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Transcript assembly and differential gene expression analysis

TM Tony Kipkoech Maritim
MM Mamta Masand
RS Romit Seth
RS Ram Kumar Sharma
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Raw reads were trimmed to remove adapter sequences, ambiguous nucleotides (N) and low-quality reads (Phred quality score ≤ Q30) using NGS QC Toolkit58. High quality clean reads were analyzed according to Tuxedo protocol59. In brief, high quality clean reads were assembled using the reference tea genome (Camellia sinensis var. sinensis25 using TOPHAT ver2.1.0. Functional annotation of assembled transcripts was performed by BLAST alignment of the sequences against public databases such as Swiss-Prot, KEGG and TAIR10. GO and KEGG annotations were performed using AgriGO toolkit and KEGG pathway database, respectively60,61. The Transcription factor (TF) families were identified using Plant transcription factor database (PTFDB)62.

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