Computational protocol: Transcriptional profiling analysis of Penicillium digitatum, the causal agent of citrus green mold, unravels an inhibited ergosterol biosynthesis pathway in response to citral

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Protocol publication

[…] Transcriptome de novo assembly of the short reads was carried out using Trinty software []. After filtration of the low quality reads, clean reads were randomly clipped into 25-bp k-mers and assembled using de Bruijin graph and Trinty software. Furthermore, the reads producing large fragment without N is named contig and the result sequences of trinity is called unigenes. Then unigenes were clustered using TGI Clustering tools to obtain the finally unigenes []. Finally, blastx alignment (e value < 0.00001) between unigenes and protein databases (non-redundant protein (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Clusters of Orthologous Groups of proteins (COG)) were performed, and the best aligning results were selected as a priority order of NR, Swiss-Prot, KEGG and COG to determine the sequence orientation. When a unigene was not aligned to the above databases, ESTScan software [] was used to predict its coding regions and to determine its sequence orientation. Gene ontology (GO) terms annotations of unigenes were performed with the Blast2GO program according to the NR annotation. The COG and KEGG pathway annotations were analyzed using Blastall software against the cluster of orthologous groups’ database and the kyoto encyclopedia of genes and genomes database. […]

Pipeline specifications

Software tools Trinity, BLASTX, ESTScan, Blast2GO
Databases COGs UniProt KEGG KEGG PATHWAY
Application Transcription analysis
Organisms Penicillium digitatum
Chemicals Ergosterol, Fatty Acids, Unsaturated, Lanosterol, Nitrogen, Steroids, Sulfur