Computational protocol: Influence of water deficit on the molecular responses of Pinus contorta × Pinus banksiana mature trees to infection by the mountain pine beetle fungal associate, Grosmannia clavigera

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Protocol publication

[…] Expressed sequence tags are publicly accessible at National Center for Biotechnology Information (NCBI) under accession numbers GW738148-GW774480 (P. banksiana) and GT229582-GT270713 (P. contorta). The corresponding transcriptome resources are described in . Contigs corresponding to putative AQP, DREB, CHI and TPS genes were identified by BLASTX using previously characterized sequences from other species as queries. Sequences used for subsequent analyses are provided in File S1 available as Supplementary Data at Tree Physiology Online. Open reading frames were predicted using Geneious 4.8.2 (). Multiple sequence alignments of deduced amino acid sequences and neighbor-joining phylogenetic analyses were performed in MEGA v4.0 (). Dendrograms were constructed using pairwise deletion and 1000 bootstrap replicates. The phylogenetic analyses were used to select genes for qRT-PCR based on position relative to functionally characterized genes from other species. […]

Pipeline specifications

Software tools BLASTX, Geneious, MEGA-V
Applications Phylogenetics, GWAS
Organisms Pinus contorta, Grosmannia clavigera
Diseases Infection, Mycoses
Chemicals Carbon, Nitrogen