The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2014 |
| Outros Autores: | , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | LOCUS Repositório Institucional da UFV |
| Texto Completo: | https://doi.org/10.1371/journal.pone.0090618 http://www.locus.ufv.br/handle/123456789/12894 |
Resumo: | Número de páginas não informado. |
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Vieira, Leila do NascimentoFaoro, HelissonRogalski, MarceloFraga, Hugo Pacheco de FreitasCardoso, Rodrigo Luis AlvesSouza, Emanuel Maltempi dePedrosa, Fábio de OliveiraNodari, Rubens OnofreGuerra, Miguel Pedro2017-11-08T15:01:52Z2017-11-08T15:01:52Z2014-03-041932-6203https://doi.org/10.1371/journal.pone.0090618http://www.locus.ufv.br/handle/123456789/12894Número de páginas não informado.Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.engPlos OneVolume 9, Issue 3, e90618, March 2014Genome sequencePodocarpus lambertiiGenome structureEvolutionary aspectsGene contentSSR detectionThe complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detectioninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALjournal.pone.0090618.PDFjournal.pone.0090618.PDFtexto completoapplication/pdf767492https://locus.ufv.br//bitstream/123456789/12894/1/journal.pone.0090618.PDF41b0b45a373c9ffac963f28f48dc24a5MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/12894/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILjournal.pone.0090618.PDF.jpgjournal.pone.0090618.PDF.jpgIM Thumbnailimage/jpeg6585https://locus.ufv.br//bitstream/123456789/12894/3/journal.pone.0090618.PDF.jpgaa241cdd21d319d7db4f2fa251fc88b7MD53123456789/128942017-11-08 22:00:45.529oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452017-11-09T01:00:45LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false |
| dc.title.en.fl_str_mv |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| title |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| spellingShingle |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection Vieira, Leila do Nascimento Genome sequence Podocarpus lambertii Genome structure Evolutionary aspects Gene content SSR detection |
| title_short |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| title_full |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| title_fullStr |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| title_full_unstemmed |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| title_sort |
The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection |
| author |
Vieira, Leila do Nascimento |
| author_facet |
Vieira, Leila do Nascimento Faoro, Helisson Rogalski, Marcelo Fraga, Hugo Pacheco de Freitas Cardoso, Rodrigo Luis Alves Souza, Emanuel Maltempi de Pedrosa, Fábio de Oliveira Nodari, Rubens Onofre Guerra, Miguel Pedro |
| author_role |
author |
| author2 |
Faoro, Helisson Rogalski, Marcelo Fraga, Hugo Pacheco de Freitas Cardoso, Rodrigo Luis Alves Souza, Emanuel Maltempi de Pedrosa, Fábio de Oliveira Nodari, Rubens Onofre Guerra, Miguel Pedro |
| author2_role |
author author author author author author author author |
| dc.contributor.author.fl_str_mv |
Vieira, Leila do Nascimento Faoro, Helisson Rogalski, Marcelo Fraga, Hugo Pacheco de Freitas Cardoso, Rodrigo Luis Alves Souza, Emanuel Maltempi de Pedrosa, Fábio de Oliveira Nodari, Rubens Onofre Guerra, Miguel Pedro |
| dc.subject.pt-BR.fl_str_mv |
Genome sequence Podocarpus lambertii Genome structure Evolutionary aspects Gene content SSR detection |
| topic |
Genome sequence Podocarpus lambertii Genome structure Evolutionary aspects Gene content SSR detection |
| description |
Número de páginas não informado. |
| publishDate |
2014 |
| dc.date.issued.fl_str_mv |
2014-03-04 |
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2017-11-08T15:01:52Z |
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2017-11-08T15:01:52Z |
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info:eu-repo/semantics/publishedVersion |
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1932-6203 |
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1932-6203 |
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https://doi.org/10.1371/journal.pone.0090618 http://www.locus.ufv.br/handle/123456789/12894 |
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Volume 9, Issue 3, e90618, March 2014 |
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Plos One |
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