Table 4.
Less-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 | ||||||||||
|
MIR1507 |
||||||||||
| miR1507a |
TCTCATTCCATACATCGTCTGA |
22 |
13 |
25849776:25849883:+ |
3 |
93418 |
6787 |
2 73567 |
59118 |
Yes |
|
MIR1508 |
||||||||||
| miR1508d |
TAGAAAGGGAAATAGCAGTTG |
21 |
9 |
28530172:28530267:+ |
3 |
6600 |
7129 |
1596 |
1456 |
No |
| miR1508e |
CTAGAAAGGGAAATAGCAGTTG |
22 |
16 |
32903737:32903831:+ |
3 |
1347 |
1516 |
374 |
317 |
No |
|
MIR1509 |
||||||||||
| miR1509a |
TTAATCAAGGAAATCACGGTCG |
22 |
17 |
10099759:10099871:+ |
5 |
7221 |
8003 |
21070 |
17929 |
Yes |
| miR1509c |
TTAATCAAGGAAATCACGGTTG |
22 |
5 |
7774098:7774206: − |
5 |
316 |
531 |
2125 |
2125 |
No |
| miR1509d |
TTAATCAAGGAAATCACGGTC |
21 |
17 |
10099759:10099871:+ |
5 |
45 |
50 |
130 |
117 |
No |
|
MIR1510 |
||||||||||
| miR1510b-3p |
TGTTGTTTTACCTATTCCACC |
21 |
2 |
6599300:6599391:+ |
3 |
75 |
125 |
139 |
162 |
Yes |
| miR1510b-5p |
AGGGATAGGTAAAACAACTACT |
22 |
2 |
6599292:6599401:+ |
5 |
1462 |
3478 |
968 |
1980 |
Yes |
| miR1510c |
AGGGATAGGTAAAACAACTAC |
21 |
2 |
6599292:6599401:+ |
5 |
750 |
851 |
697 |
1377 |
No |
| miR1510d |
AGGGATAGGTAAAACAATGAC |
21 |
16 |
31518900:31519009:+ |
5 |
136 |
266 |
245 |
822 |
No |
|
MIR2109 |
||||||||||
| miR2109a |
TGCGAGTGTCTTCGCCTCTGA |
21 |
4 |
28532444:28532532: − |
5 |
50 |
6 |
181 |
220 |
No |
|
MIR3522 |
||||||||||
| miR3522a |
TGAGACCAAATGAGCAGCTGAC |
22 |
15 |
4318787:4318887:+ |
5 |
139 |
115 |
7 |
0.01 |
No |
|
Family undefined | ||||||||||
| miR1511 |
AACCAGGCTCTGATACCATGG |
21 |
18 |
21161229:21161335:+ |
3 |
1099 |
1034 |
5415 |
8419 |
Yes |
| miR1511a |
AACCAGGCTCTGATACCATGGT |
22 |
18 |
21161229:21161335:+ |
3 |
31 |
28 |
77 |
113 |
No |
| miR1512b |
TAACTGGAAATTCTTAAAGCAT |
22 |
2 |
8618690:8618783: − |
5 |
0.01 |
8 |
72 |
102 |
No |
| miR3508 |
TAGAAGCTCCCCATGTTCTCA |
21 |
15 |
5418778:5418967:+ |
3 |
75 |
355 |
120 |
104 |
No |
| miR4345 |
TAAGACGGAACTTACAAAGATT |
22 |
14 |
49067429:49067781:+ |
5 |
77 |
92 |
151 |
139 |
Yes |
| miR4345a |
TTAAGACGGAACTTACAAAGATT |
23 |
14 |
49067429:49067781:+ |
5 |
131 |
158 |
314 |
260 |
No |
| miR4345b |
CTAAGACGGAACTTACAAAGAT |
22 |
14 |
49069094:49069198:+ |
5 |
127 |
141 |
0.01 |
0.01 |
No |
| miR4376-5p |
TACGCAGGAGAGATGACGCTGT |
22 |
13 |
40845924:40846035:+ |
5 |
250 |
154 |
0.01 |
0.01 |
Yes |
| miR4376a |
ACGCAGGAGAGATGACGCTGT |
21 |
13 |
40845924:40846035:+ |
5 |
352 |
155 |
0.01 |
0.01 |
No |
| miR4376b |
TACGCAGGAGAGATGACGCTG |
21 |
13 |
40845924:40846035:+ |
5 |
358 |
216 |
0.01 |
0.01 |
No |
| miR4413c |
TAAGAGAATTGTAAGTCACTG |
21 |
19 |
1788521:1788616: − |
5 |
46 |
65 |
120 |
119 |
No |
| miR4416a |
ACGGGTCGCTCTCACCTGGAG |
21 |
2 |
30498955:30499126: − |
3 |
0.01 |
11 |
123 |
158 |
No |
| miR4416b | ATACGGGTCGCTCTCACCTAGG | 22 | 19 | 40699080:40699213: − | 3 | 8 | 16 | 95 | 139 | No |
Soybean less-conserved miRNAs were grouped into miRNA families based on Blast analysis of mature miRNA sequences in miRBase 18.0 ( http://www.mirbase.org). For less-conserved miRNAs, homology of which can only be found in legume (legume-specific).
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.