyzed gene-rich region of the P. edulis genome, possibly along WGD (Whole genome duplication) events, but are under negative selection due to their potential deleterious impact on gene regions. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-12-01 2020-12-10T19:44:26Z 2020-12-10T19:44:26Z |
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/s11033-019-05047-4 Molecular Biology Reports. Dordrecht: Springer, v. 46, n. 6, p. 6117-6133, 2019. 0301-4851 http://hdl.handle.net/11449/196423 10.1007/s11033-019-05047-4 WOS:000503243500043 |
url |
http://dx.doi.org/10.1007/s11033-019-05047-4 http://hdl.handle.net/11449/196423 |
identifier_str_mv |
Molecular Biology Reports. Dordrecht: Springer, v. 46, n. 6, p. 6117-6133, 2019. 0301-4851 10.1007/s11033-019-05047-4 WOS:000503243500043 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Molecular Biology Reports |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
6117-6133 |
dc.publisher.none.fl_str_mv |
Springer |
publisher.none.fl_str_mv |
Springer |
dc.source.none.fl_str_mv |
Web of Science 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_ |
1808128839638843392 |