The gene expression landscape of pine seedling tissues

Conifers dominate vast regions of the Northern hemisphere and are the main source of raw materials for timber industry and a wide range of biomaterials. Despite their inherent difficulties as experimental models for classical plant biology research, new 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 one-month-old maritime pine (Pinus pinaster) seedlings have been isolated and their transcriptomes analyzed. The results increased the sequence information and number of full-length transcripts from a previous reference transcriptome and added 39,841 new transcripts. A total of 2,376 transcripts were ubiquitously expressed in all of the examined tissues. These transcripts and the significant functions shared in all tissues could be considered the core "housekeeping genes" in pine. Using the WGCNA software, the number of gene expression profiles was reduced to 38, most of them are 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://congenie.org/). 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 new and valuable resource for functional genomics research in conifers.

Cañas, R., Li, Z., Pascual, M.B., Castro-Rodríguez, V., Avila, C., Sterck, L., Van de Peer, Y., Canovas, F. (2017) The gene expression landscape of pine seedling tissues. The Plant Journal (In Press).

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