Table 1. Summary of transcriptome and small RNA sequencing data.

Sample	Sample replicate	Transcriptome sequencing		Small RNA sequencing
		No. of clean reads	Percentage of mapped reads	raw reads	No. of clean reads	17 nt < Reads <33 nt	Repeat reads	rRNA reads	tRNA reads	snRNA reads	miRNA reads
ES1	L01	174,683,830	76.32	25,927,605	24,095,270	24,094,597	133,724	208,381	17,766	446	106,044
	L02	166,992,924	79.98	23,865,315	22,321,800	22,320,871	141,021	395,043	14,084	684	148,547
	L03	149,408,286	79.82	32,115,499	29,998,859	29,997,913	187,042	344,301	19,841	648	211,084
FS2	L04	138,978,770	80.06	21,378,200	20,333,242	20,330,797	92,533	905,305	97,290	2,787	286,047
	L05	141,222,622	84.71	23,317,399	22,270,590	22,266,892	102,186	486,652	50,227	1,061	499,324
	L06	139,989,810	81.51	15,117,444	14,387,309	14,385,108	58,805	292,689	49,024	1,352	285,295
ES2	L07	153,472,418	80.64	26,286,171	24,518,825	24,518,144	159,900	1,034,571	50,200	1,601	171,786
	L08	142,547,416	76.26	29,131,977	27,250,685	27,248,979	148,601	296,936	36,413	631	365,179
	L09	128,383,618	78.67	18,473,381	17,240,894	17,240,236	102,292	209,377	32,750	541	201,224
FS1	L11	154,290,016	80.96	24,627,110	23,088,334	23,087,243	113,446	296,534	17,196	470	227,489
	L12	185,704,656	79.65	24,673,614	23,078,309	23,077,146	113,972	316,806	12,650	565	211,848
Total		1,675,674,366		264,913,715	248,584,117	248,567,926	1,353,522	4,786,595	397,441	10,786	2,713,867

Notes: E denoted EC16; F denoted Fushu No. 7–6; S1 denoted 65 days after planting; S2 denoted 85 days after planting. L01-L12 denoted different sample.