Table 2.
Identification of novel microRNAs in wild soybean
| miR_namea | Sequenced sequence | Length | genome ID | strand | dG | CG% | MFEI | raw_Al-free | raw_Al-treated | Glycine max Genomeb | Glycine soja Genomec |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PCd-1-5p |
TGGCCTGTGATGCATCAATTTGTC |
24 |
Gm12 |
+ |
−26.6 |
44 |
0.7 |
49 |
10 |
yes |
no |
| PC-1-3p |
GTCTCTGATGAATGCTCAAATTCT |
24 |
Gm12 |
+ |
−26.6 |
44 |
0.7 |
7 |
11 |
yes |
no |
| PC-4-5p |
GTCGTTGTAGTATAGTGGTAAGT |
23 |
Gm05 |
+ |
−33.5 |
37.3 |
0.7 |
26 |
8 |
yes |
yes |
| PC-4-3p |
GTCGTTGTAGTATAGTGGTAAGTA |
24 |
Gm05 |
+ |
−33.5 |
37.3 |
0.7 |
84 |
48 |
yes |
yes |
| PC-8-5p |
ATTGTTGAGACGATTCTGTAGACG |
24 |
Gm09 |
+ |
−16.8 |
28.3 |
0.6 |
12 |
9 |
yes |
no |
| PC-12-5p |
AAATCTACATGCGGATCAAGTTGA |
24 |
Gm17 |
+ |
−34.2 |
39.7 |
1.1 |
0 |
12 |
yes |
yes |
| PC-20-3p |
CAACGGTCATAATGTAGATTTA |
22 |
Gm05 |
+ |
−29 |
40.6 |
0.7 |
10 |
16 |
yes |
yes |
| PC-21-5p |
CAAAGATTCATCGTAGGCTAGACT |
24 |
Gm08 |
+ |
−25.1 |
55.4 |
0.7 |
14 |
12 |
yes |
yes |
| PC-25-3p |
CTACATAAGGCACGAGATCATC |
22 |
Gm18 |
- |
−17 |
38.2 |
0.7 |
7 |
29 |
yes |
yes |
| PC-26-3p |
CATCGGTCGAGAGCGTTCTT |
20 |
Gm06 |
- |
−48.8 |
46.2 |
0.9 |
14 |
6 |
yes |
no |
| PC-28-3p |
CATTTGGGCACCTATTTTGACTC |
23 |
Gm06 |
+ |
−18.8 |
40 |
0.8 |
24 |
2 |
yes |
yes |
| PC-32-3p |
TATATTCGGATATTCACATT |
20 |
Gm02 |
+ |
−26.7 |
34.3 |
0.8 |
15 |
10 |
yes |
no |
| PC-33-3p |
GGAGAACAAAGAAGCAGCTAAATTC |
25 |
Gm16 |
+ |
−22.4 |
32.6 |
0.7 |
4 |
29 |
yes |
no |
| PC-35-5p |
AAAAGGACACATGACTCACACCTA |
24 |
Gm10 |
- |
−11.9 |
31.2 |
0.5 |
10 |
10 |
yes |
yes |
| PC-36-5p |
GAGTTGGCGAGTTGGACACGTGGC |
24 |
Gm08 |
- |
−38 |
59.5 |
0.8 |
9 |
12 |
yes |
no |
| PC-39-5p |
TAGATTTTAAAGTTGCGGATCA |
22 |
Gm04 |
- |
−42.3 |
38.5 |
1.1 |
10 |
32 |
yes |
yes |
| PC-40-3p |
AATACGTAAGGCTTGAGCTTGACT |
24 |
Gm01 |
- |
−37.8 |
42.9 |
1 |
8 |
17 |
yes |
yes |
| PC-41-3p |
AAATCAGATGATATGGACTTAAAT |
24 |
Gm13 |
- |
−21.2 |
28.3 |
0.8 |
19 |
20 |
yes |
yes |
| PC-42-5p |
AAGAAACGTTGACTCTCCGTGTT |
23 |
Gm03 |
- |
−39.9 |
38.5 |
0.8 |
11 |
5 |
yes |
no |
| PC-43-5p |
ATCGGGATGCTCAGTTCGCATGGT |
24 |
Gm10 |
+ |
−33.9 |
46.6 |
1 |
5 |
11 |
yes |
yes |
| PC-44-3p |
ATGAACCCTTTGAGATCACTGGTT |
24 |
Gm06 |
- |
−26.2 |
47.1 |
0.7 |
17 |
13 |
yes |
yes |
| PC-45-5p |
AGACGGTAAGAAGAGAATTTCAAT |
24 |
Gm01 |
- |
−14.3 |
23.8 |
0.8 |
11 |
4 |
yes |
yes |
| PC-46-5p |
CTATATGATGAAGATA |
16 |
Gm18 |
+ |
−28.3 |
34 |
0.9 |
52 |
26 |
yes |
yes |
| PC-47-3p |
CGTTGTAGTATAGTGGTAAGTATT |
24 |
Gm19 |
+ |
−31.1 |
46 |
0.5 |
9 |
11 |
yes |
yes |
| PC-48-3p |
TTAGCTTCTTTCACCTTTCCC |
21 |
Gm17 |
- |
−41.8 |
41.5 |
1.2 |
135 |
137 |
yes |
no |
| PC-52-5p |
TGAGGGCAAAGATATTAGAGAA |
22 |
Gm05 |
- |
−26 |
35.9 |
0.7 |
5 |
12 |
yes |
yes |
| PC-56-3p |
GGCGAGGAATCTGGGCTCATT |
21 |
Gm15 |
+ |
−37.5 |
47.6 |
1 |
16 |
19 |
yes |
yes |
| PC-57-3p |
GCATACAGGGAGTCAAGCAGA |
21 |
Gm09 |
- |
−48 |
43 |
1.2 |
20 |
27 |
yes |
no |
| PC-58-5p |
TTAGTTGAATGGTACTGTAGTAGT |
24 |
Gm06 |
+ |
−29.2 |
37 |
0.7 |
6 |
11 |
yes |
yes |
| PC-60-3p |
TTTCCCGGCAATGGAACCA |
19 |
Gm17 |
+ |
−19.3 |
38 |
0.5 |
298 |
208 |
yes |
no |
| PC-61-5p | AACTTACTGACTCGTTGACTCGGT | 24 | Gm14 | + | −21.1 | 39.4 | 0.8 | 10 | 5 | yes | yes |
Genomic locations of the pre-miRNA are based on the Glycine max assembly Gmax_109_repeatmasked.fa downloaded from ftp.plantgdb.org/download/Genomes/GmGDB/. Identification of known miRNAs was based on miRBase 18.0.
a, miR_name is the name that was assigned to the detected miRNA sequences.
b, G. max Genome is the precursor sequences whether they could be mapped to Glycine max [56].
c, G. soja Genome is the precursor sequences whether they could be mapped to Glycine soja EST or GSS [92].
d, PC means 'predicted candidate'.