Computational protocol: Sugarcane genes associated with sucrose content

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Protocol publication

[…] Comparative analysis of sugarcane sugar-responsive genes was done by constructing phylogenetic trees containing the corresponding most similar plant sequences. A tblastx search [] with the sugar-regulated SAS against a green plants protein data set including 365,187 proteins sequences obtained from several genomes (Arabidopsis thaliana, version 7.0 – ; Populus trichocarpa, version 1.1 – ; Glycine max, version 0.1 – ; Oryza sativa, version 5.0 – ; Sorghum bicolor, version 1.4 – ; Selaginella moellendorffii, version 1.0 – ; Physcomitrella patens patens, version 1.1 – ; Volvox carteri, version 1.0 – ; Chlamydomonas reinhardtii, version 3.0 – ; Ostreococcus lucimarinus, version 2.0 – ; Ostreococcus tauri, version 2.0 – ; Micromonas pusilla CCMP1545, version 2.0 – ; Micromonas strain RCC299, version 2.0 – ) was performed. For each SAS, the first 40 best matches, or all matches obtained if this number were lower than 40, were selected for further analysis. The conserved domains found among the 40 selected sequences were aligned using ClustalW [] to produce ungapped alignments. The phylogenetic relationship of these aligned sequences was then constructed using the Neighbor-Joining method [] using p-distance. All analysis were conducted in MEGA4 software []. This process allowed identifying the most probable orthologues sequences of the SAS. The Arabidopsis orthologues and the Arabidopsis more closely related homologues (usually one sister clade which may include at least two Arabidopsis sequences) were compared with the set of Arabidopsis genes regulated by glucose [] and/or sucrose [] using VennMaster 0.37.3 . […]

Pipeline specifications

Software tools TBLASTX, Clustal W, MEGA, VennMaster
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Sucrose