Open Access

Grapevine microRNAs responsive to exogenous gibberellin

BMC Genomics201415:111

DOI: 10.1186/1471-2164-15-111

Received: 1 July 2013

Accepted: 3 February 2014

Published: 8 February 2014

Abstract

Background

MicroRNAs (miRNAs), involving in various biological and metabolic processes, have been discovered and analyzed in quite a number of plants species, such as Arabidopsis, rice and other plants. However, there have been few reports about grapevine miRNAs in response to gibberelline (GA3).

Results

Solexa technology was used to sequence small RNA libraries constructed from grapevine berries treated with GA3 and the control. A total of 122 known and 90 novel grapevine miRNAs (Vvi-miRNAs) were identified. Totally, 137 ones were found to be clearly responsive to GA3, among which 58 were down-regulated, 51 were up-regulated, 21 could only be detected in the control, and seven were only detected in the treatment. Subsequently, we found that 28 of them were differentially regulated by GA3, with 12 conserved and 16 novel Vvi-miRNAs, based on the analysis of qRT-PCR essays. There existed some consistency in expression levels of GA3-responsive Vvi-miRNAs between high throughput sequencing and qRT-PCR essays. In addition, 117 target genes for 29 novel miRNAs were predicted.

Conclusions

Deep sequencing of short RNAs from grapevine berries treated with GA3 and the control identified 137 GA3-responsive miRNAs, among which 28 exhibited different expression profiles of response to GA3 in the diverse developmental stages of grapevine berries. These identified Vvi-miRNAs might be involved in the grapevine berry development and response to environmental stresses.

Keywords

Grapevine Berry microRNAs Exogenous gibberellin High throughput sequencing

Background

MicroRNAs (miRNAs) are endogenous gene regulators distributed widely in plant genomes, and they play important roles in plant growth, development, signal transduction and response to environmental stimuli [15]. Identification of miRNAs is a key step in gaining insight into sRNA-based regulatory functions with many conserved miRNAs having been identified by traditional sequencing approaches such as the Sanger sequencing method [6]. However, most species-specific or tissue-specific miRNAs are hard to be detected probably because of their low accumulation and/or insufficient stringency of the sequencing approach [79]. The advent of new sequencing technologies could make it possible to mine even species-/tissue- specific miRNAs with low abundance, and they havebeen successfully used on Arabidopsis thaliana, Oryza sativa, Poplus tricocarpa, Medicago tuncatula, Gossypiumhirsutum, Zea mays, Arachis hypogaea L., Solanumlycopersicum, Citrus trifoliate, Vitis vinifera and Vitis amurensis Rupr. [1021].

Grapevine (Vitis vinifera L.) is one of the most economically important fruit crops worldwide and has nutritional and processing properties [22]. In recent years, sequencing of small RNA libraries from different grapevine cultivars or tissues has severally been reported where a large number of Vvi-miRNAs were identified [7, 1821]. Despite this, there are no reports on the study of response of Vvi-miRNAs to phytohormones. Phytohormones are important endogenous signals and regulators involved in plant growth and development [23], and they are classified into auxins, gibberellins(GA3), cytokinins, abscisic acid(ABA) and ethylene. All of these phytohormones act at low concentrations to regulate different aspects of plant growth and development to varying degrees [2325]. Among the hormones, GA3 play significant regulatoryroles in early berry expansion, berry set and berry ripening [26, 27]. Till now, it is still unclear on how GA3 participates in the regulation of the complicated developmental processes of grapevine berry.

It has been reported that phytohormone signaling pathways can be effectively controlled by modulation of positive and negative regulators during plant growth and development [4]. Among the modulators of phytohormones, miRNA was recently found to be a new growth regulator involved in phytohormone signaling [2830], with several studies showing the interactions between miRNAs and phytohormones in various plant responses. For instance, GA3 modulates the expression of miR159, while miR159 regulates the development of Arabidopsi s anthers and seeds by cleaving the GAMYB gene, during Arabidopsis anther development [28] and seed germination [29]. In strawberry, miR159 interacts with GAMYB during the course of receptacle development, and both of them act in a joint fashion to respond, in part, to changes in endogenous GA3 levels [30]. These studies strongly demonstrated that miRNAs are involved in the GA3 signaling process.

To account for the roles of miRNAs in response to GA3 during grapevine berry development, we constructed two small RNA libraries from mixed tissue samples of grapevine berries sprayed with GA3 (treatment) and with water (the control). The grapevine cultivar used for this study is ‘Summer Black’ (hybrid of V. vinifera?×?V. labrusca), an elite table grapevine cultivar native to Japan. After high-throughput sequencing, we identified a number of conserved and non-conserved Vvi-miRNAs responsive to GA3, and we further analyzed their potential role in mediation of GA3-induced regulation of grapevine berry growth and development. Further, qRT-PCR was utilized to analyze the expression of Vvi-miRNAs in different development stages of the grapevine berries subjected to exogenous GA3 and in exogenous GA3-free berries. Lastly, an attempt to elucidate the regulatory functions of Vvi-miRNAs being responsive to GA3 during grapevine berry development was done.

Results

Characterization of the Vvi-miRNAs from deep sequencing of grapevine sRNA libraries

To identify GA3-responsive miRNAs in grapevine berries, two small RNA libraries from grapevine berries treated with GA3 (GA3 treatment) and sprayed with water (the control) were constructed. Solexa, a high throughput sequencing technology, was employed to sequence these libraries, leading to a generation of 16,231,320 and 16,486,660 clean reads from GA3 treatment and the control libraries, respectively. All these clean reads were those from removal of adaptor, insert, polyA, and RNAs shorter than 18nt in length (Table 1). About 4,265,160 (GA3 treatment) and 4,326,915 (the control) clear reads could be mapped to the grapevine genome published in 2007 [31], and miRNA, tRNA, siRNA, snRNA, snoRNA, rRNA, repeat regions, exon and intron RNA reads were annotated. In addition, 9,075,238 and 9,207,588 un-annotated reads were used for prediction of new Vvi-miRNAs in GA3 treatment and the control grapevine berries, respectively (Table 1).
Table 1

Distribution of small RNAs among different categories in control and GA 3 Treated grapevine berries

Category

Control

GA3 treatment

Unique

Percent (%)

Redundant

Percent (%)

Unique

Percent (%)

Redundant

Percent (%)

Exon_antisense

88740

2.28%

232050

1.41%

67193

1.40%

157256

0.98%

Exon_sense

136907

3.52%

449869

2.73%

130285

2.71%

289348

1.80%

Intron_antisense

35335

0.91%

72189

0.44%

32881

0.68%

52624

0.33%

Intron_sense

41391

1.06%

106364

0.65%

39164

0.81%

72984

0.46%

miRNA

1724

0.04%

683061

4.14%

1726

0.04%

812099

5.07%

rRNA

51658

1.33%

1099955

6.67%

72149

1.50%

1108756

6.92%

Repeat

15219

0.39%

27556

0.17%

12601

0.26%

22740

0.14%

snRNA

4408

0.11%

19905

0.12%

4553

0.09%

19873

0.12%

snoRNA

1780

0.05%

5172

0.03%

1895

0.04%

6403

0.04%

tRNA

13078

0.34%

1285951

7.80%

20052

0.42%

1210840

7.55%

unann

3501164

89.97%

9207588

55.85%

4190436

87.17%

9075238

56.60%

Mapping to genome

838267

21.54%

43326915

26.24%

765402

15.92%

4265160

26.60%

Total

3891404

100.00%

16486660

100.00%

4807290

100%

16033016

100%

The size distribution of all sRNAs was found to be uneven ranging from 18nt to 30nt long, with the majority being 19-25nt long (Figure 1). The sRNAs of 21 nt and 24nt formed two major classes, occupying 38.35% and 32.06% (Figure 1) of the total, respectively, an observation which is in agreement with some previous reports in grapevine and tomato [11, 16, 21, 31], but contrasts to those reported in Arabidopsis, rice and peanut [3235]. The two main peaks of sRNAs in this study were 24 and 21nt long, while the most common sRNAs in Taxus chinensis[35] and Citrus trifoliate[17] were those with 21 nt in length. These cases suggested that some differences might exist in the sRNA biogenesis pathways in various plants. In addition, analysis of the first nucleotide of 18-25nt long sRNAs indicated that many sRNAs started with a uridine (U) at their 5’-ends and most of them are 21 nt and 22 nt long, with the former being most outstanding in number (Figure 2). Similar to other plants, most miRNAs here were those with 21 and 22 nt in length and they also begin with a 5’uridine, which is one of the important characteristic features of miRNAs [10, 11, 36].
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig1_HTML.jpg
Figure 1

Size distribution of unique small RNA sequences from grapevine.

https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig2_HTML.jpg
Figure 2

First nucleotide bias of 18-30nt sRNA tags.

High throughput sequencing can verify a large number of known miRNAs together with the identification of novel specific miRNAs even with the low abundance in organisms. From two sRNA libraries in this study, we first searched for known Vvi-miRNAs by comparing our libraries with known miRNAs from other plant species in miRBase 19.0 (http://​www.​mirbase.​org/​). A total of 122 known Vvi-miRNAs were sequenced both in the control and GA3-treatment libraries, and they belonged to 27 conserved miRNA families according to a comparative genomics-based analysis in different plant species [37]. Eighteen of the 27 Vvi-miRNA families contained many members (Table 2), with four families (Vvi-miR169, Vvi-miR156, Vvi-miR166, Vvi-miR171 and Vvi-miR399) possessing 19, 8, 7, 8, and 7 members, respectively. Another nine Vvi-miRNA families (Vvi-miR162, Vvi-miR168, Vvi-miR390, Vvi-miR397, Vvi-miR408, Vvi-miR477, Vvi-miR479, Vvi-miR482, and Vvi-miR828) had only one member each. Among the known Vvi-miRNAs, the Vvi-miR166 family had the most abundant reads accounting for 63.2% of all the conserved miRNA reads. In this family, the number of Vvi-miR166h reads was over 500,000 in the two libraries, followed by Vvi-miR156, Vvi-miR168, Vvi-miR167, Vvi-miR479, Vvi-miR482 families, whose redundancies were more than several ten thousands. However, other miRNA families like Vvi-miR393, Vvi-miR394, Vvi-miR398 and Vvi-miR399 had only a few or tens of reads. Interestingly, the number and abundance of members of different Vvi-miRNA families between control and GA3 libraries were significant divergence (Table 2; Figure 3), which in turn could reflect the discrepancy in their potential functions during the development of grapevine berries responsive to gibberellin.
Table 2

Conserved Vv-miRNAs identified and normalized counts (NC) in control and GA 3 treated grapevine berries

Control

GA3treatment

Identity

miRNA ID

Sequences

NC

miRNA ID

Sequences

NC

Vvi-miR156a

TTGACAGAAGAGAGGGAGCAC

8.81

vv-miR156a

TTGACAGAAGAGAGGGAGCAC

513.79

Vvi-miR156b

AACTGACAGAAGAGAGTGAGCAC

2308.90

vv-miR156b

AACTGACAGAAGAGAGTGAGCAC

0.61

Vvi-miR156c

TGACAGAAGAGAGTGAGCACAC

2214.31

vv-miR156c

TGACAGAAGAGAGTGAGCACAC

0.17

Vvi-miR156d

TGACAGAAGAGAGTGAGCAC

2321.38

vv-miR156d

TGACAGAAGAGAGTGAGCAC

2331.59

Vvi-miR156e

TGACAGAGGAGAGTGAGCAC

3.40

vv-miR156e

TGACAGAGGAGAGTGAGCAC

14.83

Vvi-miR156f

CTGTTGACAGAAGATAGAGAGCAC

5215.88

vv-miR156f

CTGTTGACAGAAGATAGAGAGCAC

3.93

Vvi-miR156g

GCTCTCTAGACTTCTGTCATC

5214.31

vv-miR156g

GCTCTCTAGACTTCTGTCATC

0.61

Vvi-miR156i

TTGACAGAAGATAGAGAGCAC

5214.31

vv-miR156i

TTGACAGAAGATAGAGAGCAC

6093.28

  

0.00

vv-miR159b

CCTTGGAGTGAAGGGAGCT

0.17

Vvi-miR159c

TTTGGATTGAAGGGAGCTCTA

74.61

vv-miR159c

TTTGGATTGAAGGGAGCTCTA

582.11

Vvi-miR160a

TCCTAGTTGGCATCAGAGGAG

1.66

vv-miR160a

TCCTAGTTGGCATCAGAGGAG

0.09

Vvi-miR160b

GCATGAGGGGAGTCAAGCAGG

1.66

vv-miR160b

GCATGAGGGGAGTCAAGCAGG

4.19

Vvi-miR160c

GCGTGCGAGGAGCCAAGCATA

3.75

vv-miR160c

GCGTGCGAGGAGCCAAGCATA

4.54

Vvi-miR160d

TGCCTGGCTCCCTGTATGCCA

4.71

  

0.00

Vvi-miR160e

GCGTATGAGGAGCCATGCATA

4.71

vv-miR160e

GCGTATGAGGAGCCATGCATA

2.27

  

0.00

vv-miR160f

TGCCTGGCTCCCTGTATGCCA

43.98

Vvi-miR162

TCGATAAACCTCTGCATCCAG

236.04

vv-miR162

TCGATAAACCTCTGCATCCAG

231.76

Vvi-miR164a

TTGGAGAAGCAGGGCACGTGC

43.02

vv-miR164a

TTGGAGAAGCAGGGCACGTGC

0.17

Vvi-miR164c

TGGAGAAGCAGGGCACGTGCAT

43.19

vv-miR164c

TGGAGAAGCAGGGCACGTGCAT

6.72

Vvi-miR164d

TGGAGAAGCAGGGCACGTGCA

43.02

vv-miR164d

TGGAGAAGCAGGGCACGTGCA

798.08

Vvi-miR166a

TCTCGGACCAGGCTTCATTCCT

762.04

vv-miR166a

TCTCGGACCAGGCTTCATTCCT

7.85

Vvi-miR166b

TCGGACCAGGCTTCATTCCTC

3280.28

vv-miR166b

TCGGACCAGGCTTCATTCCTC

15371.38

Vvi-miR166c

TCGGACCAGGCTTCATTCCCC

21467.36

  

0.00

Vvi-miR166d

GATTGTTGTCTGGCTCGAGGC

21492.15

vv-miR166d

GATTGTTGTCTGGCTCGAGGC

1.05

Vvi-miR166e

GGAATGTTGTCTGGCTCGAGG

21467.36

vv-miR166e

GGAATGTTGTCTGGCTCGAGG

311.87

Vvi-miR166f

GGAATGTTGGCTGGCTCGAGG

21506.81

vv-miR166f

GGAATGTTGGCTGGCTCGAGG

18.24

Vvi-miR166g

TTCGGACCAGGCTTCATTCCC

21509.60

vv-miR166g

TTCGGACCAGGCTTCATTCCC

82.11

Vvi-miR166h

TCGGACCAGGCTTCATTCCCC

22171.73

vv-miR166h

TCGGACCAGGCTTCATTCCCC

22520.68

Vvi-miR167a

TGAAGCTGCCAGCATGATCTGG

32.81

vv-miR167a

TGAAGCTGCCAGCATGATCTGG

11.78

Vvi-miR167b

TGAAGCTGCCAGCATGATCTAAG

616.06

vv-miR167b

TGAAGCTGCCAGCATGATCTAAG

38.48

Vvi-miR167c

TGAAGCTGCCAGCATGATCTC

134.12

vv-miR167c

TGAAGCTGCCAGCATGATCTC

1901.57

Vvi-miR167d

TGAAGCTGCCAGCATGATCTAG

424.87

vv-miR167d

TGAAGCTGCCAGCATGATCTAG

1.75

Vvi-miR167e

TGAAGCTGCCAGCATGATCTA

613.09

vv-miR167e

TGAAGCTGCCAGCATGATCTA

2349.30

Vvi-miR168

TCGCTTGGTGCAGGTCGGGAA

2963.35

vv-miR168

TCGCTTGGTGCAGGTCGGGAA

2654.62

Vvi-miR169a

CAGCCAAGGATGACTTGCCGG

13.09

  

0.00

Vvi-miR169b

GGTCGAATTGAGCCAAGGATGG

5.58

vv-miR169b

GGTCGAATTGAGCCAAGGATGG

0.35

Vvi-miR169c

TCCGGCAAGTTGTCCTTGGCTAC

13.09

vv-miR169c

TCCGGCAAGTTGTCCTTGGCTAC

0.70

Vvi-miR169d

CAGCCAAGAATGATTTGCCGG

35.25

vv-miR169d

CAGCCAAGAATGATTTGCCGG

105.50

Vvi-miR169e

TAGCCAAGGATGACTTGCCT

0.44

  

0.00

Vvi-miR169f

TGGGCAAGTTGTGTTTGGCTAC

0.35

vv-miR169f

TGGGCAAGTTGTGTTTGGCTAC

0.26

Vvi-miR169g

CAGCCAAGGATGACTTGCCGA

0.44

vv-miR169g

CAGCCAAGGATGACTTGCCGA

6.54

Vvi-miR169h

TGAGCCAAGGATGGCTTGCCGT

5.50

vv-miR169h

TGAGCCAAGGATGGCTTGCCGT

7.42

Vvi-miR169i

CTGGTCATGCACGGCTGGTTA

1.83

vv-miR169i

CTGGTCATGCACGGCTGGTTA

0.09

Vvi-miR169j

CAGCCAAGGATGACTTGCCGG

13.09

  

0.00

Vvi-miR169k

AGCCAAGGATGACTTGCCGGA

13.09

vv-miR169k

AGCCAAGGATGACTTGCCGGA

0.26

Vvi-miR169l

TGAGCCAAGGATGACTTGCCGT

58.12

vv-miR169l

TGAGCCAAGGATGACTTGCCGT

0.96

Vvi-miR169m

TGAGCCAAGGATGACTTGCCG

54.45

  

0.00

Vvi-miR169n

AAGCATCTGAGGCTCTATTTC

16.32

vv-miR169n

AAGCATCTGAGGCTCTATTTC

186.82

Vvi-miR169o

TGAGCCAAGGATGACTTGCCG

54.80

vv-miR169o

TGAGCCAAGGATGACTTGCCG

13.53

Vvi-miR169p

GCAAGCATCCGAGGCTCTGT

55.50

vv-miR169p

GCAAGCATCCGAGGCTCTGT

3.66

Vvi-miR169q

TAGAGCCAAGGATGACTTGCCG

16.40

vv-miR169q

TAGAGCCAAGGATGACTTGCCG

6.37

Vvi-miR169r

TGAGTCAAGGATGACTTGCCGA

4.71

vv-miR169r

TGAGTCAAGGATGACTTGCCGA

0.79

Vvi-miR169s

CAGCCAAGGATGACTTGCCGG

13.18

  

0.00

Vvi-miR169t

GGCAAGTTGACTTGACTCAGT

1.66

vv-miR169t

GGCAAGTTGACTTGACTCAGT

6.81

Vvi-miR169u

GGCAAGTTGACTTGACTCTGT

2.71

vv-miR169u

GGCAAGTTGACTTGACTCTGT

4.01

Vvi-miR169v

AAGCCAAGGATGAATTGCCGG

4.36

vv-miR169v

AAGCCAAGGATGAATTGCCGG

2.62

Vvi-miR169w

CAGCCAAGGATGACTTGCCGG

13.18

vv-miR169w

CAGCCAAGGATGACTTGCCGG

12.39

Vvi-miR169x

TGAGTCAAGGATGACTTGCCGA

0.52

vv-miR169x

TGAGTCAAGGATGACTTGCCGA

0.70

Vvi-miR171a

TGTTGGGACGGCTCAATCAAA

4.71

vv-miR171a

TGTTGGGACGGCTCAATCAAA

5.67

Vvi-miR171b

TTGAGCCGCGTCAATATCTCC

4.36

vv-miR171b

TTGAGCCGCGTCAATATCTCC

35.69

Vvi-miR171c

GGATATTGGTGCGGTTCAATA

5.15

vv-miR171c

GGATATTGGTGCGGTTCAATA

4.54

Vvi-miR171d

TTGATTGAGCCGTGCCAATAT

5.15

vv-miR171d

TTGATTGAGCCGTGCCAATAT

2.53

  

0.00

vv-miR171e

TGATTGAGCCGCGCCAATATC

0.09

  

0.00

vv-miR171f

TTGAGCCGCGCCAATATCACT

2.01

  

0.00

vv-miR171h

TTGAGCCGCGCCAATATCCCG

0.96

Vvi-miR171i

TGATTGAGCCGTGCCAATATC

4.71

vv-miR171i

TGATTGAGCCGTGCCAATATC

85.43

Vvi-miR172c

GGAGCATCATCAAGATTCACA

0.09

vv-miR172c

GGAGCATCATCAAGATTCACA

103.40

Vvi-miR172d

AGAATCTTGATGATGCTGCAT

184.47

vv-miR172d

AGAATCTTGATGATGCTGCAT

117.63

Vvi-miR319b

TTGGACTGAAGGGAGCTCCC

0.35

  

0.00

Vvi-miR319c

ATTGAATGATGCGGGAGACAA

0.35

vv-miR319c

ATTGAATGATGCGGGAGACAA

20.68

Vvi-miR319e

TTTGGACTGAAGGGAGCTCCT

18.59

vv-miR319e

TTTGGACTGAAGGGAGCTCCT

7.94

Vvi-miR319f

TGCTTGGACTGAAGGGAGC

0.35

vv-miR319f

TGCTTGGACTGAAGGGAGC

3.40

Vvi-miR319g

TTGGACTGAAGGGAGCTCCC

0.26

vv-miR319g

TTGGACTGAAGGGAGCTCCC

1.40

Vvi-miR390

AAGCTCAGGAGGGATAGCGCC

1.75

vv-miR390

AAGCTCAGGAGGGATAGCGCC

160.73

  

0.00

vv-miR393a

ATCATGCTATCCCTTAGGAAC

1.66

  

0.00

vv-miR393b

GGAGGAGGCATCCAAAGGGAT

0.79

Vvi-miR394a

TTGGCATTCTGTCCACCTCC

2.71

  

0.00

Vvi-miR394b

TATTGGCATTCTGTCCACCTCC

2.53

vv-miR394b

TATTGGCATTCTGTCCACCTCC

0.09

Vvi-miR394c

TTGGCATTCTGTCCACCTCC

2.71

vv-miR394c

TTGGCATTCTGTCCACCTCC

0.79

Vvi-miR395a

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395b

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395c

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395d

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395e

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395f

CACTGAAGTGTTTGGGGGAAC

22.08

vv-miR395f

CACTGAAGTGTTTGGGGGAAC

0.09

Vvi-miR395g

GTTCCCCTGAGCACTTCATTG

22.16

vv-miR395g

GTTCCCCTGAGCACTTCATTG

0.52

Vvi-miR395h

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395i

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395j

CTGAAGTGTTTGGGGGAACTC

22.08

  

0.00

Vvi-miR395k

GTTCCCTTGACCACTTCACTG

22.08

vv-miR395k

GTTCCCTTGACCACTTCACTG

0.44

Vvi-miR395l

CCCCTAGAGTTCCCCTGACCA

22.08

vv-miR395l

CCCCTAGAGTTCCCCTGACCA

0.09

Vvi-miR395m

CTGAAGTGTTTGGGGGAACTC

22.08

vv-miR395m

CTGAAGTGTTTGGGGGAACTC

11.61

Vvi-miR396a

CTCAAGAAAGCTGTGGGAGG

25.04

vv-miR396a

CTCAAGAAAGCTGTGGGAGG

35.17

Vvi-miR396b

TTCCACAGCTTTCTTGAACTT

53.23

vv-miR396b

TTCCACAGCTTTCTTGAACTT

35.86

Vvi-miR396c

TTCCACAGCTTTCTTGAACTG

13.53

vv-miR396c

TTCCACAGCTTTCTTGAACTG

18.41

Vvi-miR396d

GTTCAATAAAGCTGTGGGAAG

14.22

vv-miR396d

GTTCAATAAAGCTGTGGGAAG

6.20

Vvi-miR397a

TCATTGAGTGCAGCGTTGATG

7.59

vv-miR397a

TCATTGAGTGCAGCGTTGATG

29.41

Vvi-miR398a

CAAGGGAGTGGCACCTGAGAACA

0.09

vv-miR398a

CAAGGGAGTGGCACCTGAGAACA

6.98

Vvi-miR398b

GGTGTGACCTGAGAATCACATG

0.61

vv-miR398b

GGTGTGACCTGAGAATCACATG

0.26

Vvi-miR398c

TGTGTTCTCAGGTCGCCCCTG

0.61

vv-miR398c

TGTGTTCTCAGGTCGCCCCTG

1.13

Vvi-miR399a

GTGTGATTCTCCTTTGGCAGA

0.70

vv-miR399a

GTGTGATTCTCCTTTGGCAGA

1.57

Vvi-miR399b

TGCCAAAGGAGAGTTGCCCTG

0.26

  

0.00

Vvi-miR399c

TGCCAAAGGAGAGTTGCCCTG

0.26

vv-miR399c

TGCCAAAGGAGAGTTGCCCTG

0.09

Vvi-miR399d

TCTGCCAAAGGAGATTTGCTC

1.48

vv-miR399d

TCTGCCAAAGGAGATTTGCTC

0.26

Vvi-miR399e

TGCCAAAGGAGATTTGCCCGG

3.58

vv-miR399e

TGCCAAAGGAGATTTGCCCGG

10.56

Vvi-miR399g

TGCCAAAGGAGATTTGCCCCT

9.08

vv-miR399g

TGCCAAAGGAGATTTGCCCCT

1.31

Vvi-miR399h

TGCCAAAGGAGAATTGCCCTG

0.52

vv-miR399h

TGCCAAAGGAGAATTGCCCTG

0.96

Vvi-miR399i

CGCCAAAGGAGAGTTGCCCTG

29.49

vv-miR399i

CGCCAAAGGAGAGTTGCCCTG

14.05

Vvi-miR403a

TTAGATTCACGCACAAACTCG

52.27

  

0.00

Vvi-miR403b

TTAGATTCACGCACAAACTCG

52.62

  

0.00

Vvi-miR403c

CGCACAAACTCGTGATCTGTC

52.27

vv-miR403c

CGCACAAACTCGTGATCTGTC

0.09

Vvi-miR403d

AGTTTGTGCGCGAATCCAACC

52.62

vv-miR403d

AGTTTGTGCGCGAATCCAACC

4.36

Vvi-miR403e

TTAGATTCACGCACAAACTCGC

52.18

vv-miR403e

TTAGATTCACGCACAAACTCGC

0.17

Vvi-miR403f

TTAGATTCACGCACAAACTCG

52.36

vv-miR403f

TTAGATTCACGCACAAACTCG

586.04

Vvi-miR408

ACGGGGACGAGGTAGTGCATG

22.34

vv-miR408

ACGGGGACGAGGTAGTGCATG

62.04

Vvi-miR477

TCCCTCAAAGGCTTCCAATTT

98.25

vv-miR477

TCCCTCAAAGGCTTCCAATTT

21.82

Vvi-miR479

TGTGGTATTGGTTCGGCTCATC

2922.60

vv-miR479

TGTGGTATTGGTTCGGCTCATC

1131.41

Vvi-miR482

AATTGGAGAGTAGGAAAGCTT

45.11

vv-miR482

AATTGGAGAGTAGGAAAGCTT

1056.46

Vvi-miR535a

TGACAACGAGAGAGAGCACGC

763.18

  

0.00

Vvi-miR535b

ACGAGAGAGAGCACGCTAGTCAG

763.18

vv-miR535b

ACGAGAGAGAGCACGCTAGTCAG

0.09

Vvi-miR535c

TGACAACGAGAGAGAGCACGC

763.18

vv-miR535c

TGACAACGAGAGAGAGCACGC

83.42

Vvi-miR828a

AGATGCTCATTTGAGGAAGCAA

1.13

vv-miR828a

AGATGCTCATTTGAGGAAGCAA

5.32

Notes: ,,▲ ,, denote up-regulated, down-regulated, induced, repressed, un-affected, respectively.

https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig3_HTML.jpg
Figure 3

Number of members from Vv-miRNA families in control and GA 3 treated grapevine berries.

Bioinformatics analysis of the sequencing data could identify novel Vvi-miRNAs based on the criteria of novel miRNA annotations developed by Meyers et al. (2008) [38]. The genomic sequences with flanking un-announced sequences were extracted. Among these sequences, 90 candidate Vvi-miRNAs were firstly uncovered, and the hairpin structures of their precursors’ could be predicted (Additional file 1). The miRNA* sequences available is of vital evidence supporting the release of miRNA duplex from the predicted foldback structure [16]. Among these 90 potential novel Vvi-miRNAs, 28 had their Vvi-miRNA* sequences were detected (Additional file 2), and the sequences of 45 novel potential Vvi-miRNAs started with a 5’ uridine, the important feature of miRNAs (Additional file 2). All these confirmed the existence of these novel candidate Vvi-miRNAs in grapevine. In this study, it was also noted that the novel Vvi-miRNAs had fewer reads than the conserved ones. 72% of the former had only several or dozens of copies except for Vvi-miRC20, Vvi-miRC36, Vvi-miRC43, Vvi-miRC44, Vvi-miRC45, Vvi-miRC46, Vvi-miRC50, Vvi-miRC51, Vvi-miRC52, Vvi-miRC71, and Vvi-miRC74 that were sequenced more than one thousand times (Additional file 2). This agreed with other previously reported results [10, 11, 36], where most novel species-specific miRNAs were usually expressed at lower levels than their conserved counterparts and were much more spatiotemporally expressed.

Discovery of miRNAs responsive to exogenous GA3 in grapevine

To identify Vvi-miRNAs responsive to exogenous GA3, we normalized the counts of reads sequenced based on the systematical analysis, and compared the members and the normalized counts (NC) of different members of Vvi-miRNA families between the control and GA3 libraries. The results revealed that seven known Vvi-miRNAs (Vvi-miR159b, Vvi-miR160f, Vvi-miR171e, Vvi-miR171f, Vvi-miR171h, Vvi-miR393a and Vvi-miR393b) were found only in the GA3 treated grapevine tissues not in the control, suggesting they were probably those induced by GA3; another 21 known Vvi-miRNAs (Vvi-miR160d, Vvi-miR166c, Vvi-miR169a, Vvi-miR169e, Vvi-miR169j, Vvi-miR169m, Vvi-miR169s, Vvi-miR319b, Vvi-miR394a, Vvi-miR395a, Vvi-miR395b, Vvi-miR395c, Vvi-miR395d, Vvi-miR395e, Vvi-miR395h, Vvi-miR395i, Vvi-miR395j, Vvi-miR399b, Vvi-miR403a, Vvi-miR403b and Vvi-miR535a) were strongly repressed in GA3 treatment for they could only be detected in the control but not in the GA3 treatment (Table 2).

Thirty novel Vvi-miRNAs (Vvi-miRC02, Vvi-miRC03, Vvi-miRC05, Vvi-miRC08, Vvi-miRC10, Vvi-miRC11, Vvi-miRC13, Vvi-miRC14, Vvi-miRC16, Vvi-miRC17, Vvi-miRC21-Vvi-miRC26, Vvi-miRC33, Vvi-miRC39, Vvi-miRC41, Vvi-miRC42, Vvi-miRC54, Vvi-miRC55, Vvi-miRC57, Vvi-miRC59, Vvi-miRC61, Vvi-miRC64, Vvi-miRC65, Vvi-miRC68 and Vvi-miRC72) were found to be responsive to exogenous GA3, for they could only be detected in GA3 treated grapevines (Table 2); while another 16 novel Vvi-miRNAs (from Vvi-miRC75 to Vvi-miRC90) were repressed by exogenous GA3, and found only in control but not in GA3 treatment (Table 2). These results demonstrate that these groups of Vvi-miRNAs could be responsive to GA3 treatment.

Further comparison of the normalized counts of Vvi-miRNAs identified in GA3 treated and the control plants indicated that many Vvi-miRNAs exhibited drastic variations (increases/decreases over several times) in expression frequencies. As shown in Table 2 and Table 3, the expression of 137 Vvi-miRNAs was strongly responsive to exogenous GA3, with 58 of them induced by GA3, showing conspicuously up-regulated expression under GA3 treatment (pointed as ↑ in Table 2 and 3).Conversely, 51 Vvi-miRNAs were repressed by exogenous GA3 (pointed as ↓ in Table 2 and 3), leading to drastic reduction in their expression levels in GA3-treated grapevines. An interesting revelation was that diverse members of the same Vvi-miRNA family could exhibit conspicuous discrepancy in their responses to exogenous GA3. This aspect is best exemplified by Vvi-miR166 family, where Vvi-miR166d/e/f/g had more than 246,000 reads in control samples, but possessed only several dozen or even a little more reads in the GA3 treatment samples, while Vvi-miR166b was detected 37,952 times in control and 176,156 times in GA3 treatment (Table 2). Vvi-miR166h, however, had no distinct variations between the control and GA3 treatment (Table 2). Similar situations were found in other Vvi-miRNA families like Vvi-miR156, Vvi-miR164, Vvi-miR167, Vvi-miR403 and Vvi-miR535 (Table 2), suggesting the Vvi-miRNAs responsive to exogenous GA3 application possess multiple aspects and functions during the development of grapevine berries.
Table 3

Comparison of normalized counts (NC) of novel Vv-miRNAs between GA 3 treated and control grapevine berries

miRNA ID

Mature sequences

NC

Identity of frequency

Control

GA treatment

Vvi-miRC01

CTATGTTATAGGATCTTGGAT

9.16

17.19

Vvi-miRC01*

CCAAGATACTATAACATGGTC

0.00

0.17

Vvi-miRC02

TCCCTTTGGAAGTGCTAAGCG

0.00

1.83

Vvi-miRC03

AGTGGTGGCAAGGATGAGCAA

0.00

0.52

Vvi-miRC04

TTTGGAATGATTTGTTGATGA

4.62

1.48

Vvi-miRC05

AAGATCTCCCATTGCATCTGA

0.00

0.52

Vvi-miRC06

TTTTTTGGTTATGGTTGGCTG

0.61

1.40

Vvi-miRC07

CTCAAGAAAGCTGTGGGAAAA

0.61

1.05

Vvi-miRC07*

TTTCCACATCTTTCTTGAACT

0.09

0.17

Vvi-miRC08

AGAAGAACAAGTAGACTGAGC

0.00

0.96

Vvi-miRC09

TTATATAGGCTTTGAGGATGGA

0.00

1.92

Vvi-miRC10

TTTTAAAAAGGTTCGTCATTC

0.00

0.87

Vvi-miRC11

CCGTGACAAGTGGTATCAGAG

0.00

1.13

Vvi-miRC12

TCTGAAGTTTGAAGAGCTGTG

4.97

10.56

Vvi-miRC12*

AGAGCAATCTACGAACAACAGGAA

0.09

0.09

Vvi-miRC13

TTGGCTTGGAGATGGATCATT

0.00

10.56

Vvi-miRC14

TTGGCTTGGAGATGGATCATT

0.00

10.56

Vvi-miRC15

TCAATTTGAGAGCTGGAAGAA

0.61

0.70

Vvi-miRC16

ATATTGGTAAATGAATGTTCG

0.00

1.40

Vvi-miRC17

AATTTCTTATGTTCATGATTG

0.00

0.79

Vvi-miRC18

AAGAGCAGTTGAACTGAAGCA

0.70

1.57

Vvi-miRC19

TCTGTCGCAGGAGAGATGATGC

1.66

4.19

Vvi-miRC20

GGAATGGGCTGATTGGGATA

2551.57

760.03

Vvi-miRC20*

TTCCCAATGCCGCCCATTCCAA

94.07

208.55

Vvi-miRC21

CCAAGAGGGTGGAGTTCAGAT

0.00

1.48

Vvi-miRC21*

CTGAACTCTCTCCCTCATGGCC

0.00

0.87

Vvi-miRC22

CTAAATTGCTTCGGGTCCTGC

0.00

6.63

Vvi-miRC22*

AGGAGATGAGGTATGTTTACAT

0.00

5.93

Vvi-miRC23

AAACATGAGTCTGGACCTTGA

0.00

0.79

Vvi-miRC24

AAACATGAGTCTGGACCTTGA

0.00

0.79

Vvi-miRC25

TCTGTTTTCACTCTCATTAAG

0.00

1.13

Vvi-miRC25*

TAGTGAGAATGAGTTGGGGAAG

0.00

0.09

Vvi-miRC26

TCGGAGAAGTGTGATGTGTAT

0.00

0.70

Vvi-miRC27

ATACCATGTGGAAAAGAGGAATC

6.72

5.85

Vvi-miRC28

ATTGGCAGAATATTCAAGGTTT

0.44

0.87

Vvi-miRC29

TTATTAGGAGGACATTTAGGTAT

2.88

3.49

Vvi-miRC30

TGCGGGTGGAAGAGAAGGAAG

5.67

3.49

Vvi-miRC31

TTCCTGCGGTTTCTCGGCGAC

0.96

0.96

Vvi-miRC32

TTTTCCTATGATTTCTTGGCA

0.87

0.79

Vvi-miRC32*

CTGGGAAAGCGTGGGAAAACA

0.00

0.09

Vvi-miRC33

TTCCTATCGTTCCCGGGATTT

0.00

1.22

Vvi-miRC34

TGACCGGCTCTTATCTCTCATG

1.48

3.93

Vvi-miRC34*

TGAAGATAAAGAGTCTCGTCTGG

0.35

0.09

Vvi-miRC35

GGAATGGATGGCATGGGAACCA

0.52

0.52

Vvi-miRC36

TGAGTAGTGGACTATCGCATG

14.57

1728.01

Vvi-miRC36*

TGAGATAAGTCTGCTGCTCCAT

0.61

94.76

Vvi-miRC37

TGGATGCATGTAGCTTGTCAA

16.06

0.87

Vvi-miRC37*

GACAAGTTACATACATCCAAG

1.05

0.17

Vvi-miRC38

TCCTTCGGCGTCGGCAAATCC

1.75

1.22

Vvi-miRC39

AAGGGTTTCTCACAGAGTTTA

0.00

0.79

Vvi-miRC39*

AGCTCTGTTGGACTCTCTTTG

0.00

0.17

Vvi-miRC40

GAGGAGAATGTAGTGGGGTTA

0.52

0.44

Vvi-miRC41

CTTTGATCAGATATTGGATTG

0.00

1.40

Vvi-miRC41*

AGCAGAGTTTGATAGAGGGC

0.00

0.09

Vvi-miRC42

AATGACATGAGTTGGAACTAA

0.00

0.87

Vvi-miRC43

GTTGGAAGCCGGTGGGGGACC

4389.70

425.65

Vvi-miRC44

GTTGGAAGCCGGTGGGGGACC

4389.70

425.65

Vvi-miRC45

GTTGGAAGCCGGTGGGGGACC

4389.70

425.65

Vvi-miRC46

GTTGGAAGTCGGTGGGGGAAC

1990.92

272.69

Vvi-miRC47

GGCGATTGTAAATATGGGTAA

3.75

1.13

Vvi-miRC48

TCTAGATTTGGAAGTAGGTCA

0.70

0.44

Vvi-miRC49

GTTGGAAGTCGGTGGGGGACC

1089.01

72.95

Vvi-miRC50

GTTGGAAGCCGGTGGGGGACC

4389.70

425.65

Vvi-miRC51

TGGGCTTGTGGAGAAGAAAGTGA

0.96

0.52

Vvi-miRC52

CATGGGCGGTTTGGTAAGAGG

2805.93

1401.92

Vvi-miRC52*

TCTTACCAACACCTCCCATTCC

140.49

198.43

Vvi-miRC53

GGTATGGGAGGATTGGGGAGA

1305.32

437.43

Vvi-miRC53*

TTCCCAAGACCCCCCATGCCAA

62.48

327.23

Vvi-miRC54

TCATACCTCGATCTTCGGTTTC

0.00

0.70

Vvi-miRC54*

AATCTGAGATCGAGAATGAAA

0.00

0.09

Vvi-miRC55

ATTCGAACTCAAGACTAAGGT

0.00

41.54

Vvi-miRC56

GAAGCTCTTGAGGGGGACTG

378.18

60.38

Vvi-miRC56*

ACTCTCCCTCAAGGGCTTCTG

12.13

1.31

Vvi-miRC57

AGGTGTAGATGCAAGTGCAGA

0.00

1.05

Vvi-miRC58

TTTAATTTACTAGAGATCTCT

1.13

1.40

Vvi-miRC59

GGAGTGAAATTGCAGTGACGG

0.00

1.13

Vvi-miRC60

TCAGCAGGAATTGGACCAGAA

2.88

3.75

Vvi-miRC61

ACAGTAGGAAATTGAAAGAGA

0.00

0.70

Vvi-miRC61*

TCTTTCATTTTCCTACTTTTT

0.00

0.52

Vvi-miRC62

AAAGGCGAAGAAAAAGAAGATA

1.75

0.79

Vvi-miRC63

AATATGGAGGACTGTGTTCTT

0.61

1.75

Vvi-miRC63*

GAACTCAGTTCCGGTACCATCTTCA

0.09

0.09

Vvi-miRC64

TTGGATTCGCGCACAAACTCG

0.00

1.13

Vvi-miRC65

TTGGATTCGCGCACAAACTCG

0.00

1.13

Vvi-miRC66

CAGCAGTTGCTATTGTGGTTG

0.87

8.38

Vvi-miRC67

AGAAGAGAGAGAGTACAGCTA

1.31

9.60

Vvi-miRC68

TGGTACCAGGAGGGCAACTGTC

0.00

1.05

Vvi-miRC68*

TGTTGCCCTCCTGGTACCATC

0.00

0.09

Vvi-miRC69

TCAAGGGTCGAACGGCTTTGC

1.31

2.36

Vvi-miRC70

TTATGTGAGTGTTCGGCAAATC

0.79

2.62

Vvi-miRC71

TTAGATGATCATCAACAAACA

436.74

517.54

Vvi-miRC71*

TTTTGTTGCTGGTCATCTAGTC

2.09

3.05

Vvi-miRC72

TGCTTATTAGGTCTGCTGGCA

0.00

0.61

Vvi-miRC73

TCAAAAGAGAAAATGTGGATG

0.52

0.79

Vvi-miRC73*

TCCATCTTCTCTCTTTTTACA

0.00

0.09

Vvi-miRC74

TCGCAGGAGAGATGACGCCGT

52.97

110.21

Vvi-miRC74*

AGCATCATTTCTCCTGCATAG

1.13

4.28

Vvi-miRC75

ATATTAGCAGCTGAGAACACA

1.40

0.00

Vvi-miRC76

CAGGACTGGCAGTGATGGTTA

1.13

0.00

Vvi-miRC77

GTGTTTTGCAGGATCAGACGG

0.70

0.00

Vvi-miRC78

TGGCTGAGAACTTGATGGTTA

2.71

0.00

Vvi-miRC79

TTCAAGTCAAAGTCGAACAAG

0.87

0.00

Vvi-miRC80

AGCGAAGTAGTTGTAGGGCTT

0.96

0.00

Vvi-miRC81

TTCGGAGGGAACTGACCGGTT

0.70

0.00

Vvi-miRC82

TGCCAAGAAGCACATTCCTCC

16.84

0.00

Vvi-miRC82*

AGGAATGTGCTTCTTGGCATA

0.09

0.00

Vvi-miRC83

CAAGTGTGGGATTTTGGGTGGCT

0.52

0.00

Vvi-miRC84

GCAGCATCATGAAGATTCACA

0.52

0.00

Vvi-miRC84*

GGAATCTTGATGATGCTGCAT

0.17

0.00

Vvi-miRC85

AGGTGCAGGTGAAGGTGCAGA

1.75

0.00

Vvi-miRC85*

TGCATTTGCACCTGCACCTTA

0.96

0.00

Vvi-miRC86

GTAGCATCATCAAGATTCACA

1.66

0.00

Vvi-miRC87

GGAATGTTGTCTGGCTCGAGGT

0.70

0.00

Vvi-miRC88

ATGTATTTGAGGGAAAGCAAA

0.44

0.00

Vvi-miRC88*

TGTTTTCCCTCAAAAACATGT

0.09

0.00

Vvi-miRC89

CTGCGGGTGGAAAAGGATTAGGC

6.81

0.00

Vvi-miRC89*

CTCATCCTTTTCCATCGGCAGCA

0.35

0.00

Vvi-miRC90

TCTCAGCAACCAAGTAGAGCC

5.93

0.00

Notes: ,,▲ ,, denote up-regulated, down-regulated, induced, repressed, un-affected, respectively; the symbol * denotes the complementary strands of miRNAs.

Expression patterns of Vvi-miRNAs responsive to exogenous GA3 during grapevine berry development

Spatiotemporal expression of grapevine miRNAs could not only provide clues to their physiological functions, but also give fundamental evidence supporting the existence of the miRNAs in grapevine. In this study, 53 Vvi-miRNAs (27 conserved Vvi-miRNAs and 26 novel candidate Vvi-miRNAs) detected in grapevine berries treated with GA3 were subjected to qRT-PCR expression analysis as described in Section 2. This could also be applied to the analysis of the degree of response of these Vvi-miRNAs to GA3 treatments. We screened for the expression profiles of miRNAs responsive to GA3 treatments in the diverse stages of grapevine berries by qRT-PCR. The results showed that the expression levels of 15 Vvi-miRNAs (Vvi-miR169d, Vvi-miR319c, Vvi-miR393a, Vvi-miR396a, Vvi-miR398a, Vvi-miR399a, Vvi-miRC03, Vvi-miRC04, Vvi-miRC05, Vvi-miRC08, Vvi-miRC10, Vvi-miRC13, Vvi-miRC19, Vvi-miRC26 and Vvi-miRC37) were up-regulated by GA3, while 13 (Vvi-miR167a, Vvi-miR171d, Vvi-miR395f, Vvi-miR397a, Vvi-miR408, Vvi-miR482, Vvi-miRC06, Vvi-miRC14, Vvi-miRC15, Vvi-miRC24, Vvi-miRC27, Vvi-miRC30, Vvi-miRC38) were down-regulated by GA3, and seven (Vvi-miR156d, Vvi-miR166h, Vvi-miR390, Vvi-miR477, Vvi-miRC23, Vvi-miRC29, and Vvi-miRC36) were un-affected by GA3 (see Figure 4).
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig4_HTML.jpg
Figure 4

Expression patterns of miRNAs in grapevine berries underdifferent GA 3 treatments and control.

Further analysis of the expression results of 16 known Vvi-miRNAs responsive to GA3 both from qRT-PCR and high throughput sequencing revealed that the qRT-PCR expressions of 11 were consistent with the results from high throughput sequencing, which could not only demonstrated the reliability of these two technologies, but confirm the characteristics of these known GA3 responsive Vvi-miRNAs. On the other hand, it was discernible that the expression analysis results of 18 novel GA3 responsive Vvi-miRNAs from both qRT-PCR and high throughput sequencing were not of the same phenomenon, for only three (Vvi-miRC19, Vvi-miRC14 and Vvi-miRC29) was in the same way. This discrepancy in behavior of conserved and novel Vvi-miRNAs requires further research; while the consistency of the expression results, for the most conserved and a few novel Vvi-miRNAs, from the assays of the qRT-PCR and high throughput may provide some evidence supporting the fact about these Vvi-miRNAs responsive to GA3.

Characterization of potential target genes for novel Vvi-miRNAs responsive to GA3

To further comprehend the functions of these newly identified species-specific Vvi-miRNAs, it was essential to search for their target genes. Following the rules suggested by Schwab et al. (2005) [39], we searched the grapevine transcript database (http://​www.​genoscope.​cns.​fr/​spip), and predicted a total of 117 putative target genes for 29 novel Vvi-miRNAs (Additional file 3). Among the 29 novel Vvi-miRNAs, 11 had multiple target genes, as exemplified by Vvi-miRC03 with 19 target genes, indicating these Vvi-miRNAs might possess comprehensive functions in grapevine. Based on orthologous functional annotation in other plants, these target genes seemed to be functionally involved in glucose metabolism (DNA glycosylase domain-containing protein), aromatic substance biosynthesis in berry (lipoxygenase, nigralipoxygenase), signal transduction (receptor-like protein kinase, serine-threonine protein kinase, protein phosphatase), stress resistance (ankyrin repeat-containing protein, disease resistance protein,cc-nbs-lrrresistance protein, domain-containing disease resistance protein, leucine-rich repeat receptor-like protein kinase), etc. (Figure 5; Additional file 3). We also noted that there were a large number of potential target genes with unknown functions for novel Vvi-miRNAs, especially those responsive to GA3 (Additional file 3). More in depth investigation on their functions would be essential for thorough understanding of the mechanisms of grapevine flower and fruit development and of the formation of berry quality.
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig5_HTML.jpg
Figure 5

Functional classification of target genes for novel Vv-miRNAs responsive to exogenous GA 3 .

Verification of potential Vvi-miRNA target genes using 5’-RLM-RACE

To verify the nature of potential miRNA targets and to study the Vvi-miRNAs’ regulation on their target genes, a modified RLM-RACE experiment was set up and used to map the cleavage sites in four predicted Vvi-miRNA target genes. Results showed that the cleavage sites of these four miRNA target genes GSVIVT01000639001, GSVIVT01026728001, GSVIVT01037667001 and GSVIVT01037667001 for Vvi-miRC15, Vvi-miRC23, Vvi-miRC60 and Vvi-miRC72 in this study is at the nucleotide that pairs with the 9th and/or 10th and/or 11th nucleotide of the corresponding miRNAs (Figure 6), consistent with previous related reports [7, 16, 18, 19, 40]. The GSVIVT01000639001, GSVIVT01026728001, GSVIVT01037667001 and GSVIVT01037667001 were confirmed as the true targets of Vvi-miR015, Vvi-miR023, Vvi-miR060 andVvi-miR072, respectively. Functional analysis indicated that GSVIVT01000639001, GSVIVT01026728001, GSVIVT01037667001 and GSVIVT01037667001 could be of cc-nbs-lrr resistance protein, nbs-lrrresistance protein, leucine-rich repeat family protein, and lipoxygenase (Additional file 3).
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig6_HTML.jpg
Figure 6

Verification of target genes for Vvi-miRNAs by RLM-5’-RACE.

Discussion

To verify the hypothesis that miRNAs play some role inregulating plant response to GA3[28], two small RNA libraries from grapevine berries treated with GA3 and without GA3 were constructed and used for high-throughput sequencing of sRNAs, from which a total of 212 Vvi-miRNAs (both known and novel), with 137 of them being firstly found to be responsive to GA3 in grapevine. Further comparison of our dataset from this work to Vvi-miRNAs reported earlier by us [20] revealed that since the grapevine materials used in these studies was the same grapevine cultivar, most of the Vvi-miRNAs could be observed in these two studies, while only a few members (such as Vvi-miR171f, Vvi-miR171h) could be discovered in one of both studies, which may be derived from the differences in the development stages of grapevine materials used in these studies or GA3 induced/depressed Vvi-miRNAs in this work.

The breakthroughs in sequencing technology have provided the most powerful tool for miRNA discovery, and one of the advantages of the thorough approach is its ability to reveal novel miRNAs. In this work, a large number of novel candidate Vvi-miRNAs were uncovered, with the miRNAs* for some novel Vvi-miRNAs being detected too. The identification of miRNAs*of the candidate miRNAs provides convincing evidence for consideration of these Vvi-miRNAs as authentic [38]. Importantly, the expression levels of some novel Vvi-miRNAs and their miRNAs* under GA3 treatments had much more diverse variation compared to the control. The best examples of this phenomenon are Vvi-miRC20/Vvi-miRC20*, Vvi-miRC34/Vvi-miRC34*, Vvi-miRC52/Vvi-miR C52* and Vvi-miRC53/Vvi-miRC53* (Figure 7). The expressions of Vvi-miRC20 and Vvi-miRC34 were up-regulated in GA3 treatments compared to the control, while the expression of their miRNAs* was down-regulated. On the contrary, the expressions of Vvi-miRC52 and Vvi-miRC53 were down-regulated in GA3 treatments, while those of their miRNAs* were up-regulated (Figure 7). The reasons for these discrepancies have not been clearly elucidated. The drastic variation in expression levels of the Vvi-miRNA* under GA3 treatments could indicate these miRNAs* were important regulatory genes like Vvi-miRNAs [41].
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-15-111/MediaObjects/12864_2013_Article_5769_Fig7_HTML.jpg
Figure 7

Comparison of expression modes for Vv-miRNAs and Vv-miRNAs*.

From high throughput sequencing and qRT-PCR analysis, it was further revealed that the conserve Vvi-miRNAs responsive to GA3 had the higher consistency between these two assays, while the novel ones showed some distinct discrepancy. This might be derived from the fact that the conserved Vvi-miRNAs possessed the higher conservation of development and function, while the novel ones had high specificity. Other, the samples used in the high throughput sequencing were the mixed materials from grapevine berries of several development stages, while those used for the qRT-PCR were of three stages berries (1 week after flowering (WAF), 5 WAF, 9 WAF). These could be the reasons explaining the expression levels of novel Vvi-miRNAs from qRT-PCR and high throughput sequencing had more apparent differences than those of conserved Vvi-miRNAs. In addition, the predication of potential target genes for novel Vvi-miRNAs responsive to exogenous GA3 and functional annotations of their orthologous target genes in other plants revealed that 20 genes were related to stress resistance. Whether or how these GA3 responsive novel Vvi-miRNAs are involved in the regulation of stress resistance can call for further research. The functions of one-third of the novel Vvi-miRNAs were unknown, indicating that more studies need to be performed on these novel miRNAs to elucidate their functions in the growth of grapevine.

Conclusions

Deep sequencing of short RNAs from grapevine berries in GA3 treatment and the control identified 137 GA3-responsive miRNAs, of which 28 exhibited different expression profiles of response to GA3 in the diverse developmental stages of grapevine berries. These Vvi-miRNAs identified might be involved in the grapevine berry development and response to various environments.

Methods

Plant material

Mixed samples of young berries (one week after flowering, WAF1) large berries (five week after flowering, WAF5), and old berries(nine week after flowering, WAF9) treated with 50 mg/lGA3, were collected in 2011 from four-year old ‘Summer Black’ grapevine (hybrids of V. vinifera and V. labrusca) trees grown under common field conditions at the Nanjing Agricultural University fruit farm, Nanjing, China. Each type of samples had three replicates during deep sequencing and qRT-PCR. All the samples were immediately frozen in liquid nitrogen and stored at −80°C until use.

Small RNA library construction and sequencing

Mixed Summer Black’ grapevine young berries (one week after flowering), large berries (five week after flowering after flowering), and old berries (nine week after flowering) treated with GA3, wereusedforRNAextraction. The total RNA samples were first extracted usingour modified CTAB method [20]. Isolation of small RNAs and preparation of small RNA libraries were performed based on the procedure of Wang et al. (2011) [20]. sRNAs were first separated from the total RNA by size fractionation with 15% TBE urea polyacrylamide gel (TBU) and small RNA regions correspondingto the 18–30 nucleotide bands in the marker lane were excised and recovered. The 18–30 nt small RNAs were 5’ and 3’ RNA adapter-ligated by T4 RNA ligase and at each step, length validated and purified by TBU electrophoretic separation. The adapter-ligated smallRNA was subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen) and PCR amplified using primers that annealed to the ends of the adapters. The amplified cDNA constructs were purified and recovered. 18 ng cDNA was loaded into the Illumina 1 G Genome Analyzer for sequencing.

Bioinformatics analysis and identification of Vvi-miRNA

To identify conserved and potential Vvi-miRNAs in grapevine, the raw sequences were processed as described by Sunkaret al. (2005) [8]. All sRNAs sequences from 18nt to 30nt obtained were removed from the vector sequences, then the modified sequences were further subjected to removal of rRNA, tRNA, snRNA, snoRNA and those containing the polyA tails, and finally the remaining sequences were compared against known plant Vvi-miRNAs in the miRBase [33]. Only the high matching (0-3mismatches) sequences were considered as conserved Vvi-miRNAs. To study potential Vvi-miRNAs precursor sequences, all sRNAs from grapevine were aligned against the grapevine genome and then the miRNA candidates were processed by miRCat (http://​srna-tools.​cmp.​uea.​ac.​uk/​) [33], using default parameters, to generate the secondary structures (Additional file 1).

qRT-PCR validation of miRNA expression

The template for RT-PCR was the miRNA-enriched library mentioned above. To amplify the Vvi-miRNAs from the reverse transcribed cDNAs, we used the Vvi-miRNA precise sequences as the forward primers and the mirRacer 3’Primer as the reverse primer [9] (Additional file 3). RT-PCR was conducted with the Rotor-Gene 3000 (Corbett Robotics, Australia) and the Rotor-Gene software version 6.1. For each reaction, 1 μL of diluted cDNA (equivalent to about 100 pg of total RNA) was mixed with 10 μL of 2X SYBR green reaction mix (SYBR® Green qRT-PCR Master Mix; Toyobo, Osaka, Japan), and 5 pmol each of the forward and the reverse primers were added in a final volume of 20 μL. The conditions for the PCR amplification were as follows: polymerase activation at 95°C for 1 min, then 95°C for 1 min, followed by 50 cycles of 95°C for 15 s, 95°C for 15 s, 60°C for 20 s, and 72°C for 20 s. The comparative quantification procedure was used to determine relative expression levels, and the homologous genes of the Arabidopsis 5.8S rRNA in grapevine berries was previously used as a reference gene in the qPCR detection of miRNAs in Arabidopsis[41]. The data were analyzed with an R2 above 0.998 using the LinRegPCR program [42].

Prediction of potential target mRNAs for Vvi-miRNAs

Target predictions were performed based on methods described by Schwab et al.(2005) [39]. Putative Vvi-miRNAs were first blasted against the grapevine unigene database on the Genoscope (http://​www.​genoscope.​cns.​fr/​). BLASTn hits possessing less than four mismatches were chosen as the candidate targets, and then BLASTx was used to obtain their putative functions. The sequences of predicted targets and their functions are shown in Additional file 4.

Data access

The sRNA sequence data from this study have been submitted to Gene Expression Omnibus (GEO) under accession No. at website: http://​www.​ncbi.​nlm.​nih.​gov/​geo/​query/​acc.​cgi?​token=​dlihnquimuscezm&​acc=​GSE3973.

Declarations

Acknowledgements

This research was supported by Project Funded by the Natural Science Foundation of China (NSFC) (No. 31301759), China Postdoctoral Science Foundation(2013 M531373), Postdoctoral Science Foundation of Jiangsu Province(1301116C), the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), the National Science Foundation of China (No. 60901053), and the Nanjing Agricultural University Youth Science and Technology Innovation Fund (KJ2013013).

Authors’ Affiliations

(1)
College of Horticulture, Nanjing Agricultural University
(2)
Institute of Pomology

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© Han et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.

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