Transcriptome Analysis of Oryza longistaminata

Libraries were prepared with the TruSeq Standard mRNA Library Prep Kit (Illumina, San Diego, CA, USA) using 1 µg of total RNA. Sequence analysis of 40-M reads was performed with a NovaSeq 6000 Sequencing System (Illumina). Library preparation and sequencing were conducted by Macrogen Japan, Inc. (Tokyo, Japan). The sequencing reads were mapped to the O. longistaminata genome obtained from the O. longistaminata Information Resource (http://olinfres.nig.ac.jp/; Reuscher et al., 2018 (link)) using HISAT2 (Kim et al., 2019 (link)), followed by featureCounts (Liao et al., 2014 (link)) for counting reads and edgeR (Robinson et al., 2009 (link)) for differential expression analysis. Low expression genes were removed using filterByExpr function of edgeR with the default setting. We obtained the presumed function and MAPMAN BIN code for each gene and the presumed corresponding gene ID of O. sativa from Supplemental data 2 of Reuscher et al. (2018) (link). GO analysis was performed using the corresponding O. sativa gene ID list with the analysis tool agriGO (http://systemsbiology.cau.edu.cn/agriGOv2/) (Du et al., 2010 ; Tian et al., 2017 (link)).