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RNA-seq analysis in forest tree species: bioinformatic problems and solutions

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Abstract

Direct sequencing of RNA (RNA-seq) using next-generation sequencing platforms has allowed a growing number of gene expression studies focused on forest trees in the last 5 years. Bioinformatic analyses derived from RNA-seq of forest trees are particularly challenging, because the massive genome length (~20.1 Gbp for loblolly pine) and the absence of annotated reference genomes require specific bioinformatic pipelines to obtain sound biological results. In the present manuscript, we review common bioinformatic challenges that researchers need to consider when analyzing RNA-seq data from forest tree species at the light of the experience acquired from recent studies. Furthermore, we list bioinformatic pipelines and data processing software available to overcome RNA-seq limitations. Finally, we discuss the impact of novel computation solutions, such as the cloud computing paradigm that allows RNA-seq analysis even for small research centers with limited resources.

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Acknowledgments

This manuscript was written in the frame of the Master of Bioinformatics of ENS-ISCIII (Spain) and of the SPIP2014-01093: PersPiCan (Persistence of the Canary Island Pine after a disturbance of great magnitude) research project, funded by the OAPN (Spanish Ministry of Agriculture, Food and Environment). We wish to thank Dr. M. Venturas for a review of English and style.

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Authors and Affiliations

  1. Forest Genetics and Ecophysiology Research Group, E.T.S. Forestry Engineering, Technical University of Madrid (UPM), Ciudad Universitaria s/n 28040, Madrid, Spain

    Unai López de Heredia

  2. Distributed Systems Architecture Research Group, Department of Computer Architecture and Automation, Complutense University, C/Profesor José García Santesmases, s/n Ciudad Universitaria 28040, Madrid, Spain

    José Luis Vázquez-Poletti

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  1. Unai López de Heredia
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  2. José Luis Vázquez-Poletti
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Correspondence to Unai López de Heredia.

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Communicated by J. L. Wegrzyn

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López de Heredia, U., Vázquez-Poletti, J.L. RNA-seq analysis in forest tree species: bioinformatic problems and solutions. Tree Genetics & Genomes 12, 30 (2016). https://doi.org/10.1007/s11295-016-0995-x

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  • DOI: https://doi.org/10.1007/s11295-016-0995-x

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