title: Illumina RNA sequencing of root sample from wild rice Oryza rufipogon
design: Dongxiang wild rice used in this study was growing under natural conditions in a paddy field at the experimental station of Jiangxi Academy of Agricultural Sciences, Nanchang, China. In order to reduce the heterogeneous rate and avoid the interference from extraneous pollen, the wild rice had been subjected to selfpollination by bagging cultivation for more than ten years. The seedlings had been planted in the growth chamber before DNA and RNA extraction. The DNA was extracted from the seedling leaves and the total RNA was from seedling leaves and seedling roots at the four-leaf stage, separately. One DNA-seq and two non-strand-specific RNA-seq libraries were constructed using Illumina TruSeq DNA/RNA Sample Prep Kits and sequenced on the Illumina HiSeq 2000 system, separately. The DNA-seq library used 500 bp insert size and 90 bp pairedend sequencing, while the RNA-seq library used 200 bp insert size and 100 bp pairedend sequencing. The cleaning and quality control of the DNA-seq and RNA-seq data were conducted using the pipeline Fastq_clean. Low quality (<Q20) and adapter contained reads were removed from the DNA-seq data. Low quality (<Q20) nucleotides and adapter on both ends of the raw reads were trimmed from the RNA-seq data.