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Transcriptome profiles have been widely captured using short-read sequencing technology, but there are still limitations partially due to the read length. Here, we generated long reads using Oxford Nanopore PromethION™ technology and short reads using the Illumina sequencing platform to study the transcriptome of root, stem, and leaf of Camellia sinensis cv. Fudingdabai. We mapped the Nanopore reads to the Shuchazao of C. sinensis genome sequence, and the mapping rates ranged from 82.63% to 90.59% (average 86.44%); this is lower than t