Taxus cuspidata RNA-Seq analysis

This project is to analyze the over-wintering transcriptomic changes of Taxus cuspidata. RNA was extracted from the leaves (needles) of north-facing branches of three male T. cuspidata trees (height: around 8 m) which grow in front of the Institute of Low Temperature Science, Hokkaido University (43.1°N, 141.3°E). These leaves were at around 10 am on January 18, 2022 and July 20, 2022. 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.