Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

Zhai, Rongrong; Ye, Shenghai; Zhu, Guofu; Lu, Yanting; Ye, Jing; Yu, Faming; Chu, Qiren; Zhang, Xiaoming

doi:10.1186/s12864-020-6637-6

Table 3 Summary of small RNA (sRNA) sequencing data

From: Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing

	lib	Raw reads	3ADT&length filter	Junk reads	Rfam	mRNA	Repeats	valid reads	rRNA	tRNA	snoRNA	snRNA	other Rfam RNA
CK1	Total	13,774,024	3,390,537	38,220	1,054,000	847,233	4749	8,495,423	863,173	139,387	5115	1723	44,602
	% of Total	100.00	24.62	0.28	7.65	6.15	0.03	61.68	6.27	1.01	0.04	0.01	0.32
	uniq	2,453,175	841,448	20,791	18,859	14,165	185	1,558,672	15,033	2264	332	159	1071
	% of uniq	100.00	34.30	0.85	0.77	0.58	0.01	63.54	0.11	0.02	0.00	0.00	0.01
CK2	Total	13,852,706	2,934,133	33,314	1,258,384	973,925	6008	8,708,898	1,083,866	115,231	4395	1803	53,089
	% of Total	100.00	21.18	0.24	9.08	7.03	0.04	62.87	7.82	0.83	0.03	0.01	0.38
	uniq	2,405,519	874,287	17,335	19,294	14,955	214	1,480,435	15,747	1975	291	149	1132
	% of uniq	100.00	36.35	0.72	0.80	0.62	0.01	61.54	0.11	0.01	0.00	0.00	0.01
CK3	Total	11,305,213	751,727	31,484	861,890	947,345	4370	8,761,939	698,077	121,230	4076	1822	36,685
	% of Total	100.00	6.65	0.28	7.62	8.38	0.04	77.50	6.17	1.07	0.04	0.02	0.32
	uniq	2,072,418	519,795	17,449	18,638	13,555	182	1,503,706	14,936	2174	299	140	1089
	% of uniq	100.00	25.08	0.84	0.90	0.65	0.01	72.56	0.13	0.02	0.00	0.00	0.01
GLY1	Total	10,234,674	3,616,701	19,106	1,149,522	967,205	17,295	4,557,991	961,780	124,212	6855	2549	54,126
	% of Total	100.00	35.34	0.19	11.23	9.45	0.17	44.53	9.40	1.21	0.07	0.02	0.53
	uniq	1,828,494	917,707	7845	18,067	13,035	282	872,751	14,296	2195	320	142	1114
	% of uniq	100.00	50.19	0.43	0.99	0.71	0.02	47.73	0.14	0.02	0.00	0.00	0.01
GLY2	Total	14,038,269	7,373,691	39,460	857,843	617,980	1416	5,187,783	722,433	94,555	3929	2256	34,670
	% of Total	100.00	52.53	0.28	6.11	4.40	0.01	36.95	5.15	0.67	0.03	0.02	0.25
	uniq	2,749,254	1,226,291	25,154	14,288	11,708	77	1,472,281	11,735	1340	291	145	777
	% of uniq	100.00	44.60	0.91	0.52	0.43	0.00	53.55	0.08	0.01	0.00	0.00	0.01
GLY3	Total	9,915,965	5,677,422	8527	550,744	474,821	12,345	3,247,324	426,107	89,633	4243	1279	29,482
	% of Total	100.00	57.26	0.09	5.55	4.79	0.12	32.75	4.30	0.90	0.04	0.01	0.30
	uniq	1,472,793	870,393	4467	13,287	8952	246	576,405	10,643	1523	211	76	834
	% of uniq	100.00	59.10	0.30	0.90	0.61	0.02	39.14	0.11	0.02	0.00	0.00	0.01

3ADT&length filter: reads removed due to 3ADT not found and length with < 18 nt and > 25 nt were removed (for plants); length with< 18 and > 26 were remove (for animals); Junk reads: Junk: > = 2 N, > = 7A, > = 8C, > = 6G, > = 7 T, > = 10Dimer, > = 6Trimer, or > =5Tetramer; Rfam: Collection of many common non-coding RNA families except micro RNA; Repeats:Prototypic sequences representing repetitive DNA from different eukaryotic species

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ISSN: 1471-2164

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