Table 6.
Target genes of P-responsive miRNAs in soybean
|
miRNA |
Target gene |
Target description |
Cleavage site (nt) |
Abundance |
Target site location |
|---|---|---|---|---|---|
| (TP10M) | |||||
|
UP-regulated miRNAs by -Pi | |||||
| m |
Glyma20g37690.1 |
No annotationc |
2526 |
|
CDS |
| miR166u |
Glyma05g06070.1 |
Mybb |
1806 |
|
CDS |
| miR169o |
Glyma06g03940.1 |
Peptidase S24-likea |
584 |
38.429 |
CDS |
| miR169q |
Glyma18g07890.1 |
NF-YAb |
949 |
|
CDS |
| miR396j |
Glyma02g45340.1 |
LRR/NB-ARC domain/TIR domainb |
710 |
|
CDS |
| |
Glyma10g00320.1 |
Protease family S9Bb |
1252 |
|
CDS |
| |
Glyma12g28570.1 |
Core-2/I-Branching enzymeb |
753 |
|
CDS |
| |
Glyma16g00260.1 |
Core-2/I-Branching enzymeb |
711 |
|
CDS |
| |
Glyma17g35500.1 |
Syntaxin 6, N-terminalb |
988 |
|
CDS |
| miR396k |
Glyma12g01390.1 |
Cytokinin dehydrogenasec |
730 |
|
CDS |
| miR397a |
Glyma11g19150.1 |
Male sterility proteina |
1484 |
34.8634 |
CDS |
| |
Glyma12g09270.1 |
Male sterility proteina |
1475 |
34.8634 |
CDS |
| miR399a/b/c/d |
Glyma10g04230.1 |
Phosphate transporterb |
407 |
|
CDS |
| |
Glyma01g13410.1 |
AP2b |
27 |
|
CDS |
| |
Glyma14g36650.1 |
Phosphate transporterb |
240 |
|
CDS |
| |
Glyma13g31290.1 |
PHO2b |
1050 |
|
5’UTR |
| miR399e |
Glyma10g04230.1 |
Phosphate transporterc |
407 |
|
CDS |
| |
Glyma13g31290.1 |
PHO2c |
1050 |
|
5’UTR |
| miR408c |
Glyma06g12680.1 |
Plastocyanin-like domaina |
207 |
55.8606 |
CDS |
| |
Glyma08g13510.1 |
Plastocyanin-like domaina |
198 |
18.224 |
CDS |
| miR1510b-5p |
Glyma10g16090.1 |
PCI domain/eIF3 subunit 6 N terminal domainc |
1451 |
|
3’UTR |
| miR1510d |
Glyma11g04630.1 |
Domain of unknown function (DUF296)c |
1152 |
|
3’UTR |
| miR482f |
Glyma05g01650.1 |
PPRc |
521 |
|
CDS |
| miR482g |
Glyma05g01650.1 |
PPRc |
521 |
|
CDS |
| miR482j |
Glyma05g06070.1 |
Mybb |
282 |
|
CDS |
| miR482k |
Glyma05g06070.1 |
Mybb |
282 |
|
CDS |
| miR482b-3p |
Glyma09g39410.1 |
LRR/NB-ARC domain/leucine-rich repeat-containing proteinc |
513 |
|
CDS |
| miR1512b |
Glyma08g17790.1 |
D-mannose binding lectin/Domain of unknown function (DUF3403)b |
1209 |
|
CDS |
| miR3508 |
Glyma06g42170.1 |
Protein of unknown function (DUF_B2219)/Polyphenol oxidase middle domainb |
1048 |
|
CDS |
| |
Glyma07g31290.1 |
Protein of unknown function (DUF_B2220)/Polyphenol oxidase middle domainb |
2569 |
|
CDS |
| |
Glyma07g31310.1 |
Protein of unknown function (DUF_B2221)/Polyphenol oxidase middle domainb |
1117 |
|
CDS |
| |
Glyma13g25150.1 |
Polyphenol oxidase middle domain/Common central domain of tyrosinaseb |
1096 |
|
CDS |
| |
Glyma13g25180.1 |
Protein of unknown function (DUF_B2219)/Polyphenol oxidase middle domainb |
1025 |
|
CDS |
| |
Glyma13g25260.1 |
Protein of unknown function (DUF_B2220)/Polyphenol oxidase middle domainb |
1199 |
|
CDS |
| |
Glyma15g07710.1 |
Protein of unknown function (DUF_B2221)/Polyphenol oxidase middle domainb |
1077 |
|
CDS |
| miR4416a |
Glyma10g06650.1 |
Uncharacterized nodulin-like proteinb |
1544 |
|
CDS |
| miRnov_2 |
Glyma08g21620.1 |
START domaina |
2712 |
19.0164 |
CDS |
| |
Glyma08g21620.2 |
START domaina |
1892 |
13.8661 |
CDS |
| |
Glyma18g51750.1 |
LRR/NB-ARC domaina |
1840 |
46.3525 |
CDS |
| miRnov_7 |
Glyma19g37520.1 |
Enolasea |
755 |
904.8633 |
CDS |
|
Down-regulated miRNAs by -Pi | |||||
| miR159e-3p |
Glyma13g25716.1 |
Myba |
1340 |
97.459 |
CDS |
| |
Glyma15g35860.1 |
Myba |
937 |
198.4836 |
CDS |
| miR169c |
Glyma10g10240.1 |
NF-YAc,d |
1174 |
|
3’UTR |
| miR169r |
Glyma18g07890.1 |
NF-YAb |
949 |
|
CDS |
| miR2109 |
Glyma16g29650.1 |
Heavy-metal-associated domaina |
297 |
56.653 |
CDS |
| |
Glyma16g33950.1 |
Leucine-rich repeat-containing proteina |
86 |
25.3552 |
CDS |
| |
Glyma16g33980.1 |
Plant basic secretory proteina |
833 |
51.8989 |
CDS |
| |
Glyma16g34060.1 |
transmembrane receptor activitya |
185 |
28.9208 |
CDS |
| |
Glyma16g34060.2 |
transmembrane receptor activitya |
185 |
28.9208 |
CDS |
| miR3522 |
Glyma07g31270.1 |
Protein of unknown function (DUF_B2219)/Polyphenol oxidase middle domainc |
418 |
|
CDS |
| miR4376a |
Glyma09g36420.1 |
F-box/LRRc |
1297 |
|
|
| miRnov_5a |
Glyma06g08730.1 |
No annotationa |
681 |
60.2186 |
CDS |
| |
Glyma06g08730.2 |
No annotationa |
926 |
60.2186 |
CDS |
| |
Glyma06g08730.4 |
No annotationa |
968 |
318.9207 |
CDS |
| miRnov_5b |
Glyma06g08730.1 |
No annotationa |
681 |
60.2186 |
CDS |
| |
Glyma06g08730.2 |
No annotationa |
926 |
60.2186 |
CDS |
| |
Glyma06g08730.4 |
No annotationa |
968 |
318.9207 |
CDS |
| miRnov_6a |
Glyma05g07780.1 |
DEAD/DEAH box helicasea |
1019 |
19.8087 |
CDS |
| |
Glyma06g23290.1 |
DEAD/DEAH box helicasea |
1036 |
19.8087 |
CDS |
| |
Glyma14g40680.1 |
EamA-like transporter familya |
818 |
72.1038 |
CDS |
| |
Glyma17g13230.1 |
DEAD/DEAH box helicasea |
268 |
47.9372 |
CDS |
| |
Glyma18g22940.1 |
DEAD/DEAH box helicasea |
1005 |
19.8087 |
CDS |
| miRnov_9 |
Glyma05g00880.1 |
Sensor histidine kinase-relatedb |
1165 |
|
CDS |
| |
Glyma04g39860.1 |
Peroxidaseb |
260 |
|
CDS |
| |
Glyma06g15030.1 |
Peroxidaseb |
256 |
|
CDS |
| miRnov_10 |
Glyma08g20840.1 |
Dof domain, zinc fingerb |
1001 |
|
CDS |
| |
Glyma20g26290.1 |
Cyclinb |
895 |
|
CDS |
| |
Glyma10g40990.1 |
Cyclinb |
626 |
|
CDS |
| Glyma13g17410.1 | CAAX amino terminal protease family alpha/beta hydrolase domain containingb | 3678 | CDS | ||
The potential targets of soybean P-responsive miRNAs in leaves and roots were predicted by degradome sequencing and computationally using Pairfinder and psRNAtarget. The Glycine max transcriptome is available in Phytozome ( http://www.phytozome.org). For conserved miRNAs, homology of which can be found in other plant species apart from legume; for less-conserved miRNAs, homology of which can be found in legume (legume-specific); for novel miRNAs, which were not previously in miRBase and not assigned into any family were denoted by miRnov (soybean-specific).
a: predicted from degradome;
b: predicted with Pairfinder developed by BGI ( http://www.bgi.cn);
c: predicted from psRNAtarget ( http://plantgrn.noble.org/psRNATarget/?function=3);
d: experimentally confirmed target [20,27,28].
AP2, AP2 domain protein; CDS: coding sequence; Cleavage site: nucleotide position in cDNA cleaved by miRNA from 5’ to 3’; Myb, Myb family of transcription factors; NF-Y, NUCLEAR FACTOR Y (also CCAAT, CCAAT-binding transcription factor); TP10M: transcripts per 10 million reads; UTR: untranslated region.