Computational protocol: Galactinol synthase transcriptional profile in two genotypes of Coffea canephora with contrasting tolerance to drought

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Protocol publication

[…] Searches for GolS sequences in the HarvEST:Coffea v.0.16 platform (http://harvest.ucr.edu/) yielded only one assembled contig with full-length cDNA (Unigene 2798). This sequence was compared with those in the Brazilian Coffee Genome Project Consortium () and the NCBI database using BlastX (http://www.ncbi.nlm.nih.gov/BLAST) (). The reference accession for CcGolS1 in NCBI is GT646983.1 and Contig 7664 in the Brazilian Coffee Genome Project Consortium. The open reading frame (ORF) of the unigene was predicted using the ORF Finder program (NCBI). Multiple sequence alignments were done using CLC Main Workbench v.5.0 based on the deduced amino acid sequence of coffee CaGolS1 and CcGolS1. A phylogenetic tree was constructed using the neighbor-joining method () with Poisson-corrected distances and pairwise deletion in MEGA6 software (). The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1,000 replicates) were shown next to the branches (). The phylogenetic tree was drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the tree. The analysis involved 30 amino acid sequences from different organisms with 275 positions in the final dataset. The 3D structure of CcGolS1 was generated using the I-TASSER server (). […]

Pipeline specifications

Software tools BLASTX, Open Reading Frame Finder, CLC Main Workbench, MEGA, I-TASSER
Databases Full Length cDNA
Application Phylogenetics
Organisms Coffea canephora
Chemicals Raffinose