DOI: 10.5061/dryad.xsj3tx9j1
title: Evolutionary targets of gene expression divergence in a complex of closely related pine species

description: The environment is a powerful selective pressure for sessile organisms,
 such as plants, and adaptation to the environment is particularly
 important for long-lived species, like trees. Despite the importance of
 adaptive trait variation to the survival and success of trees, the
 molecular basis of adaptation is still poorly understood. Gene expression
 patterns in three closely related, but phenotypically and ecologically
 divergent, pine species were analyzed to detect differentiation that may
 be associated with their adaptation to distinct
 environments. Total RNA of Pinus mugo, P.
 uncinata and P. sylvestris samples grown under
 common garden conditions was used for de
 novo transcriptome assembly, providing a new reference dataset
 that includes species from the taxonomically challenging Pinus
 mugo complex. Gene expression profiles were found to be very
 similar with only 121 genes significantly diverged in any of the pairwise
 species comparisons. Functional annotation of these genes revealed major
 categories of distinctly expressed transcripts including: wood
 trait properties, oxidative stress response, and response to abiotic
 factors such as salinity, drought and temperature. We discuss
 putative associations between gene expression profiles and adaptation to
 different environments, for example: upregulation of genes involved in
 lignin biosynthesis in the species which have adapted to mountainous
 regions characterized by strong winds and thick snow cover. Our study
 provides valid candidates for verification of the importance of the gene
 expression role, in addition to evidence for selection within genomic
 regions, in the process of ecological divergence and adaptation to higher
 altitudes in pine taxa.
description: Genetic material was obtained from
 needles of 11 two year-old seedlings of three pine species (<em>P.
 mugo</em> – 4 samples, M; <em>P. uncinata</em> – 3
 samples, UN; <em>P. sylvestris </em>L. – 4 samples, PS) grown
 in a glasshouse facility of the UK Centre of Ecology and Hydrology in
 Edinburgh. The seedlings were derived from open-pollinated seeds collected
 in natural populations in Europe (for details, see Wachowiak et al.,
 2018). Raw paired-end Illumina reads from teams’ previous RNA-sequencing
 attempts were used, data is deposited in the European Nucleotide Archive
 under accession number PRJEB6877 (for precise sample identifiers, please
 see Table 1 in the article). Details regarding RNA isolation, library
 preparation and sequencing are specified in Wachowiak et al.
 (2015). The raw reads of
 all 11 samples were quality checked in FASTQC v0.11.9
 (www.github.com/s-andrews/FastQC) and used for <em>de
 novo</em> transcriptome construction by TRINITY v2.11.0 (Haas et
 al., 2013). The paired-end assembly procedure adapted default parameter
 values, except it was run with simultaneous cleaning and trimming of reads
 provided by TRIMMOMATIC v0.39 (Bolger et al., 2014) and contigs below 200
 bp were rejected. TRIMMOMATIC parameters used:
 "ILLUMINACLIP:anaconda3/envs/Trinity/share/adapters/TruSeq2-PE.fa:2:30:10:2:keepBothReads SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:30"
description: The only change in the file made was deletion of the
 'TRINITY_' part from the generated sequence names. No more
 alternations have been introduced.