Tree Genetics & Genomes

, 12:30 | Cite as

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

  • Unai López de Heredia
  • José Luis Vázquez-Poletti
Part of the following topical collections:
  1. Gene Expression


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.


Cloud computing De novo assembly Differential expression Functional annotation RNA-seq Transcriptome 



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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11295_2016_995_MOESM1_ESM.xlsx (203 kb)
ESM 1 (XLSX 202 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Unai López de Heredia
    • 1
  • José Luis Vázquez-Poletti
    • 2
  1. 1.Forest Genetics and Ecophysiology Research Group, E.T.S. Forestry EngineeringTechnical University of Madrid (UPM)MadridSpain
  2. 2.Distributed Systems Architecture Research Group, Department of Computer Architecture and AutomationComplutense UniversityMadridSpain

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