Computational protocol: Metabolic Flux Redirection and Transcriptomic Reprogramming in the Albino Tea Cultivar ‘Yu-Jin-Xiang’ with an Emphasis on Catechin Production

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Protocol publication

[…] The unigene sequences of the mixed tea leaf sample aligned using BLASTX against the COG, GO, KEGG, Swissprot, TrEMBL and NR databases (E-value < = 1E-5) to retrieve functional annotations based on sequence similarity. Unigenes that could not be aligned to any of these databases were analyzed by the ESTScan software. Gene ontology (GO) analysis was conducted using the TopGO package. The GO terms with p-values <0.05 were considered significantly enriched. The biological processes of enriched GO terms were then visualized using TopGO. [...] All usable reads were normalized into RPKM values (reads per kb per million reads). Differential expression of unigenes between two RNAseq samples were calculated based on “base mean” value obtained from the DESeq package. Only unigenes with an PL/SL RPKM ratio >2 and a false discovery rate (FDR) multiple test score of P < 0.05, were considered to be differentially expressed unigenes. […]

Pipeline specifications

Software tools BLASTX, ESTScan, TopGO, DESeq
Databases KEGG
Applications RNA-seq analysis, Transcription analysis
Organisms Camellia sinensis
Chemicals Catechin, Chlorophyll, Quercetin