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The gene expression landscape of pine seedling tissues

(2017) PLANT JOURNAL. 91(6). p.1064-1087
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Conifers dominate vast regions of the Northern hemisphere. They are the main source of raw materials for timber industry as well as a wide range of biomaterials. Despite their inherent difficulties as experimental models for classical plant biology research, the technological advances in genomics research are enabling fundamental studies on these plants. The use of laser capture microdissection followed by transcriptomic analysis is a powerful tool for unravelling the molecular and functional organization of conifer tissues and specialized cells. In the present work, 14 different tissues from 1-month-old maritime pine (Pinus pinaster) seedlings have been isolated and their transcriptomes analysed. The results increased the sequence information and number of full-length transcripts from a previous reference transcriptome and added 39 841 new transcripts. In total, 2376 transcripts were ubiquitously expressed in all of the examined tissues. These transcripts could be considered the core 'housekeeping genes' in pine. The genes have been clustered in function to their expression profiles. This analysis reduced the number of profiles to 38, most of these defined by their expression in a unique tissue that is much higher than in the other tissues. The expression and localization data are accessible at ConGenIE.org (http://v22.popgenie.org/microdisection/). This study presents an overview of the gene expression distribution in different pine tissues, specifically highlighting the relationships between tissue gene expression and function. This transcriptome atlas is a valuable resource for functional genomics research in conifers.
Keywords
SPRUCE PICEA-GLAUCA, TRANSPOSABLE ELEMENTS, ARABIDOPSIS-THALIANA, NORWAY, SPRUCE, GENOME-WIDE, TRANSCRIPTOME ANALYSIS, ASPARAGINE SYNTHETASE, LASER MICRODISSECTION, CELL-DIFFERENTIATION, NITROGEN-METABOLISM, Pinus pinaster, conifer, seedling, microdissection, gene expression, database, long terminal repeats, Myb, nitrogen metabolism

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Citation

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Chicago
Cañas, Rafael A, Zhen Li, M Belén Pascual, Vanessa Castro-Rodríguez, Concepción Ávila, Lieven Sterck, Yves Van de Peer, and Francisco M Cánovas. 2017. “The Gene Expression Landscape of Pine Seedling Tissues.” Plant Journal 91 (6): 1064–1087.
APA
Cañas, R. A., Li, Z., Pascual, M. B., Castro-Rodríguez, V., Ávila, C., Sterck, L., Van de Peer, Y., et al. (2017). The gene expression landscape of pine seedling tissues. PLANT JOURNAL, 91(6), 1064–1087.
Vancouver
1.
Cañas RA, Li Z, Pascual MB, Castro-Rodríguez V, Ávila C, Sterck L, et al. The gene expression landscape of pine seedling tissues. PLANT JOURNAL. 2017;91(6):1064–87.
MLA
Cañas, Rafael A, Zhen Li, M Belén Pascual, et al. “The Gene Expression Landscape of Pine Seedling Tissues.” PLANT JOURNAL 91.6 (2017): 1064–1087. Print.
@article{8533279,
  abstract     = {Conifers dominate vast regions of the Northern hemisphere. They are the main source of raw materials for timber industry as well as a wide range of biomaterials. Despite their inherent difficulties as experimental models for classical plant biology research, the technological advances in genomics research are enabling fundamental studies on these plants. The use of laser capture microdissection followed by transcriptomic analysis is a powerful tool for unravelling the molecular and functional organization of conifer tissues and specialized cells. In the present work, 14 different tissues from 1-month-old maritime pine (Pinus pinaster) seedlings have been isolated and their transcriptomes analysed. The results increased the sequence information and number of full-length transcripts from a previous reference transcriptome and added 39 841 new transcripts. In total, 2376 transcripts were ubiquitously expressed in all of the examined tissues. These transcripts could be considered the core 'housekeeping genes' in pine. The genes have been clustered in function to their expression profiles. This analysis reduced the number of profiles to 38, most of these defined by their expression in a unique tissue that is much higher than in the other tissues. The expression and localization data are accessible at ConGenIE.org (http://v22.popgenie.org/microdisection/). This study presents an overview of the gene expression distribution in different pine tissues, specifically highlighting the relationships between tissue gene expression and function. This transcriptome atlas is a valuable resource for functional genomics research in conifers.},
  author       = {Ca{\~n}as, Rafael A and Li, Zhen and Pascual, M Bel{\'e}n and Castro-Rodr{\'i}guez, Vanessa and {\'A}vila, Concepci{\'o}n and Sterck, Lieven and Van de Peer, Yves and C{\'a}novas, Francisco M},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {SPRUCE PICEA-GLAUCA,TRANSPOSABLE ELEMENTS,ARABIDOPSIS-THALIANA,NORWAY,SPRUCE,GENOME-WIDE,TRANSCRIPTOME ANALYSIS,ASPARAGINE SYNTHETASE,LASER MICRODISSECTION,CELL-DIFFERENTIATION,NITROGEN-METABOLISM,Pinus pinaster,conifer,seedling,microdissection,gene expression,database,long terminal repeats,Myb,nitrogen metabolism},
  language     = {eng},
  number       = {6},
  pages        = {1064--1087},
  title        = {The gene expression landscape of pine seedling tissues},
  url          = {http://dx.doi.org/10.1111/tpj.13617},
  volume       = {91},
  year         = {2017},
}

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