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Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats

BACKGROUND: Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles...

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Autores principales: Cañas, Rafael A., Feito, Isabel, Fuente-Maqueda, José Francisco, Ávila, Concepción, Majada, Juan, Cánovas, Francisco M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636790/
https://www.ncbi.nlm.nih.gov/pubmed/26545587
http://dx.doi.org/10.1186/s12864-015-2177-x
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author Cañas, Rafael A.
Feito, Isabel
Fuente-Maqueda, José Francisco
Ávila, Concepción
Majada, Juan
Cánovas, Francisco M.
author_facet Cañas, Rafael A.
Feito, Isabel
Fuente-Maqueda, José Francisco
Ávila, Concepción
Majada, Juan
Cánovas, Francisco M.
author_sort Cañas, Rafael A.
collection PubMed
description BACKGROUND: Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. RESULTS: An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95 % of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5 % for PINARRAY3 and 5.7 % for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. CONCLUSIONS: Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2177-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-46367902015-11-08 Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats Cañas, Rafael A. Feito, Isabel Fuente-Maqueda, José Francisco Ávila, Concepción Majada, Juan Cánovas, Francisco M. BMC Genomics Research Article BACKGROUND: Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. RESULTS: An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95 % of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5 % for PINARRAY3 and 5.7 % for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. CONCLUSIONS: Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2177-x) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-06 /pmc/articles/PMC4636790/ /pubmed/26545587 http://dx.doi.org/10.1186/s12864-015-2177-x Text en © Cañas et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Cañas, Rafael A.
Feito, Isabel
Fuente-Maqueda, José Francisco
Ávila, Concepción
Majada, Juan
Cánovas, Francisco M.
Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats
title Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats
title_full Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats
title_fullStr Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats
title_full_unstemmed Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats
title_short Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats
title_sort transcriptome-wide analysis supports environmental adaptations of two pinus pinaster populations from contrasting habitats
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636790/
https://www.ncbi.nlm.nih.gov/pubmed/26545587
http://dx.doi.org/10.1186/s12864-015-2177-x
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