Taxus cuspidata RNA-Seq analysis

This project is to analyze the over-wintering transcriptomic changes of Taxus cuspidata. Leaves (needles) of three north-facing branches and those of three south-facing branches of a male T. cuspidata tree (height: around 8 m) growing in front of the Institute of Low Temperature Science, Hokkaido University (43.1°N, 141.3°E) were harvested at around 10 am on September 24, 2019; October 24, 2019; November 5, 2019; December 3, 2019; December 25, 2019; February 25, 2020; March 25, 2020; April 23, 2020. RNA was extracted from these leaves and poly A+ RNA was further purified, and was analyzed with DNBSEQ. The fastP program (Chen et al. 2018) with default settings for paired-end reads was used to clean the RNA-seq reads. Subsequently, the Salmon program (Patro et al. 2017) was used to quantify the expression of the transcripts using the cleaned reads. The protein-coding region of the cDNAs obtained from the Iso-seq analysis were used as target sequences for the quantification. Transcripts per million (TPM) calculated by Salmon were used to normalize transcript read counts.