Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max

Zabala, Gracia; Campos, Edhilvia; Varala, Kranthi K; Bloomfield, Sean; Jones, Sarah I; Win, Hlaing; Tuteja, Jigyasa H; Calla, Bernarda; Clough, Steven J; Hudson, Matthew; Vodkin, Lila O

doi:10.1186/1471-2229-12-177

BMC Plant Biology

Table 2 Differential expression of soybean miRNAs

From: Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max

				Normalized counts in each library per million reads^a
	Sequence	L	miRBase	Immature seed tissue					Vegetative tissue			miRNA gene origins^b	Target glyma cDNAs	Annotation
				WS	SCR	SCM	SCW	Cot	GCot	ST	LE
1	TGAAGCTGCCAGCATGATCTT (see Figure 2A blot)	21	gma-miR167e/f	48472	54106	9009	72015	1540	8512	5	224	Gm20:37,901,914	20g02540.1	None
												Gm10:46,574,320	10g35160.1	Unknown function
2	TGAAGCTGCCAGCATGATCTG	21	gma-miR167c	65	412	37	281	782	9252	0	673	Glyma10g30370.1	20g02540.1	None
												Glyma20g36720.1*
3	TGAAGCTGCCAGCATGATCTA	21	gma-miR167a/b	225	52	14	76	597	400	15	18	Glyma19g34240.1*	18g05330.1	Auxin response factor
												Gm10:2,640,290	02g40650.1	“
												Glyma02g16230.1*	11g31940.1	“
												Glyma03g31410.1*	14g38940.1	“
4	TAACTGAACATTCTTAGAGCAT (see Figure 2B blot)	22	gma-miR1512c	94395	36802	44554	64171	72	227	5	0	Gm02:8609718	08g17790.1	Cysteine-rich receptor-like kinase
													10g21350.1	Villin
5	CAGCCAAGGATGACTTGCCGG (see Figure 3A blot)	21	gma-miR169a	14	8	12	18	0	2042	7	32	Gm10:40,332,893	14g01360.1	Nuclear transcription factor
												Glyma09g28810.1*
6	TGACAGAAGAGAGTGAGCAC_	20	gma-miR156a	3331	2150	8462	2190	20788	22007	38342	31850	Gm17:4,291,733	05g38180.5	Squamosa PB-like TF
												Glyma17g08280.1*	08g01450.1	“
												Glyma17g33830.1*	06g17700.1	“
												Gm14:9,431,608	04g37390.1	“
												Gm13:20,521,472	05g00200.1	“
												Gm06:4,013,580	17g08840.1	“
												Gm04:4,257,067	03g27200.1	“
												Gm02:41,864,174	19g32800.1	“
7	TTGACAGAAGATAGAGAGCAC	21	gma-miR156c/d/e/g	290	4381	2889	2053	25	14252	13237	5014	Gm19:8,895,400	19g26390.1	Squamosa PB-like TF
												Gm09:37,843,837	13g24590.1	“
												Gm08g05430.1*	07g31880.1	“
												Gm07:9,347,149	18g36960.1	“
												Gm02:7,812,536	02g30670.1	“
												Gm08:3,891,372	19g32800.1	“
												Gm16:5331711	03g29900.1	“
8	TTGACAGAAGAGAGAGAGCAC	21	gma-miR156b/f	214	1631	3171	2018	98674	42110	9	51	Gm14:990,353	11g36980.1	Squamosa PB-like TF
	(see Figure 3A blot)											Gm02:50,779,324	18g36960.1	“
												Gm06:19,264,024	02g30670.1	“
													19g32800.1	“
													03g29900.1	“
9	TCGCTTGGTGCAGGTCGGGAA	21	gma-miR168b	1749	3565	1891	3244	1148	2935	1189	731	Glyma09g35160.1
	(see Figure 3A blot)											Gm01:48,070,389
10	TCGGACCAGGCTTCATTCCCC (see Figure 3A blot)	21	gma-miR166a-3p	4471	11557	16665	29735	12361	5812	24375	5460	Glyma16g02380.1*	08g21620.1	HD-zip transcription factor
												Glyma02g15860.1*	07g01940.1	“
												Glyma04g38430.1*	08g21610.1	“
												Glyma08g00630.1*
11	GGAATGTTGTCTGGCTCGAGG	21	gma-miR166a-5p	10	154	500	252	230	45	23	182	Glyma16g02380.1*
												Glyma08g00630.1*
												Glyma04g38430.1*
12	TGAGACCAAATGAGCAGCTGA (see Figure 3B blot)	21	gma-miR3522	3987	1849	4478	2524	112139	43366	1478	646995	Glyma15g06080.1*	07g31270.1	Tyrosinase
13	AGGGATAGGTAAAACAACTAC (see Figure 3B blot)	21	gma-miR1510b-5p	891	3293	16652	1798	9906	2809	2825	2028	Glyma02g08410.1*
14	AGGGATAGGTAAAACAATGAC	21	gma-miR1510a-5p	428	0	5633	699	2628	221	0	0	Glyma16g27510.1*
15	TGTTGTTTTACCTATTCCACC	21	gma-miR1510a/b-3p	31	20	65	18	132	34	9	0	Glyma16g27510.1*	04g39740.1	Disease-resistance protein
												Glyma02g08410.1*	18g14660.1	“
													19g07700.2	"
16	TCTCATTCCATACATCGTCTGA (see Figure 3B blot)	22	gma-miR1507a	29315	17502	5373	15728	17964	19959	34871	10750	Glyma17g08340.1* Glyma13g22280.1*
17	AGCTCTGTTGGCTACACTTTG	21	gma-miR394a	19	693	2382	782	15	0	2412	11	Glyma17g38110.1
18	TTCCACAGCTTTCTTGAACTG	21	gma-miR396a/e/h/i -3p	53	144	27	120	0	73	388	52	Glyma13g22840.1*	19g39020.1	Unknown function
												Gm17:35,366,632	03g00550.1	Retrovirus related Pol
												Gm14:13,971,439	13g22840.1	polyprotein
												Gm17:9,044,867		none
19	AGAATCTTGATGATGCTGCAT	21	gma-miR172a/b	2	32	10	25	8	30	349	616	Gm20:40,895,751	12g07800.1	AP2-like transcription factor
												Glyma13g39860.1*	11g15650.1	“
												Gm12:6,110,723	15g04930.1	“
												Gm10:31,592,580	13g40470.1	“
												Gm10:43,474,799	02g09600.1	“
20	CAGGGGAACAGGCAGAGCATG	21	gma-miR408c/a-5p	5	0	11	0	22	3	12	4669	Glyma10g27760.1*	11g01200.1	DNA-directed RNA
												Gm02:837,430		polymerase
21	TTGGCATTCTGTCCACCTCC	20	gma-miR394c-5p	286	102	71	147	13	2	412	0	Glyma17g38110.1*	18g00870.1	F-box protein
												Gm15:3,767,188	05g28050.1	“
												Glyma14g39920.1*	08g11030.1	“
												Gm08:9,880,084	11g36960.1	“
												Glyma06g02270.1*
												Glyma05g30360.1*
22	TAGAAAGGGAAATAGCAGTTG	21	gma-miR1508a/b	464	187	52	120	913	7892	704	1063	Gm16:32,903,801	09g30500.1	Pentatricopeptide
												Gm09:28,530,237	16g27800.1	repeat-containing protein
													09g39260.1	“
													09g39250.1	“
23	TAAGAGAATTGTAAGTCACTG	21	gma-miR4413	32	29	33	46	72	109	73	91	Glyma19g02070.1	09g07250.1	Pentatricopeptide
													07g11410.1	repeat-containing protein
													07g11290.1	“
													16g31950.1	“
													09g07300.1	“
													09g30620.1	“

^aNormalized read counts higher than 5000 are in bold. Library abbreviations are in Table 1. ^bThe position of the miRNA hairpin in the Glycine max reference genome or the associated gene Model number is shown. *Low confidence gene model. L= sequence length. Underline indicates base difference between family members.

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ISSN: 1471-2229

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