Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis

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MetadadosDescriçãoIdioma
Autor(es): dc.contributorUniversidade de São Paulo (USP)-
Autor(es): dc.contributorUniversidade Estadual de Campinas (UNICAMP)-
Autor(es): dc.contributorINRA-
Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.creatorCosta, Zirlane Portugal da-
Autor(es): dc.creatorCauz-Santos, Luiz Augusto-
Autor(es): dc.creatorRagagnin, Geovani Tolfo-
Autor(es): dc.creatorVan Sluys, Marie-Anne-
Autor(es): dc.creatorDornelas, Marcelo Carnier-
Autor(es): dc.creatorBerges, Helene-
Autor(es): dc.creatorVarani, Alessandro de Mello [UNESP]-
Autor(es): dc.creatorCarneiro Vieira, Maria Lucia-
Data de aceite: dc.date.accessioned2022-02-22T00:09:23Z-
Data de disponibilização: dc.date.available2022-02-22T00:09:23Z-
Data de envio: dc.date.issued2020-12-09-
Data de envio: dc.date.issued2020-12-09-
Data de envio: dc.date.issued2019-11-30-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1007/s11033-019-05047-4-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/196423-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/196423-
Descrição: dc.descriptionA 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.-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)-
Descrição: dc.descriptionCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)-
Descrição: dc.descriptionUniv Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, BR-13418900 Piracicaba, Brazil-
Descrição: dc.descriptionUniv Sao Paulo, Inst Biociencias, Dept Bot, BR-05508090 Sao Paulo, SP, Brazil-
Descrição: dc.descriptionUniv Estadual Campinas, Inst Biol, Dept Biol Vegetal, BR-13083862 Campinas, SP, Brazil-
Descrição: dc.descriptionINRA, Ctr Natl Ressources Genom Vegetales, F-31326 Castanet Tolosan, France-
Descrição: dc.descriptionUniv Estadual Paulista, Fac Ciencias Agr & Vet, Dept Tecnol, BR-14884900 Jaboticabal, Brazil-
Descrição: dc.descriptionUniv Estadual Paulista, Fac Ciencias Agr & Vet, Dept Tecnol, BR-14884900 Jaboticabal, Brazil-
Descrição: dc.descriptionFAPESP: 2014/25215-2-
Formato: dc.format6117-6133-
Idioma: dc.languageen-
Publicador: dc.publisherSpringer-
Relação: dc.relationMolecular Biology Reports-
???dc.source???: dc.sourceWeb of Science-
Palavras-chave: dc.subjectPassiflora-
Palavras-chave: dc.subjectPassion fruit-
Palavras-chave: dc.subjectGenome evolution-
Palavras-chave: dc.subjectMobile genetic elements-
Palavras-chave: dc.subjectReverse transcriptase-
Título: dc.titleTransposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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