Computational protocol: Drought induces alterations in the stomatal development program in Populus

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Protocol publication

[…] Putative homologues of genes known to be involved in stomatal development were identified from Populus using P. trichocarpa sequence data available on phytozome v7.0 (http://phytozome.net). The protein sequences from Arabidopsis were used as a query for BLAST (BLASTp/PtPEPv2.0) searches against the databases. FAMA () and STOMAGEN (Kondo et al., 2010) orthologues in Populus have previously been reported. Poplar GeneChip (Affymetrix) probe sets were identified using the NetAffx resource (http://www.affymetrix.com/analysis/index.affx). Transcript abundance for homologues of genes implicated in stomatal development was assessed through interrogation of Populus balsamifera transcript abundance data available in the PopGenExpress compendium (Wilkins et al., 2009b) of the Bio-Array Resource (BAR, http://bar.utoronto.ca/). […]

Pipeline specifications

Software tools BLASTP, NetAffx
Databases Phytozome
Application Protein sequence analysis
Organisms Populus balsamifera