Table 3.
Conserved soybean miRNAs in four small RNA libraries
|
miRNA |
Sequence (5’ to 3’) |
Size (nt) |
Ch |
Start:end (+/-) |
Arm |
TPM in HPL |
TPM in LPL |
TPM in HPR |
TPM in LPR |
Registered in |
|---|---|---|---|---|---|---|---|---|---|---|
| miRBase or not | ||||||||||
| miR156d |
TTGACAGAAGATAGAGAGCAC |
21 |
8 |
3891352:3891504:+ |
5 |
34857 |
30879 |
18368 |
15715 |
Yes |
| miR156h |
TGACAGAAGAGAGTGAGCAC |
20 |
4 |
4990842:4990964: − |
5 |
66744 |
55303 |
22303 |
26339 |
Yes |
| miR156o |
TTGACAGAAGAGAGTGAGCAC |
21 |
17 |
37759430:37759553:+ |
5 |
1749 |
1579 |
1271 |
998 |
Yes |
| miR156p |
ACAGAAGATAGAGAGCACAG |
20 |
7 |
9347129:9347272:+ |
5 |
46 |
47 |
94 |
131 |
No |
| miR156q |
TGACAGAAGATAGAGAGCAC |
20 |
19 |
8895390:8895494:+ |
5 |
483 |
526 |
403 |
452 |
No |
| miR156r |
TGACAGAAGAGAGTGAGCACT |
21 |
13 |
20521462:20521566:+ |
5 |
75 |
57 |
159 |
206 |
No |
| miR156s |
TGACAGAAGAGAGTGAGCACT |
21 |
17 |
4291649:4291772: − |
5 |
75 |
57 |
159 |
206 |
No |
| miR156t |
TGACAGAAGAGAGTGAGCACA |
21 |
2 |
41864154:41864278:+ |
5 |
173 |
156 |
99 |
108 |
No |
| miR156u |
TGACAGAAGAGAGTGAGCACA |
21 |
4 |
4257047:4257175:+ |
5 |
173 |
156 |
99 |
108 |
No |
| miR156v |
TGACAGAAGAGAGTGAGCACA |
21 |
6 |
4013560:4013688:+ |
5 |
173 |
156 |
99 |
108 |
No |
| miR156w |
TGACAGAAGAGAGTGAGCACA |
21 |
14 |
9431588:9431718:+ |
5 |
173 |
156 |
99 |
108 |
No |
| miR156x |
TGACAGAAGAGAGTGAGCACA |
21 |
17 |
38431855:38431985: − |
5 |
173 |
156 |
99 |
108 |
No |
| miR156y |
CTGACAGAAGATAGAGAGCAC |
21 |
18 |
61442592:61442691: − |
5 |
28 |
27 |
196 |
106 |
No |
| miR156z |
GCTCACTACTCTTTCTGTCGGTT |
23 |
19 |
40699080:40699213: − |
3 |
503 |
491 |
12 |
17 |
No |
| miR156_c1 |
TTGACAGAAGAAAGGGAGCAC |
21 |
1 |
55282671:55282770:+ |
5 |
291 |
274 |
0.01 |
0.01 |
No |
| miR156_c2 |
TTGACAGAAGAAAGGGAGCAC |
21 |
11 |
453213:453312: − |
5 |
291 |
274 |
0.01 |
0.01 |
No |
| miR156_c3 |
TTGACAGAAGAGAGAGAGCAC |
21 |
2 |
50779230:50779334: − |
5 |
182 |
139 |
45 |
32 |
No |
| miR159e-3p |
TTTGGATTGAAGGGAGCTCTA |
21 |
7 |
9524916:9525128: − |
5 |
191 |
250 |
293 |
109 |
Yes |
| miR160f |
GCGTATGAGGAGCCAAGCATA |
21 |
10 |
43851636:43851757: − |
3 |
56 |
46 |
117 |
128 |
No |
| miR160g |
GCGTATGAGGAGCCAAGCATA |
21 |
20 |
40554887:40554987:+ |
3 |
56 |
46 |
117 |
128 |
No |
| miR162c |
TCGATAAACCTCTGCATCCAG |
21 |
17 |
10181487:10181612:+ |
3 |
97 |
111 |
59 |
54 |
Yes |
| miR164e |
TGGAGAAGCAGGGCACGTGCA |
21 |
2 |
1511590:1511686:+ |
5 |
1621 |
2713 |
969 |
1532 |
No |
| miR164f |
TGGAGAAGCAGGGCACGTGCA |
21 |
3 |
45537767:45537877:+ |
5 |
1621 |
2713 |
969 |
1532 |
No |
| miR164g |
TGGAGAAGCAGGGCACGTGCA |
21 |
3 |
46896220:46896314:+ |
5 |
1621 |
2713 |
969 |
1532 |
No |
| miR164h |
TGGAGAAGCAGGGCACGTGCA |
21 |
19 |
48157202:48157297:+ |
5 |
1621 |
2713 |
969 |
1532 |
No |
| miR164i |
TGGAGAAGCAGGGCACGTGCA |
21 |
20 |
45788090:45788206: − |
5 |
1621 |
2713 |
969 |
1532 |
No |
| miR166a-5p |
GGAATGTTGTCTGGCTCGAGG |
21 |
16 |
1912569:1912713: − |
5 |
171 |
362 |
89 |
110 |
Yes |
| miR166g |
TCGGACCAGGCTTCATTCCCC |
21 |
10 |
2905308:2905432: − |
3 |
16705 |
19874 |
20693 |
18766 |
Yes |
| miR166h-3p |
TCTCGGACCAGGCTTCATTCC |
21 |
8 |
14990535:14990743:+ |
3 |
520 |
620 |
5834 |
5908 |
Yes |
| miR166j-3p |
TCGGACCAGGCTTCATTCCCG |
21 |
15 |
3688752:3688943: − |
3 |
964 |
1127 |
3563 |
3670 |
Yes |
| miR166k |
TCGGACCAGGCTTCATTCCCT |
21 |
6 |
10985730:10985884:+ |
3 |
1128 |
1461 |
2223 |
2182 |
No |
| miR166l |
TCTCGGACCAGGCTTCATTC |
20 |
16 |
3661371:3661614:+ |
3 |
48 |
32 |
649 |
549 |
No |
| miR166m |
TCTCGGACCAGGCTTCATTC |
20 |
19 |
36649690:36649989: − |
3 |
48 |
32 |
649 |
549 |
No |
| miR166n |
TTTCGGACCAGGCTTCATTCC |
21 |
3 |
39519830:39519954: − |
3 |
72 |
68 |
148 |
113 |
No |
| miR166o |
TCGGACCAGGCTTCATTCCC |
20 |
6 |
12992803:12992972: − |
3 |
75 |
53 |
118 |
103 |
No |
| miR166p |
TCGGACCAGGCTTCATTCCC |
20 |
7 |
10198823:10198944:+ |
3 |
75 |
53 |
118 |
103 |
No |
| miR166q |
TCGGACCAGGCTTCATTCCC |
20 |
9 |
37125221:37125362: − |
3 |
75 |
53 |
118 |
103 |
No |
| miR166r |
GGAATGTCGTCTGGTTCGAGA |
21 |
2 |
14340754:14340878:+ |
5 |
120 |
116 |
12 |
15 |
No |
| miR166s |
TTCGGACCAGGCTTCATTCCCC |
22 |
5 |
37747448:37747571: − |
3 |
163 |
192 |
106 |
100 |
No |
| miR166t |
TTCGGACCAGGCTTCATTCCCC |
22 |
8 |
282637:282760: − |
3 |
163 |
192 |
106 |
100 |
No |
| miR166u |
GGAATGTTGTCTGGCTCGAGG |
21 |
6 |
12992922:12993135: − |
5 |
177 |
370 |
92 |
114 |
No |
| miR167e |
TGAAGCTGCCAGCATGATCTT |
21 |
20 |
37901894:37902003:+ |
5 |
1866 |
1676 |
2108 |
1984 |
Yes |
| miR167g |
TGAAGCTGCCAGCATGATCTGA |
22 |
10 |
39044864:39044969:+ |
5 |
160 |
139 |
12 |
11 |
Yes |
| miR167j |
TGAAGCTGCCAGCATGATCTG |
21 |
20 |
44765083:44765188:+ |
5 |
5198 |
6009 |
381 |
405 |
Yes |
| miR167k |
TGAAGCTGCCAGCATGATCTA |
21 |
3 |
39319064:39319173:+ |
5 |
236 |
255 |
166 |
61 |
No |
| miR167l |
TGAAGCTGCCAGCATGATCTTA |
22 |
10 |
46574251:46574360: − |
5 |
1210 |
1096 |
951 |
839 |
No |
| miR168 |
TCGCTTGGTGCAGGTCGGGAA |
21 |
9 |
41353223:41353352: − |
5 |
10469 |
8526 |
7573 |
7864 |
Yes |
| miR168c |
CCCGCCTTGCATCAACTGAAT |
21 |
1 |
48070300:48070429: − |
3 |
195 |
223 |
277 |
327 |
No |
| miR168d |
CCCGCCTTGCATCAACTGAAT |
21 |
9 |
41353223:41353352: − |
3 |
195 |
223 |
277 |
327 |
No |
| miR169c |
AAGCCAAGGATGACTTGCCGA |
21 |
9 |
5295079:5295216:+ |
5 |
29 |
12 |
119 |
95 |
Yes |
| miR169f |
CAGCCAAGGATGACTTGCCGG |
21 |
10 |
40332781:40332933: − |
5 |
103 |
99 |
29 |
32 |
Yes |
| miR169o |
CAGCCAAGGGTGATTTGCCGG |
21 |
15 |
14150055:14150198:+ |
5 |
72 |
144 |
301 |
326 |
No |
| miR169p |
AAGCCAAGGATGACTTGCCGG |
21 |
9 |
5299595:5299718:+ |
5 |
21 |
14 |
118 |
92 |
No |
| miR169q |
AAGCCAAGGATGACTTGCCGA |
21 |
15 |
14202454:14202568:+ |
5 |
0.01 |
12 |
125 |
102 |
No |
| miR169r |
AAGCCAAGGATGACTTGCCGG |
21 |
17 |
4864165:4864284: − |
5 |
0.01 |
0.01 |
122 |
0.01 |
No |
| miR172b-3p |
AGAATCTTGATGATGCTGCAT |
21 |
13 |
40401672:40401822: − |
3 |
3576 |
4906 |
584 |
689 |
Yes |
| miR172h-5p |
GCAGCAGCATCAAGATTCACA |
21 |
10 |
43474719:43474839:+ |
5 |
103 |
97 |
9 |
11 |
Yes |
| miR172k |
TGAATCTTGATGATGCTGCAT |
21 |
12 |
33560621:33560754:+ |
3 |
89 |
133 |
0.01 |
0.01 |
No |
| miR390b |
AAGCTCAGGAGGGATAGCACC |
21 |
2 |
44954748:44954865:+ |
5 |
32 |
28 |
175 |
199 |
Yes |
| miR390d |
AAGCTCAGGAGGGATAGCGCC |
21 |
11 |
30272752:30272868:+ |
5 |
515 |
328 |
230 |
268 |
No |
| miR390e |
AAGCTCAGGAGGGATAGCGCC |
21 |
18 |
53278026:53278171:+ |
5 |
515 |
328 |
230 |
268 |
No |
| miR390f |
AAGCTCAGGAGGGATAGCGCC |
21 |
18 |
5047758:5047875: − |
5 |
515 |
328 |
230 |
268 |
No |
| miR396a-5p |
TTCCACAGCTTTCTTGAACTG |
21 |
13 |
26338131:26338273: − |
5 |
75 |
110 |
323 |
299 |
Yes |
| miR396b-3p |
GCTCAAGAAAGCTGTGGGAGA |
21 |
13 |
26329939:26330049:+ |
3 |
138 |
220 |
0.01 |
0.01 |
Yes |
| miR396c |
TTCCACAGCTTTCTTGAACTT |
21 |
13 |
43804787:43804882:+ |
5 |
141 |
191 |
93 |
101 |
Yes |
| miR396j |
GTTCAATAAAGCTGTGGGAAG |
21 |
13 |
26338141:26338266: − |
5 |
0.01 |
130 |
0.01 |
0.01 |
No |
| miR396k |
GCTCAAGAAAGCTGTGGGAGA |
21 |
13 |
26329931:26330059:+ |
3 |
91 |
172 |
8 |
21 |
No |
| miR397a |
TCATTGAGTGCAGCGTTGATG |
21 |
8 |
4639045:4639154: − |
5 |
161 |
253 |
0.01 |
17 |
Yes |
| miR399a |
TGCCAAAGGAGATTTGCCCAG |
21 |
5 |
34958613:34958732: − |
3 |
21 |
712 |
8 |
280 |
No |
| miR399b |
TGCCAAAGGAGATTTGCCCAG |
21 |
5 |
34967642:34967778: − |
3 |
21 |
712 |
8 |
280 |
No |
| miR399c |
TGCCAAAGGAGATTTGCCCAG |
21 |
8 |
9118500:9118624: − |
3 |
21 |
712 |
8 |
280 |
No |
| miR399d |
TGCCAAAGGAGATTTGCCCAG |
21 |
8 |
9126508:9126640: − |
3 |
21 |
712 |
8 |
280 |
No |
| miR399e |
TGCCAAAGAAGATTTGCCCAG |
21 |
5 |
34963165:34963300: − |
3 |
0.01 |
394 |
0.01 |
0.01 |
No |
| miR2118a |
TTGCCGATTCCACCCATTCCTA |
22 |
20 |
35349746:35349875:+ |
3 |
2084 |
3812 |
2429 |
2557 |
Yes |
| miR2118b |
TTGCCGATTCCACCCATTCCTA |
22 |
10 |
48574023:48574132: − |
3 |
2084 |
3812 |
2429 |
2557 |
Yes |
| miR408b −5p |
CTGGGAACAGGCAGGGCACG |
20 |
3 |
44626682:44626839: − |
5 |
228 |
362 |
13 |
12 |
Yes |
| miR408c |
ATGCACTGCCTCTTCCCTGGC |
21 |
10 |
36556991:36557143: − |
3 |
516 |
1215 |
70 |
84 |
Yes |
| miR408d |
CTGGGAACAGGCAGGGCACGA |
21 |
3 |
44626682:44626839: − |
5 |
409 |
588 |
81 |
78 |
No |
| miR408e |
CAGGGGAACAGGCAGAGCATG |
21 |
2 |
837410:837560:+ |
5 |
380 |
295 |
12 |
14 |
No |
| miR408f |
CAGGGGAACAGGCAGAGCATG |
21 |
10 |
36556991:36557143: − |
5 |
380 |
295 |
12 |
14 |
No |
| miR408g |
GCTGGGAACAGGCAGGGCACG |
21 |
3 |
44626682:44626839: − |
5 |
100 |
167 |
21 |
22 |
No |
| miR482b-3p |
TCTTCCCTACACCTCCCATACC |
22 |
20 |
35360307:35360413:+ |
3 |
37 |
154 |
218 |
494 |
Yes |
| miR482e |
GGAATGGGCTGATTGGGAAGC |
21 |
2 |
7783811:7783923:+ |
5 |
560 |
711 |
651 |
562 |
No |
| miR482f |
TTCCCAATTCCGCCCATTCCTA |
22 |
2 |
7783811:7783923:+ |
3 |
182 |
696 |
91 |
163 |
No |
| miR482g |
TTCCCAATTCCGCCCATTCCTA |
22 |
18 |
61452897:61453007: − |
3 |
182 |
696 |
91 |
163 |
No |
| miR482h |
TATGGGGGGATTGGGAAGGAA |
21 |
10 |
48569622:48569728: − |
5 |
147 |
110 |
133 |
114 |
No |
| miR482i |
TATGGGGGGATTGGGAAGGAA |
21 |
20 |
35360307:35360413:+ |
5 |
147 |
110 |
133 |
114 |
No |
| miR482j |
TTCCCAATTCCGCCCATTCCTA |
22 |
2 |
7783818:7783913:+ |
5 |
195 |
736 |
0.01 |
186 |
No |
| miR482k | TTCCCAATTCCGCCCATTCCTA | 22 | 18 | 61452907:61453000: − | 5 | 195 | 736 | 0.01 | 186 | No |
Soybean conserved miRNAs were grouped into different miRNA families based on Blast analysis of mature miRNA sequences in miRBase ( http://www.mirbase.org). For conserved miRNAs, homology of which can be found in other plant species apart from legume.
Ch, chromosome; HPL, leaf+Pi; HPR, root+Pi; LPL, leaf-Pi; LPR, root-Pi; nt, nucleotide; TPM, transcript per million reads; +, sense strand; −, antisense strand.
miR156_c1 means new soybean miR156 candidate 1, and so on in other miRNA families.