The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

<h4>Background</h4>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 whol...

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Autores principales:	Leila do Nascimento Vieira, Helisson Faoro, Marcelo Rogalski, Hugo Pacheco de Freitas Fraga, Rodrigo Luis Alves Cardoso, Emanuel Maltempi de Souza, Fábio de Oliveira Pedrosa, Rubens Onofre Nodari, Miguel Pedro Guerra
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4756e2788ed948bdac082a3b4e421172
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spelling	oai:doaj.org-article:4756e2788ed948bdac082a3b4e4211722021-11-18T08:29:52ZThe complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.1932-620310.1371/journal.pone.0090618https://doaj.org/article/4756e2788ed948bdac082a3b4e4211722014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24594889/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusion</h4>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.Leila do Nascimento VieiraHelisson FaoroMarcelo RogalskiHugo Pacheco de Freitas FragaRodrigo Luis Alves CardosoEmanuel Maltempi de SouzaFábio de Oliveira PedrosaRubens Onofre NodariMiguel Pedro GuerraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e90618 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Leila do Nascimento Vieira Helisson Faoro Marcelo Rogalski Hugo Pacheco de Freitas Fraga Rodrigo Luis Alves Cardoso Emanuel Maltempi de Souza Fábio de Oliveira Pedrosa Rubens Onofre Nodari Miguel Pedro Guerra The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.
description	<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusion</h4>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.
format	article
author	Leila do Nascimento Vieira Helisson Faoro Marcelo Rogalski Hugo Pacheco de Freitas Fraga Rodrigo Luis Alves Cardoso Emanuel Maltempi de Souza Fábio de Oliveira Pedrosa Rubens Onofre Nodari Miguel Pedro Guerra
author_facet	Leila do Nascimento Vieira Helisson Faoro Marcelo Rogalski Hugo Pacheco de Freitas Fraga Rodrigo Luis Alves Cardoso Emanuel Maltempi de Souza Fábio de Oliveira Pedrosa Rubens Onofre Nodari Miguel Pedro Guerra
author_sort	Leila do Nascimento Vieira
title	The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and 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	complete chloroplast genome sequence of podocarpus lambertii: genome structure, evolutionary aspects, gene content and ssr detection.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/4756e2788ed948bdac082a3b4e421172
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The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

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