Comprehensive Transcriptome Analysis Workflow

To convert the transcript sequences to the orthologues, BLASTX with E-value ≤ 10⁻⁵ was applied against the Arabidopsis Information Resource (TAIR). The functional enrichment analysis of modules was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) [40 (link)] for categories of Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was also carried out in the web-based DAVID [40 (link)]. P-value < 0.01 was considered to be significant; moreover, the identification and classification of TFs, TRs, and PKs were carried out through applying the transcript sequences to BLASTX search against the iTAK database [41 (link)]. To identify transporters, BLASTX was carried out on transcript sequences against the transporter classification database (TCDB) with E-value ≤ 10⁻²⁰ [42 (link)]. Wu et al. (2012) identified 2660 mlncRNAs candidates, which were considered as an emerging class of regulators, using a computational mlncRNA identification pipeline in D. purpurea [43 (link)]. After the creation of the mlncRNAs-derived local database through CLC Genomics Workbench 11.0, the searching procedure was carried out for all of the transcripts in the significant major modules using BLASTN with a cut-off E-value ≤ 10⁻⁵ to uncover important mlncRNAs.