Small RNA sequencing in Toona sinensis

The samples of two cultivars toon sprouts (BYC2 vs GYC2) were used for four libraries construction and sequencing with each cultivar including two biological repetition. Total raw data 19,174,385, 23,020,318, 13,560,132, and 16,930,140 reads were generated in four libraries GYC2_1, GYC2_2, BYC2_1, and BYC2_2, respectively. After adapter removal and low-quality data (sequence < 17 nt) filtering, 18,596,858, 22,252,682, 13,056,247, and 15,791,016 clean reads were obtained with total small RNA reads proportion 65.82 % (12,239,853), 64.05 % (14,251,756), 68.66 % (8,964,927), and 51.41 % (8,118,129) in each library. The read length distribution was mainly centered around 20-24 nt and contained over 60 % of total reads.Among them, 487-953 thousand unique reads corresponding to 7.54-12.58 millionreads were perfectly mapped to T. sinensis transcriptome. The total counts of annotated clean reads as tRNA, rRNA, snRNA, and snoRNA were 4,207,049, 4,385,655, 2,078,935, and 1,734,949 in GYC2_1, GYC2_2, BYC2_1, and BYC2_2, respectively. The remaining clean reads were aligned and edited in Sequence Alignment Map (SAM) format and input into miRDeep2 pipeline for miRNA discovery. In comparison, 818-1,277 unique reads corresponding 40,682-76,624 reads were matched to miRBase database. 250-295 reads were found to match to known mature miRNAs collected from all plant species available in miRBase database or be novel miRNAs in T. sinensis transcriptome by miRDeep2 software