Table 4.
Representative targets of conserved miRNA in four roses
| miRNA | Sequence (5′-3′) | Va | Ma | Sa | Ha | Target (UniGene)b | PS* | Annotation |
|---|---|---|---|---|---|---|---|---|
| miR156a c |
UGACAGAAGAGAGUGAGCUC |
1,393 |
1,861 |
2,755 |
3,616 |
H_CL12502Contig1 d |
2 |
squamosa promoter-binding-like protein |
| M_CL3280Contig1 d |
2 |
squamosa promoter-binding-like protein |
||||||
| S_FJZMSUQ02I0U8Q d |
2 |
squamosa promoter-binding-like protein |
||||||
| |
|
|
|
|
|
V_CL1436Contig1 |
2 |
squamosa promoter-binding-like protein |
| miR159 c |
UUUGGAUUGAAGGGAGCUCUA |
327,436 |
271,208 |
264,412 |
187,579 |
H_F09TDQC01DKJVB |
4 |
U-box domain-containing protein |
| M_FJZMSUQ02JDPLW d |
3.5 |
r2r3-myb transcription factor |
||||||
| S_FJZMSUQ02FP8OE |
4 |
U-box domain-containing protein |
||||||
| |
|
|
|
|
|
V_F1XUE2F01EH5K8 d |
3.5 |
r2r3-myb transcription factor |
| miR160 c |
UGCCUGGCUCCCUGUAUGCCA |
682 |
739 |
1,739 |
783 |
H_F1XUE2F01ECCC8 |
0.5 |
putative auxin response factor ARF16 |
| M_FJZMSUQ02HS2DI |
0.5 |
putative auxin response factor ARF16 |
||||||
| |
|
|
|
|
|
S_FJZMSUQ02JJQL0 d |
0.5 |
putative auxin response factor ARF16 |
| miR164b c |
UGGAGAAGCAGGGCACGUGCA |
1,618 |
1,166 |
753 |
735 |
H_F1XUE2F01CXKY2 d |
3 |
NAC domain protein |
| M_CL5581Contig1 |
2.5 |
NAC domain protein |
||||||
| |
|
|
|
|
|
V_CL3217Contig1 |
2.5 |
NAC domain protein |
| miR167c c |
UGAAGCUGCCAGCAUGAUCUC |
19,155 |
21,149 |
28,997 |
17,491 |
H_CL5998Contig1 |
4 |
ARF domain class transcription factor |
| M_CL367Contig1 |
4 |
ARF domain class transcription factor |
||||||
| S_CL788Contig1 |
4 |
ARF domain class transcription factor |
||||||
| |
|
|
|
|
|
V_F1XUE2F01AFQWV |
4 |
ARF domain class transcription factor |
| miR168 c |
UCGCUUGGUGCAGGUCGGGAA |
40 |
145 |
33 |
98 |
H_F09TDQC01CTD5O |
3.5 |
argonaute protein group |
| |
|
|
|
|
|
M_CL4618Contig1 |
0.5 |
argonaute protein group |
| miR172 c |
GGAAUCUUGAUGAUGCUGCAG |
2,590 |
1,369 |
1,728 |
720 |
H_CL8041Contig1 |
1 |
AP2 domain class transcription factor |
| S_CL1813Contig1 d |
1 |
AP2 domain class transcription factor |
||||||
| |
|
|
|
|
|
V_CL10861Contig1 |
1 |
AP2 domain class transcription factor |
| miR319a c |
UUGGACUGAAGGGAGCUCCC |
392 |
1,117 |
630 |
518 |
H_F1XUE2F01EUODN |
4 |
TCP domain class transcription factor |
| M_CL839Contig1 |
3.5 |
TCP domain class transcription factor |
||||||
| S_CL7921Contig1 |
4 |
TCP domain class transcription factor |
||||||
| |
|
|
|
|
|
V_F1XUE2F01EH5K8 |
3 |
r2r3-myb transcription factor |
| miR394 c |
UUGGCAUUCUGUCCACCUCC |
227 |
2,251 |
732 |
310 |
H_F1XUE2F01DV50Z d |
1 |
F-box family protein |
| M_CL9289Contig1 |
1 |
F-box family protein |
||||||
| S_CL298Contig1 |
3.5 |
conserved hypothetical protein |
||||||
| |
|
|
|
|
|
V_CL3647Contig1 |
3.5 |
conserved hypothetical protein |
| miR396 c |
UUCCACAGCUUUCUUGAACUG |
10,509 |
20,749 |
9,975 |
6,184 |
M_CL458Contig1 |
4 |
3-dehydroquinate dehydrogenase |
| S_FJZMSUQ02FG68V |
3.5 |
ATP binding protein |
||||||
| |
|
|
|
|
|
V_CL7932Contig1 |
3 |
uncharacterized protein |
| miR482b c |
UCUUUCCUAUUCCUCCCAUCCC |
2,150 |
5,734 |
4,173 |
6,112 |
H_F09TDQC01C8RL9 |
4 |
TIR-NBS-LRR resistance protein |
| S_FJZMSUQ02IMY8Q |
4 |
TIR-NBS-LRR resistance protein |
||||||
| |
|
|
|
|
|
V_F1XUE2F01BNZWC |
3 |
TIR-NBS-LRR resistance protein |
| miR530a |
UGCAUUUGCACCUGCACCUCU |
231 |
205 |
88 |
237 |
H_CL335Contig4 |
2.5 |
BZIP domain class transcription factor |
| M_CL83Contig1 |
2.5 |
BZIP domain class transcription factor |
||||||
| S_CL3168Contig1 |
2.5 |
BZIP domain class transcription factor |
||||||
| |
|
|
|
|
|
V_CL1619Contig1 |
2.5 |
BZIP domain class transcription factor |
| miR894 |
CGUUUCACGUCAGGUUCACCA |
494 |
325 |
736 |
239 |
H_CL672Contig1 |
3 |
E3 ubiquitin-protein ligase |
| M_CL2017Contig1 |
3 |
E3 ubiquitin-protein ligase |
||||||
| |
|
|
|
|
|
V_CL3434Contig1 |
3 |
E3 ubiquitin-protein ligase |
| Ng3 e |
UCUAAGAAACAUUCCUUGAUG |
186 |
391 |
155 |
77 |
S_FJZMSUQ02GRX36 |
2 |
Probable disease resistance protein |
| S_CL7967Contig1 |
2 |
Probable disease resistance protein |
||||||
| |
|
|
|
|
|
V_CL9334Contig1 |
4 |
Probable disease resistance protein |
| Ng11 e |
GUGGAGUUCUGGGAAAGAAG |
51 |
8 |
2 |
7 |
H_CL10098Contig1 |
3.5 |
Matrix metalloprotease 1 |
| M_CL1633Contig2 |
4 |
Acyltransferase-like protein |
||||||
| S_CL7901Contig1 | 3.5 | Metalloendoproteinase 1-like |
a numbers denote normalized expression value in each Rosa. b A single capital letter in front of the UniGene ID represent the abbreviations of Rosa. For example, “M_CL3280Contig1” is unigene in ‘Maroussia’. All abbreviations of tag (V, M, S, H) are ‘Vital’, ‘Maroussia’, ‘Sympathy’, and ‘Haedang’, respectively. c miRNAs identified in strawberry libraries which downloaded from GEO (Accession No. GSE34813). d target genes successfully validated using 5’RACE (Figure 5). e Novel miRNAs identified in this study.