7 publications mentioning ppe-MIR166e

Open access articles that are associated with the species Prunus persica and mention the gene name MIR166e. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1

Moreover, TAS3 trans-acting short-interfering RNAs, which are targeted by miR390, can regulate miR166 expression that may control auxin flow via its target HD-ZIP.

The expression levels of miR171, miR168, miR408a, miR398 and miR408b were significantly upregulated in mesocarp in NAA -treated samples compared to the control fruits, whereas those of miR156, miR160, miR166, miR167, miR390, miR393, miR482, miR535 and miR2118 were downregulated following NAA treatment.

The results of real-time PCR experiments revealed the increased expression levels of miR171, miR168, miR408a, miR398 and miR408b, as well as the reduced expression levels of miR166, miR167, miR160, miR156, miR2118, miR535, miR390, miR482 and miR393 in the peach fruit after NAA treatment, respectively, suggesting the functional divergence of microRNAs in the regulation of fruit development.

miR160, miR162, miR164d, miR396b, miR408a were upregulated under NAA treatment, whereas miR166 was downregulated.

The experimental verification results were consistent with our high throughput sequencing datasets and also with previous studies that demonstrated the critical roles of miR160, miR166, miR167, miR390 and miR393 and their targeted genes in auxin signaling pathways.

Furthermore, we found that miR165/miR166 can target REV, ATHB8, ATHB14 and ATHB15 in the peach fruit with high prediction confidence (Figure 3).

Together, these studies support an direct/indirect association between miR166 and auxin [35, 36].

We also identified miR165/miR166 cleavage sites in ATHB8, ATHB14 and ATHB15 in the peach fruit under control conditions.

Of these, ten (83%) were conserved peach miRNAs, including miR160, miR162, miR164d, miR166, miR168, miR396a, miR396b, miR398, miR408a and miR482 (Table S1).

Among these miRNAs, miR160, miR166, miR167, miR390 and miR393 are known to play important roles in auxin signaling pathways [14, 16, 17, 18, 35, 36].

2

It should be noted that expression of miR165/166 was induced in leaf but inhibited in root tissues of H. vulgare after dehydration stress [9] while miR166 was down-regulated in both leaf and root tissues of P. persica.

As for miR166, although its expression was down-regulated in root tissues in response to drought, the expression level of miR166 were not changed between control and drought stressed leaves of peach (Figure 6).

Up-regulation of any miRNA expression levels was considered a positive value while negative values indicate down-regulation For miR156, miR164, miR166, miR168, miR169, miR171 and miR395, the miRNA stem-loop reverse transcription reaction was performed in a volume of 10 µL containing 2, 20, and 200 ng of total RNA samples of leaf and root samples (1 µL), 0.5 µL 10 mM dNTP mix, 1 µL stem-loop RT primer (1 µM) and 7.5 µL nuclease free water.

The target transcripts of Ppe-mir156, Ppe-mir166, Ppe-mir168, Ppe-mir169, Ppe-mir171, and Ppe-mir395 were obtained using psRNATarget (user-submitted transcripts and miRNA option) and BlastN algoritms.

This result is consistent with the previous finding that the miR166 was downregulated in roots of barley after drought stress [71].

Although the measured expression level of the miR166 did not change in leaf tissue of peach under drought stress, the qPCR results indicate that its expression level decreased in root tissue after treatment (Figure 6).

qRT-PCR was also used for detection and quantification of predicted targets of six drougt-responsive miRNAs (miR156, miR164, miR166, miR169, miR171 and miR395).

Among them, drought responsive miRNAs (miR156, miR164, miR166, miR168, miR169, miR171, and miR395) were detected and their expression levels were measured by qRT-PCR.

Among the conserved miRNAs, total reads of miR535, miR157, miR166, miR156 and miR408 accounted for vast majority of total miRNAs; LC (82,49%), LS (89,09%), RC (75,54%) and RS (55,02%).

3

miR164, miR165, miR166, miR172 and miR393 exhibited a similar phloem-specific expression pattern, i. e., they were highly expressed only in phloem tissues, whereas their expression level was relatively undetectable or very weak in the leaves and fruit at different stages.

Additionally, the four target genes of miR166 in peach also have a high level of sequence homology with those in Arabidopsis [67].

The most abundantly expressed miRNA family was miR156, which is represented by more than 1,910,151 reads (S2 Table), followed by miR166 with more than 39,453 reads.

Remarkably, we found that miR166 in peach fruit has an identical miRNA sequence, the same target gene number, the same miRNA -binding sites, and identical cleavage sites as those of miR166 in Arabidopsis [67].

The miR166 family is wi dely considered to have highly conserved targets that encode proteins of the HD-ZIP family in a wide range of plant species, such as olive [47], citrus [62], and cotton [32].

Remarkably, the degradome sequencing results verified that four HD-ZIP III subfamily genes (HB8, HB14, HB15, and REV), which were predicted but had not been previously validated, were verified to be cleaved by the miR166 family of peach fruit at nucleotides 565, 574, 589, and 615, respectively.

For example, miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR172, miR396, and miR397 are perfectly identical to the corresponding miRNAs in three other plant species (Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa) (S3 Table).

miR164, miR166, and miR397 are very similar to the corresponding miRNAs in four plant species, including Brassica napus and Vitis vinifera.

miR156, miR157, and miR166 are the three most abundant known miRNAs in the peach fruit library and are also found in abundance in most plant species [23, 58] (S2 Table).

4

The expression of 8 conserved (miR166, miR168, miR319, miR394, miR399, miR827, miR894 and miR5139) and six novel miRNAs (miRC1, miRC14, miRC16, miRC112, miRC179 and miRC181) showed no significant change in different tissues (Figs. 5A and 5B).

The miR166, miR156 and miR157 families were the largest, with 15, 11 and 10 members, respectively, whereas 14 miRNA families had only a single member (Fig. 2A).

Among the miRNA families in peach, miR156, miR159, miR160, miR166, miR171, miR319, miR390 and miR396 showed a high conservation in plants, indicating that these 12 peach miRNA families are ancient.

The abundance of miRNA families also varied drastically: miR157, miR166 and miR156 were most frequently represented in the library, with 154,908, 79,863 and 73,043 reads, whereas miR172, miR167, miR168 and miR396 were moderately abundant in the library with 6,411, 5,280, 4,373 and 2,500 copies.

5

miR156, miR159, miR166, miR172, miR390, miR396, and miR5021 are the most expressed families in bud tissues.

Most of conserved families common to Arabidopsis and peach (miR156, miR159, miR160, miR164, miR166, miR171, miR172, miR319, miR390, miR395, and miR396) did not show significant size variation (Figure 4).

6

The expression levels of a few miRNA families, such as miR166, miR1511 and miR398, were evidentially high in both libraries.

7

In some cases no mismatches were reported with the conserved sequences present in miRBase (e. g., miR403, miR394, miR166, miR156) while in some others mismatches were present and related to differences in the sequence and/or in its length.