Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.)

Yu, Rugang; Wang, Yan; Xu, Liang; Zhu, Xianwen; Zhang, Wei; Wang, Ronghua; Gong, Yiqin; Limera, Cecilia; Liu, Liwang

doi:10.1186/s12870-015-0427-3

Table 2 Summary information of known miRNA families and their transcript abundance identified in all libraries

From: Transcriptome profiling of root microRNAs reveals novel insights into taproot thickening in radish (Raphanus sativus L.)

miRNA family	No. of members	miRNA reads			Normalized read count			Fold change
miRNA family	No. of members	Stage1	Stage2	Stage3	Stage1	Stage2	Stage3	Log ₂ (stage2/stage1)	Log ₂ (stage3/stage1)	Log ₂ (stage3/stage2)
Conserved miRNA
miR156	19	1255950	197473	60169	30069.08	2684.56	950.56	−3.49	−4.98	−1.50
miR158	2	557972	982854	368856	20520.33	27460.11	11365.77	0.42	−0.85	−1.27
miR159	11	57202	53482	8715	16.29	0.01	6.67	−10.67	−1.29	9.38
miR160	5	1871124	1233815	437740	16.83	12.20	5.09	−0.46	−1.72	−1.26
miR161	1	113	15	0	6.72	0.80	0.01	−3.08	−9.39	−6.31
miR162	4	2343	1994	1126	0.01	0.27	0.06	4.73	2.55	−2.18
miR164	6	31856	9637	7293	1631.16	422.95	349.19	−1.95	−2.22	−0.28
miR166	14	560689	400549	158105	1040.43	643.12	276.19	−0.69	−1.91	−1.22
miR167	7	11164	13684	9386	96.43	151.64	120.71	0.65	0.32	−0.33
miR168	4	182143	183619	99034	10707.73	9669.95	5744.26	−0.15	−0.90	−0.75
miR169	10	30809	21665	18662	1.66	0.95	0.70	−0.80	−1.24	−0.44
miR171	5	158	470	51	0.01	12.46	2.87	10.28	8.16	−2.12
miR172	6	1234	6039	4154	19.03	26.31	53.21	0.47	1.48	1.02
miR390	5	22804	7150	2234	1301.37	358.88	118.37	−1.86	−3.46	−1.60
miR391	2	4090	5165	275	242.45	272.10	16.10	0.17	−3.91	−4.08
miR393	2	35	36	59	0.06	0.16	0.01	1.42	−2.57	−3.99
miR394	2	702	426	654	0.01	2.12	1.52	7.73	7.25	−0.48
miR395	3	39	50	18	1.90	0.01	0.01	−7.57	−7.57	0.00
miR396	10	2795	1792	1427	109.75	32.46	22.95	−1.76	−2.26	−0.50
miR397	1	2316	172	30	137.69	9.12	1.76	−3.92	−6.29	−2.38
miR398	3	804	1638	28150	47.50	86.46	0.01	0.86	−12.21	−13.08
miR399	4	65	87	26	0.01	0.05	0.18	2.41	4.13	1.73
miR403	1	2175	1604	1053	129.31	85.08	61.64	−0.60	−1.07	−0.46
miR408	3	11998	3335	400	712.19	176.31	23.42	−2.01	−4.93	−2.91
miR482	3	68	2640	2324	0.01	140.03	0.01	13.77	0.00	−13.77
miR535	2	1402	2121	709	0.65	0.80	0.41	0.28	−0.67	−0.96
miR824	2	4469	330	344	219.80	13.05	16.16	−4.07	−3.77	0.31
miR827	1	353	122	27	20.99	6.47	1.58	−1.70	−3.73	−2.03
miR828	2	56	18	33	3.33	0.95	1.05	−1.80	−1.66	0.14
miR2111	2	10	229	47	0.59	4.93	0.94	3.05	0.66	−2.40
miR2118	2	92829	15700	12723	2834.86	0.01	0.01	−18.11	−18.11	0.00
Total	144	4709767	3147905	1223824	280011.51	166968.59	71641.49	−0.75	−1.97	−1.22
Non-conserved miRNA
miR400	1	147	72	41	8.74	4.28	2.40	−1.03	−1.86	−0.83
miR774	1	307	10640	5198	18.25	632.58	304.29	5.12	4.06	−1.06
miR812	1	0	3145	1503	0.00	186.98	87.98	18.26	17.18	−1.09
miR825	1	1675	0	0	99.58	0.00	0.00	−17.35	−17.38	−0.02
miR831	1	267	295	760	15.87	17.54	44.49	0.14	1.49	1.34
miR845	2	11735	7945	1722	697.69	472.36	100.80	−0.56	−2.79	−2.23
miR858	2	22	28	153	1.31	1.66	3.40	0.35	1.38	1.03
miR859	1	444	956	347	26.40	56.84	20.31	1.11	−0.38	−1.48
miR862	1	76	224	58	4.52	13.32	3.40	1.56	−0.41	−1.97
miR1310	1	1376	273	296	81.81	16.23	17.33	−2.33	−2.24	0.09
miR1510	2	1419	0	1905	84.36	0.00	111.52	−17.11	0.40	17.52
miR1511	2	14510	22556	8500	862.67	1341.03	497.58	0.64	−0.79	−1.43
miR1513	1	484	1001	0	28.78	59.51	0.00	1.05	−15.59	−16.63
miR1520	1	36042	7457	6131	2142.82	443.34	358.90	−2.27	−2.58	−0.30
miR1885	1	3846	1383	1444	228.66	82.22	84.53	−1.48	−1.44	0.04
miR3630	2	266	52	0	15.81	3.09	0.00	−2.35	−14.72	−12.37
miR4378	1	0	9787	1082	0.00	581.87	63.34	19.90	16.70	−3.20
miR5654	1	8098	2411	738	481.45	143.34	43.20	−1.75	−3.48	−1.73
miR5763	1	0	370	669	0.00	22.00	39.16	15.18	16.01	0.83
miR5774	1	0	0	1234	0.00	0.00	72.24	0.00	16.89	16.89
miR6164	1	892	971	615	53.03	57.73	36.00	0.12	−0.56	−0.68
miR7504	1	45	113	5348	2.68	6.72	313.07	1.33	6.87	5.54
miR7510	1	218	383	171	12.96	22.77	10.01	0.81	−0.37	−1.19
miR7532	1	8125	2752	2304	483.06	163.62	134.87	−1.56	−1.84	−0.28
miR8005	1	0	1118	0	0.01	59.2998	0.01	12.53	0.00	−12.53
miR8041	1	18	62	27	1.07	3.69	1.58	1.78	0.56	−1.22
Total	31	90012	73994	40246	5351.52	3865.41	3469.08	−0.47	−0.63	−0.16
Total	175	4799779	3221899	1264070	285363.03	170834.01	75110.57	−0.74	−1.93	−1.19

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ISSN: 1471-2229

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