Acer japonicum RNA-Seq analysis during autumn leaf senescence

This project aims to analyze transcriptomic changes in sun and shade leaves of Acer japonicum during autumn leaf senescence. Three leaves from the north-facing outer canopy (sun leaves) and another three leaves from the north-facing inner canopy (shade leaves) of an adult A. japonicum tree (height: approximately 10 m, age: 50 years) grown in the arboretum of the Hokkaido Research Center, Forestry and Forest Products Research Institute (43.0°N, 141.4°E; 180 m a.s.l.) were harvested at approximately 10:00 a.m. on September 7, September 28, October 5, and October 13, 2021. RNA was extracted from these leaves, and poly A+ RNA was further purified and analyzed using DNBSEQ (MGI Tech Co. Ltd, Shenzhen, China). The fastP program (Chen et al. 2018 10.1093/bioinformatics/bty560), with default settings for paired-end reads, was used to clean the RNA-seq reads. Subsequently, the Salmon program (Patro et al. 2017 10.1038/nmeth.4197) was used to quantify the expression of the transcripts using the cleaned reads. The protein coding regions of the cDNAs obtained from the Iso-seq analysis were used as target sequences for quantification. Transcripts per million (TPM) calculated by Salmon was used to normalize the transcript read counts.