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24 publications mentioning sly-MIR167b

Open access articles that are associated with the species Solanum lycopersicum and mention the gene name MIR167b. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 126
Moreover, RNA seq analysis of very young flower buds in control and transgenic MIR167 lines showed that SpARF6A and SpARF8B were most significantly down-regulated (3 and 1.7-fold respectively), whereas SpARF8A was not down-regulated in these tissues (Supplementary Table S2 available at JXB online). [score:7]
As miR167 regulates ARF6 and ARF8 genes in both species, we expected that plasmid pB7WG2-MIR167a, which expresses Arabidopsis MIR167a under the control of the CaMV 35S promoter (Wu et al., 2006), would target tomato SpARF6 and SpARF8 genes. [score:6]
It has been experimentally determined in Arabidopsis that miRNA167 regulates expression of ARF6 and ARF8 and that overexpression of the miR167 precursor gene MIR167a phenocopies the arf6 arf8 double mutant (Ru et al., 2006; Wu et al., 2006). [score:6]
Therefore, the data demonstrated that increased miR167 expression in the transgenic tomato plants led to reduced expression of ARF6 and ARF8 resulting in altered developmental phenotypes. [score:6]
of RNA isolated from anthesis-stage flowers showed that the lines with strong phenotypes had a significant reduction in the expression of SpARF6A and SpARF8A/B (Fig. 5A) as well as increased miR167 expression over endogenous levels (Fig. 5B). [score:5]
b, The 185 genes that were differentially expressed both owing to overexpression of MIR167 in tomato and in the Arabidopsis arf6 arf8 double mutant. [score:5]
Cultivated tomato miR167 was initially identified in a conventional small RNA cloning approach, and its expression pattern was developmentally regulated based on small RNA gel blot (Itaya et al., 2008) and deep sequencing (http://smallrna. [score:5]
The Arabidopsis miR167 regulates the expression of AtARF6 and AtARF8. [score:4]
Identification of MIR167 in tomatoThe Arabidopsis miR167 regulates the expression of AtARF6 and AtARF8. [score:4]
The putative importance of ARF6 and ARF8 in plant development is suggested by the observation that they are probably targets of microRNA167 (miR167) in all analysed plants (Axtell and Bartel, 2005; Oh et al., 2008; Remington et al., 2004; Xing et al., 2011; Yang et al., 2006). [score:4]
Tomato provides an excellent mo del to test the potentially conserved role of ARF6 and ARF8 in flower development as well as their regulation by miR167. [score:3]
We attempted to find and validate additional targets of miR167 in tomato, which are listed in the miSolRNA database (www. [score:3]
Fig. 5. Gene expression analysis in MIR167 transgenic and wild-type tomato flower and floral organs. [score:3]
The results indicated that these tomato genes are targets of miR167, as are the orthologous ARF6 and ARF8 genes in Arabidopsis. [score:3]
a, All 687 differentially expressed genes between wild-type tomato and MIR167 transgenic lines. [score:3]
Genome biology 14, R36 23618408 Kinoshita N Wang H Kasahara H Liu J Macpherson C Machida Y Kamiya Y Hannah MA Chua NH 2012 IAA-Ala Resistant3, an evolutionarily conserved target of miR167, mediates Arabidopsis root architecture changes during high osmotic stress. [score:3]
In addition to targeting ARF6 and ARF8, it was recently shown that miR167 also guides cleavage of IAA-Ala Resistant 3 (IAR3) transcripts in Arabidopsis (Kinoshita et al., 2012). [score:3]
However, none of them was validated as a likely target of miR167 in the SoMART degradome RNA library database. [score:3]
In addition to SlARF6A and SlARF8A/B, three putative candidate genes (Solyc04g077220, Solyc04g073990, and Solyc11g011980) could be targeted by miR167. [score:3]
IAR3 is important for lateral root growth and thus, further studies on tomato root samples may help clarify whether miR167 could mediate regulation of tomato IAR3. [score:2]
Differentially expressed genes in MIR167 lines compared with LA1589 control in two comparisons. [score:2]
The regulation of ARF6 and ARF8 by miR167 is likely to be highly conserved. [score:2]
Thus far, there is no evidence that miR167 in tomato regulates guided cleavage of any gene other than ARF6A, ARF8A, and ARF8B, consistent with findings from another study (Karlova et al., 2013). [score:2]
Thus, we concluded that tomato has four MIR167 genes that produce miR167, which regulates SlARF6 and SlARF8 genes. [score:2]
Thus, regulation of ARF6 and ARF8 by the miR167 family is conserved between Solanaceae and Brassicaceae. [score:2]
edu) was employed to validate miR167 -mediated regulation of SlARF6A, SlARF8A, and SlARF8B. [score:2]
of MIR167 transgenic lines. [score:1]
In parallel, LA1589 pollen was used to pollinate MIR167-transgenic flowers. [score:1]
The genome sequences surrounding these four putative genes share sequence homology to Ath-MIR167a and Sly-MIR167. [score:1]
Flower buds of LA1589 were emasculated one day before anthesis and pollinated using MIR167- transgenic pollen. [score:1]
Together, this suggests the presence of four MIR167 genes encoding miR167 precursors (Supplementary Fig. S1B available at JXB online). [score:1]
However, we were unable to validate these as bona fide MIR167 genes based on the absence of a strongly supported predicted stem-loop precursor structure using in silico folding analysis (Supplementary Fig. S1C available at JXB online), extremely low reads in small RNA deep sequencing (fewer than 10 reads), and the lack of miRNA* sequences for these candidate genes in deep sequencing data (http://smallrna. [score:1]
Mapped Sly-miR167 -mediated cleaved SlARF6A/SlARF8A/SlARF8B RNAs and the predicted folding of the Sly-miR167 genes. [score:1]
Floral organ lengths of MIR167 and LA1589 control flowers. [score:1]
By using the SoMART degradome RNA library analysis, we demonstrate that miR167 guides the cleavage of SlARF6A, SlARF8A, and SlARF8B transcripts in cultivated tomato, consistent with a previous report (Moxon et al., 2008). [score:1]
We employed the newly developed online software tool SoMART and available small RNA sequencing data from VF36 and Microtom (Li et al., 2012) to evaluate whether SlARF6A and SlARF8A were also targets of miR167. [score:1]
For the hormone experiments, selected floral buds were tagged before the petals in the MIR167- transgenic lines turned white, which corresponded to 1–2 days before anthesis in wild-type plants. [score:1]
No significant differences were found in MIR167 transgenics treated with or without methyl jasmonate. [score:1]
In MIR167, the second inflorescence forms either after 3 or 4 internodes from the first inflorescence. [score:1]
Cross-sections of style and ovary showed similar cellular organization in wild type and transgenic lines, except possibly for the placenta, which seemed smaller in the MIR167 plants (Fig. S3D–M). [score:1]
Fig. 6. SEM of floral organs from MIR167 and control tomato plants. [score:1]
miR167 -mediated cleavage products were found for SlARF6A, SlARF8A, and SlARF8B (Supplementary Fig. S1A available at JXB online). [score:1]
We also found the corresponding miR167* sequences (from the other strand of the stem-loop precursors) for these four genes in the small RNA deep sequencing database (http://smallrna. [score:1]
Identification of MIR167 in tomato. [score:1]
Antisense miR167 (5′-TAGATCATGCTGGCAGCTTCA-3′) and miR166 (5′-GGGGAATGAAGCCTGGTCCGA-3′) probes were prepared by end-labelling with T4-polynucleotide kinase (New England Biolabs, Ipswich MA, USA) in the presence of γ [32]P-ATP. [score:1]
Fig. 4. Phenotypes of the MIR167 transgenic tomato plants. [score:1]
Close-up of the corresponding style regions boxed in white are shown in (F–H) for MIR167 and (N–P) for control. [score:1]
Style morphology of the MIR167 transgenic (E–H) and wild-type (M–P) plants. [score:1]
Pollen tube growth and gynoecium structure in MIR167 and the wild-type LA1589. [score:1]
Thus, we renamed the registered Sly-MIR167 as Sly-MIR167a-1 and the additional three genes as Sly-MIR167a-2, Sly-MIR167a-3, and Sly-MIR167a-4. The predicted precursor structures of these four Sly-MIR167 genes are shown in Supplementary Figure S1B available at JXB online. [score:1]
Identification of ARF6, ARF8, and MIR167 genomic sequences from tomatoBy using the DNA -binding domain of Arabidopsis ARF6 and 8 proteins (defined as amino acids 1 to ~350 by Ulmasov et al., 1999b) as query sequences, four cultivated tomato genes were identified that share a likely common ancestor: SlARF6A (Solyc00g196060), SlARF6B (solyc07g043610/043620), SlARF8A (Solyc03g031970), and SlARF8B (Solyc02g037530). [score:1]
The tomato genome has two additional sequences with high similarity to mature miR167. [score:1]
Previously, tomato miR167 -mediated cleavage of SlARF8B was confirmed by 5′-RACE (Moxon et al., 2008). [score:1]
Mature Sly-miR167 shares an identical sequence with the Arabidopsis miR167. [score:1]
miR167 is found in seed-producing plants from gymnosperms to flowering plants (Axtell and Bartel, 2005). [score:1]
For MIR167, we used the mature microRNA sequence as a query to search for possible MIR167 gene candidates in the tomato genome (http://solgenomics. [score:1]
Identification of ARF6, ARF8, and MIR167 genomic sequences from tomato. [score:1]
However, application of exogenous MeJA did not restore the trichome defect of MIR167 styles, and application of IAA, MeJA, or GA did not restore female fertility (data not shown). [score:1]
The tomato genome contains four putative precursor genes that could encode miR167 even though only one, Sly-MIR167, is registered in miRBase (Griffiths-Jones, 2004; Tomato Genome Consortium, 2012). [score:1]
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2
[+] score: 95
A schematic presentation of miRNA-target pairs and their role in regulation of male-sterility in 7B- 1 mutant is illustrated in Fig.   7. 5′-RACE validation of these miRNA targets in 7B- 1 anther and stem showed that they were active and directed the cleavage of their targets in these tissues, except for miR167 in 7B- 1 stem. [score:9]
MiR167 and miR396 were down-regulated in all stages of 7B- 1 anthers; more strongly at stage 1. MiR#M was strongly down-regulated in all stages of 7B- 1 anthers, while miR#A and miR#B were not differentially expressed and their sequenced miRNA* strands were not detected by our RT-qPCR analysis. [score:9]
MiR390, miR166, miR159 were up-regulated and miR530, miR167, miR164, miR396, miR168, miR393, miR8006 and two new miRNAs, miR#W and miR#M were down-regulated in 7B- 1 anthers. [score:7]
Among the known miRNAs, miR390, miR166, miR159 were up-regulated and miR530, miR167, miR164, miR396, miR168, miR393, and miR8006 were down-regulated in 7B- 1 anthers (Table  2). [score:7]
In 7B- 1 stem, miR159, miR390, miR167 and miR#M were all up-regulated, while miR396, miR#A and miR#B were not differentially expressed. [score:6]
Although up-regulation of miR167 and ARF8 in 7B- 1 stem could be independently associated and/or affected by 7B- 1 mutation, understanding their functions with respect to anther development and male-sterility in 7B- 1 requires further functional analysis. [score:6]
RT-qPCR analysis showed strong down-regulation of miR167 in 7B- 1 anthers, which was negatively correlated with regulation of ARF8 in anthers. [score:5]
Analysis showed a consistent negative correlation between miRNAs expression and accumulation level of their targets, except for miR390- TAS3-tasi ARFs (in anthers and stem), and miR167- ARF8 (in stem). [score:5]
The results showed a very distinct anther- or stem-specific expression pattern of miR167, miR396, and miR#M, which suggests that they may regulate different biological processes in these tissues. [score:4]
Among these miRNAs, miR159, miR167, miR396, miR390 and miR#M were those of particular interest as their targets had potential roles in anther development, microsporogenesis and production of ta-siRNAs as the case of miR390. [score:4]
MiR167 targets ARF6/ 8, which regulate ovule and anther development [31]. [score:4]
MiR167, miR396, and miR#M had distinctively different expression patterns in anthers and stem, which strongly suggested that these miRNAs regulate different biological processes in these tissues. [score:4]
In Arabidopsis thaliana, overexpression of miR167 led to male-sterility [37]. [score:3]
Therefore, proper regulation of miR167- ARF6/8 is required for normal female and male organ development. [score:3]
Cleavage products of ARF8, target of miR167, were identified from anther, but not stem. [score:3]
Tomato overexpressing miR167 had lower levels of ARF6/8 transcripts and a shorter hypocotyl [76], while other researchers reported that light-grown Arabidopsis thaliana arf8- 1 mutant had elongated hypocotyl [78]. [score:3]
Tomato overexpressing miR167 and arf6- arf8 double -null mutant of Arabidopsis thaliana both had flowers with severe defects associated with female and male-sterilities, respectively [76, 77]. [score:3]
In 7B- 1 stem, neither the ARF8 cleavage products were found nor the ARF8 expression was correlated with miR167 level. [score:3]
Although differential regulation of miR167- ARF8 cleavage cascade in 7B- 1 anthers could be linked and due to 7B- 1 mutation, its actual function with respect to anther development and male-sterility in 7B- 1 remains to be further characterized. [score:2]
There are increasing evidences showing that the function of miRNAs, including miR156, miR159, miR164, miR167, miR172 and miR319 is crucial during flower development and microsporogenesis [31– 33]. [score:2]
MiR167 cleaves ARF6/8 transcripts [76]; however we only identified ARF8 in our target prediction, which was also validated by 5′-RACE in 7B- 1 anther. [score:2]
1 Aldehyde dehydrogenase Solyc03g118350.2.1 Actin-fragmin kinase Solyc05g053090.1.1GRAS transcription factor [a] Solyc06g007320.2.1 Ubiquitin-activating enzyme E1 Solyc06g059760.2.1 Transcriptional corepressor SEUSS Solyc07g019640.1.1 Transposase Solyc07g045480.2.1 Phytochrome F Solyc09g057910.2.1 N-alpha-acetyltransferase 25 Solyc10g047270.1.1 Potassium transporter family protein Solyc11g006680.1.1 Pentatricopeptide repeat-containing protein Solyc11g020100.1.1 Cc-nbs-lrr, resistance protein Solyc12g013840.1.1 G-protein beta WD-40 repeat miR164 Solyc03g115850.2.1No Apical Meristem (NAM) [a] Solyc06g084350.2.1 U6 snRNA -associated Sm-like protein LSm2 Solyc11g066150.1.1 Bifunctional polymyxin resistance protein ArnA miR167 Solyc02g037530.2.1Auxin response factor 8 [a] Solyc01g010020.2. [score:1]
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3
[+] score: 46
Other miRNAs from this paper: sly-MIR160a, sly-MIR167a
In roots, SlARF8A was highly up-regulated after 24 hours of salt treatment while no strong changes occurred in the expression of miR167 precursors. [score:6]
Knowing that ARF8A is implicated in control and development of vegetative and floral organs in Dicots, the downregulation of miR167 gene precursors might enhance the auxin response and thus enhance shoot and leaf development. [score:6]
In cassava (Manihot esculenta), Xia et al., (2014) [89] showed that miR167 expression was modified in response to extreme temperature and could induce the cleavage of its target gene, ARF8, due to the presence of the miR167 cleavage sites on it. [score:5]
The expression of miR167 precursors and their target gene SlARF8A were modified by salt and drought stresses (Fig 7). [score:5]
SlARF8 and SlARF6 are known to be targeted by miR167 and SlARF10 is specifically regulated by miR160 [41, 63]. [score:4]
Some miRNAs, including miR160 and miR167, known to regulate the levels of transcription factor transcripts and protein abundance showed altered expression profiles in salt and drought conditions. [score:4]
Our results show that the downregulation of miR167 precursors (miR167a, miR167b, miR167c and miR167d) was negatively correlated with the accumulation of SlARF8A transcripts in leaves after 24 hours of salt exposure. [score:4]
0193517.g007 Fig 7 SlARF8A and miR167s (miR167a, miR167b, miR167c, miR167d) expression under salt and drought stress conditions. [score:3]
In salt stressed leaves, SlARF8A was highly induced up to 16 times after 24 hours of salt treatment while the expression miR167b was in a concurring of way highly repressed. [score:3]
SlARF8A and miR167s (miR167a, miR167b, miR167c, miR167d) expression under salt and drought stress conditions. [score:3]
After 48 hours of drought stress exposure, SlARF8A gene expression in leaves was not strongly affected while miR167a and miR167c genes were highly induced when miR167b was repressed. [score:3]
[1 to 20 of 11 sentences]
4
[+] score: 41
Other miRNAs from this paper: osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR160a, osa-MIR160b, osa-MIR160c, osa-MIR160d, osa-MIR162a, osa-MIR164a, osa-MIR164b, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR169a, osa-MIR171a, osa-MIR394, osa-MIR395b, osa-MIR395d, osa-MIR395e, osa-MIR395g, osa-MIR395h, osa-MIR395i, osa-MIR395j, osa-MIR395k, osa-MIR395l, osa-MIR395s, osa-MIR395t, osa-MIR395c, osa-MIR395a, osa-MIR395f, osa-MIR395u, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR156k, osa-MIR156l, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR160e, osa-MIR160f, osa-MIR162b, osa-MIR164c, osa-MIR164d, osa-MIR164e, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR171b, osa-MIR171c, osa-MIR171d, osa-MIR171e, osa-MIR171f, osa-MIR171g, osa-MIR172a, osa-MIR172b, osa-MIR172c, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR408, osa-MIR172d, osa-MIR171i, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, osa-MIR396e, gma-MIR156d, gma-MIR156e, gma-MIR156c, gma-MIR159a, gma-MIR160a, gma-MIR166a, gma-MIR166b, gma-MIR167a, gma-MIR167b, gma-MIR172a, gma-MIR172b, gma-MIR156a, gma-MIR396a, gma-MIR396b, gma-MIR156b, gma-MIR169a, osa-MIR395m, osa-MIR395n, osa-MIR395o, osa-MIR395p, osa-MIR395q, osa-MIR395v, osa-MIR395w, osa-MIR395r, osa-MIR169r, gma-MIR159b, gma-MIR159c, gma-MIR162a, gma-MIR164a, gma-MIR167c, gma-MIR169b, gma-MIR169c, gma-MIR171a, gma-MIR171b, gma-MIR482a, sly-MIR160a, sly-MIR166a, sly-MIR166b, sly-MIR167a, sly-MIR169a, sly-MIR169b, sly-MIR169c, sly-MIR169d, sly-MIR171a, sly-MIR171b, sly-MIR171c, sly-MIR171d, sly-MIR395a, sly-MIR395b, sly-MIR156a, sly-MIR156b, sly-MIR156c, sly-MIR159, sly-MIR162, sly-MIR172a, sly-MIR172b, osa-MIR396f, gma-MIR167d, gma-MIR396c, mdm-MIR482a, gma-MIR167e, gma-MIR167f, gma-MIR172c, gma-MIR172d, gma-MIR172e, osa-MIR396g, osa-MIR396h, osa-MIR396d, osa-MIR395x, osa-MIR395y, gma-MIR396d, gma-MIR482b, gma-MIR167g, gma-MIR156f, gma-MIR169d, gma-MIR172f, gma-MIR171c, gma-MIR169e, gma-MIR394b, gma-MIR156g, gma-MIR159d, gma-MIR394a, gma-MIR396e, gma-MIR156h, gma-MIR156i, gma-MIR160b, gma-MIR160c, gma-MIR160d, gma-MIR160e, gma-MIR162b, gma-MIR164b, gma-MIR164c, gma-MIR164d, gma-MIR166c, gma-MIR166d, gma-MIR166e, gma-MIR166f, gma-MIR166g, gma-MIR166h, gma-MIR169f, gma-MIR169g, gma-MIR171d, gma-MIR171e, gma-MIR171f, gma-MIR171g, gma-MIR394c, gma-MIR408d, gma-MIR482c, gma-MIR171h, gma-MIR171i, gma-MIR169h, gma-MIR167h, gma-MIR169i, gma-MIR396f, gma-MIR396g, gma-MIR167i, sly-MIR482e, sly-MIR482a, gma-MIR171j, gma-MIR395a, gma-MIR395b, gma-MIR395c, gma-MIR408a, gma-MIR408b, gma-MIR408c, gma-MIR156j, gma-MIR156k, gma-MIR156l, gma-MIR156m, gma-MIR156n, gma-MIR156o, gma-MIR159e, gma-MIR159f, gma-MIR162c, gma-MIR166i, gma-MIR166j, gma-MIR169j, gma-MIR169k, gma-MIR169l, gma-MIR169m, gma-MIR169n, gma-MIR171k, gma-MIR172g, gma-MIR172h, gma-MIR172i, gma-MIR172j, gma-MIR396h, gma-MIR396i, gma-MIR482d, gma-MIR167j, gma-MIR171l, gma-MIR156p, gma-MIR171m, gma-MIR172k, gma-MIR171n, gma-MIR156q, gma-MIR171o, gma-MIR172l, gma-MIR169o, gma-MIR171p, gma-MIR394d, gma-MIR169p, gma-MIR156r, gma-MIR396j, gma-MIR171q, gma-MIR156s, gma-MIR169r, gma-MIR169s, gma-MIR396k, gma-MIR166k, gma-MIR156t, gma-MIR482e, gma-MIR171r, gma-MIR394e, gma-MIR169t, gma-MIR171s, gma-MIR166l, gma-MIR171t, gma-MIR394f, gma-MIR171u, gma-MIR395d, gma-MIR395e, gma-MIR395f, gma-MIR395g, gma-MIR166m, gma-MIR169u, sly-MIR482b, sly-MIR482c, gma-MIR156u, gma-MIR156v, gma-MIR156w, gma-MIR156x, gma-MIR156y, gma-MIR156z, gma-MIR156aa, gma-MIR156ab, gma-MIR160f, gma-MIR164e, gma-MIR164f, gma-MIR164g, gma-MIR164h, gma-MIR164i, gma-MIR164j, gma-MIR164k, gma-MIR166n, gma-MIR166o, gma-MIR166p, gma-MIR166q, gma-MIR166r, gma-MIR166s, gma-MIR166t, gma-MIR166u, gma-MIR169v, gma-MIR394g, gma-MIR395h, gma-MIR395i, gma-MIR395j, gma-MIR395k, gma-MIR395l, gma-MIR395m, mdm-MIR156a, mdm-MIR156b, mdm-MIR156c, mdm-MIR156d, mdm-MIR156e, mdm-MIR156f, mdm-MIR156g, mdm-MIR156h, mdm-MIR156i, mdm-MIR156j, mdm-MIR156k, mdm-MIR156l, mdm-MIR156m, mdm-MIR156n, mdm-MIR156o, mdm-MIR156p, mdm-MIR156q, mdm-MIR156r, mdm-MIR156s, mdm-MIR156t, mdm-MIR156u, mdm-MIR156v, mdm-MIR156w, mdm-MIR156x, mdm-MIR156y, mdm-MIR156z, mdm-MIR156aa, mdm-MIR156ab, mdm-MIR156ac, mdm-MIR156ad, mdm-MIR156ae, mdm-MIR159a, mdm-MIR159b, mdm-MIR160a, mdm-MIR160b, mdm-MIR160c, mdm-MIR160d, mdm-MIR160e, mdm-MIR162a, mdm-MIR162b, mdm-MIR164a, mdm-MIR164b, mdm-MIR164c, mdm-MIR164d, mdm-MIR164e, mdm-MIR164f, mdm-MIR166a, mdm-MIR166b, mdm-MIR166c, mdm-MIR166d, mdm-MIR166e, mdm-MIR166f, mdm-MIR166g, mdm-MIR166h, mdm-MIR166i, mdm-MIR167a, mdm-MIR167b, mdm-MIR167c, mdm-MIR167d, mdm-MIR167e, mdm-MIR167f, mdm-MIR167g, mdm-MIR167h, mdm-MIR167i, mdm-MIR167j, mdm-MIR169a, mdm-MIR169b, mdm-MIR169c, mdm-MIR169d, mdm-MIR171a, mdm-MIR171b, mdm-MIR171c, mdm-MIR171d, mdm-MIR171e, mdm-MIR171f, mdm-MIR171g, mdm-MIR171h, mdm-MIR171i, mdm-MIR171j, mdm-MIR171k, mdm-MIR171l, mdm-MIR171m, mdm-MIR171n, mdm-MIR172a, mdm-MIR172b, mdm-MIR172c, mdm-MIR172d, mdm-MIR172e, mdm-MIR172f, mdm-MIR172g, mdm-MIR172h, mdm-MIR172i, mdm-MIR172j, mdm-MIR172k, mdm-MIR172l, mdm-MIR172m, mdm-MIR172n, mdm-MIR172o, mdm-MIR394a, mdm-MIR394b, mdm-MIR395a, mdm-MIR395b, mdm-MIR395c, mdm-MIR395d, mdm-MIR395e, mdm-MIR395f, mdm-MIR395g, mdm-MIR395h, mdm-MIR395i, mdm-MIR396a, mdm-MIR396b, mdm-MIR396c, mdm-MIR396d, mdm-MIR396e, mdm-MIR396f, mdm-MIR396g, mdm-MIR408a, mdm-MIR482b, mdm-MIR482c, mdm-MIR408b, mdm-MIR408c, mdm-MIR408d, mdm-MIR482d, mdm-MIR159c, mdm-MIR171o, mdm-MIR169e, mdm-MIR169f, sly-MIR164a, sly-MIR164b, sly-MIR394, sly-MIR166c, sly-MIR156d, sly-MIR156e, sly-MIR396a, sly-MIR482d, sly-MIR169e, sly-MIR396b, sly-MIR171e, gma-MIR167k, gma-MIR167l, gma-MIR169w, sly-MIR172c, sly-MIR408, sly-MIR172d, sly-MIR169f, sly-MIR171f, mdm-MIR159d, mdm-MIR159e, mdm-MIR159f, mdm-MIR166j, mdm-MIR395j, mdm-MIR169g, mdm-MIR169h, mdm-MIR169i, mdm-MIR169j, mdm-MIR171p, mdm-MIR395k, mdm-MIR171q, mdm-MIR169k, mdm-MIR169l, mdm-MIR169m, mdm-MIR169n, mdm-MIR172p, mdm-MIR395l, mdm-MIR169o
miR167 targets auxin response factors, which are the transcription factors that regulate the expression of auxin-responsive genes and play critical roles in plant development [38], [39], [40]. [score:7]
Targeted gene families were mostly involved in developmental processes and auxin response factors were targeted by two miRNA families - miR160 and miR167. [score:6]
However, target genes for miR167 were detected only in predicted gene mo dels, and miR171 had predicted target genes only in mesocarp cDNA sequences. [score:5]
In Ptc2, the miR167 locus was tandemly duplicated. [score:1]
Relationship between date palm contigPDK_30s943301 containing an miR167 locus and orthologous segments from seven other plant species. [score:1]
However, only one of two orthologous segments in Arabidopsis thaliana, Oryza sativa and Citrus sinensis had an miR167 locus. [score:1]
However, one contig containing the miR167 locus showed collinearity between both monocots and dicots (Figure 1). [score:1]
Evolution of an miR167 Locus within a Conserved Contig between Plant Species. [score:1]
Our analysis of orthologous contigs containing miR167 between remotely related plant species indicated that genomic duplications significantly influenced the conservation and expansion of miR167 locus (Figure 1). [score:1]
In Osa7, the miR167 locus was shuffled to a nearby region. [score:1]
Of 18 orthologous regions, 14 (78%) had an miR167 locus in the collinear region, and four orthologous regions - Ath4, Osa3, Osa10 and Csi5 - lost the miR167 locus. [score:1]
Phoenix dactylifera and Solanum lycopersicum had one orthologous miR167 locus, indicative of the ancient state of this unduplicated region. [score:1]
Adding this monocot species into a comparative analysis between different land plants, we analyzed the evolution of an miR167 locus in an orthologous DNA segment shared between eight species from different families. [score:1]
These observations imply that copies of miR167 can be lost or retained due to different species evolutionary histories, with genome-wide duplication as a major factor, but that conservation of a single copy is universally selected for. [score:1]
The miR167 locus along with its flanking region was duplicated in seven species from different families, with the miRNA loci maintained in this region (Figure 1 and 4). [score:1]
Detailed alignments and comparison of orthologous regions in date palm contigPDK_30s943301 (containing one miR167 locus) were conducted to highlight the variation and divergence between date palm and the other reference genomes (Figure 4). [score:1]
Plants belonging to the Fabids (Populus trichocarpa, Malus domestica and Glycine max) had the highest number of conserved segments, and all miR167 loci were preserved. [score:1]
Red arrows represent the miR167 loci. [score:1]
Previous studies have observed that there are two miR167 loci [12], and our analysis showed that one of the two loci was preserved in genomic duplication. [score:1]
miR167 was predicted to be involved in auxin response transcription factors, which are important for plant architecture. [score:1]
The results suggest that this miR167 locus may be crucial for both monocots and dicots, as it is far more highly preserved in the process of genomic duplication and new species formation than other miRNAs. [score:1]
The gain and loss of the conserved miR167 loci implies that conserved miRNAs are maintained despite sequence divergence between different plants as a result of genomic duplication. [score:1]
Although miR167 was conserved in most orthologous regions from different plants, the flanking genes varied. [score:1]
Our analysis of duplicated miRNA-containing segments indicated that two miR167 segments in poplar and soybean were duplicated very recently. [score:1]
The black bars represent the conserved segment, and the triangles indicate the presence of an miR167 locus in the extant plant genomes. [score:1]
Our analysis indicated that these ancient and conserved segments varied in their maintenance of miR167. [score:1]
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5
[+] score: 21
Other miRNAs from this paper: sly-MIR167a, sly-MIR390a, sly-MIR390b
Mir167, mir390, D7 tasiRNA were all up regulated in 5-azaC -treated 7B-1 seedlings, which expectedly down regulated the expression of their target ARF transcripts except for ARF4; ARF4 was slightly up regulated. [score:8]
Mir167, mir390, D7 tasiRNA were all strongly up regulated in response to 5-azaC, while D8 tasiRNA expression remained unaffected. [score:4]
To investigate if these miRNAs were linked to auxin signaling pathway in response to 5-azaC, expressions of mir167, mir390, TAS3-derived tasiRNAs (D7 and D8) and their target ARF transcripts (ARF2/3/4/8) were analyzed in 5-azaC -treated 7B-1 seedlings using qRT-PCR (Fig 8). [score:3]
Mir167 and mir390 are tightly connected to auxin signaling pathway via down regulation of ARF8 and ARF2/3/4 transcripts, respectively [34]. [score:2]
Mir167 and mir390 regulate auxin response factors in response to 5-azaC. [score:2]
Mir167 cleaves ARF8 transcripts and mir390 triggers the production of tasiRNAs from TAS3 mRNA, which in turns cleave and down regulate ARF2, 3, and 4 [34]. [score:2]
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6
[+] score: 16
Other miRNAs from this paper: osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR169a, osa-MIR171a, osa-MIR393a, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR397a, osa-MIR397b, osa-MIR398a, osa-MIR398b, osa-MIR399a, osa-MIR399b, osa-MIR399c, osa-MIR399d, osa-MIR399e, osa-MIR399f, osa-MIR399g, osa-MIR399h, osa-MIR399i, osa-MIR399j, osa-MIR399k, osa-MIR156k, osa-MIR156l, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR168a, osa-MIR168b, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR171b, osa-MIR171c, osa-MIR171d, osa-MIR171e, osa-MIR171f, osa-MIR171g, osa-MIR172a, osa-MIR172b, osa-MIR172c, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR393b, osa-MIR408, osa-MIR172d, osa-MIR171i, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR396e, mtr-MIR166a, mtr-MIR169a, mtr-MIR399b, mtr-MIR399d, mtr-MIR393a, mtr-MIR399c, mtr-MIR399a, mtr-MIR399e, mtr-MIR156a, mtr-MIR171a, mtr-MIR156b, mtr-MIR167a, mtr-MIR166b, mtr-MIR169c, mtr-MIR169d, mtr-MIR169e, mtr-MIR171b, mtr-MIR166c, mtr-MIR166d, mtr-MIR169f, mtr-MIR156c, mtr-MIR156d, mtr-MIR399f, mtr-MIR399g, mtr-MIR399h, mtr-MIR399i, mtr-MIR399j, mtr-MIR399k, mtr-MIR166e, mtr-MIR156e, mtr-MIR171c, mtr-MIR398a, mtr-MIR172a, mtr-MIR393b, mtr-MIR398b, mtr-MIR168a, mtr-MIR169g, mtr-MIR156f, mtr-MIR399l, mtr-MIR156g, mtr-MIR399m, mtr-MIR399n, mtr-MIR399o, mtr-MIR398c, mtr-MIR156h, mtr-MIR166f, mtr-MIR166g, mtr-MIR171d, mtr-MIR171e, mtr-MIR396a, mtr-MIR396b, mtr-MIR169h, mtr-MIR169b, mtr-MIR156i, mtr-MIR171f, mtr-MIR399p, osa-MIR169r, sly-MIR166a, sly-MIR166b, sly-MIR167a, sly-MIR169a, sly-MIR169b, sly-MIR169c, sly-MIR169d, sly-MIR171a, sly-MIR171b, sly-MIR171c, sly-MIR171d, sly-MIR397, sly-MIR156a, sly-MIR156b, sly-MIR156c, sly-MIR172a, sly-MIR172b, sly-MIR399, osa-MIR827, osa-MIR396f, mtr-MIR2118, osa-MIR2118a, osa-MIR2118b, osa-MIR2118c, osa-MIR2118d, osa-MIR2118e, osa-MIR2118f, osa-MIR2118g, osa-MIR2118h, osa-MIR2118i, osa-MIR2118j, osa-MIR2118k, osa-MIR2118l, osa-MIR2118m, osa-MIR2118n, osa-MIR2118o, osa-MIR2118p, osa-MIR2118q, osa-MIR2118r, mtr-MIR169k, mtr-MIR169j, mtr-MIR399q, osa-MIR396g, osa-MIR396h, osa-MIR396d, osa-MIR5072, mtr-MIR4414a, mtr-MIR4414b, mtr-MIR482, mtr-MIR172b, mtr-MIR172c, mtr-MIR171h, mtr-MIR168b, mtr-MIR399r, mtr-MIR156j, sly-MIR482e, sly-MIR482a, mtr-MIR167b, mtr-MIR168c, mtr-MIR408, mtr-MIR396c, mtr-MIR171g, stu-MIR6024, sly-MIR6024, stu-MIR482c, stu-MIR482b, stu-MIR482a, stu-MIR482d, stu-MIR482e, sly-MIR482b, sly-MIR482c, stu-MIR6025, stu-MIR6026, sly-MIR6026, sly-MIR168a, sly-MIR168b, mtr-MIR169i, mtr-MIR172d, mtr-MIR397, mtr-MIR169l, mtr-MIR399s, mtr-MIR399t, stu-MIR7980a, stu-MIR7983, stu-MIR8007a, stu-MIR8007b, stu-MIR7980b, stu-MIR399a, stu-MIR399b, stu-MIR399c, stu-MIR399d, stu-MIR399e, stu-MIR399f, stu-MIR399g, stu-MIR399h, stu-MIR3627, stu-MIR171b, stu-MIR166a, stu-MIR166b, stu-MIR166c, stu-MIR166d, stu-MIR171a, stu-MIR171c, stu-MIR399i, stu-MIR827, stu-MIR172b, stu-MIR172c, stu-MIR172a, stu-MIR172d, stu-MIR172e, stu-MIR156a, stu-MIR156b, stu-MIR156c, stu-MIR156d, stu-MIR171d, stu-MIR167c, stu-MIR167b, stu-MIR167a, stu-MIR167d, stu-MIR399j, stu-MIR399k, stu-MIR399l, stu-MIR399m, stu-MIR399n, stu-MIR399o, stu-MIR393, stu-MIR398a, stu-MIR398b, stu-MIR396, stu-MIR408a, stu-MIR408b, stu-MIR397, stu-MIR171e, stu-MIR156e, stu-MIR156f, stu-MIR156g, stu-MIR156h, stu-MIR156i, stu-MIR156j, stu-MIR156k, stu-MIR169a, stu-MIR169b, stu-MIR169c, stu-MIR169d, stu-MIR169e, stu-MIR169f, stu-MIR169g, stu-MIR169h, sly-MIR403, sly-MIR166c, sly-MIR156d, sly-MIR156e, sly-MIR396a, sly-MIR482d, sly-MIR169e, sly-MIR396b, sly-MIR171e, sly-MIR172c, sly-MIR408, sly-MIR172d, sly-MIR827, sly-MIR393, sly-MIR398a, sly-MIR399b, sly-MIR6025, sly-MIR169f, sly-MIR171f
Although no target gene was predicted for miR167 under the strict criterion used in this study, miR167 has been evidenced to regulate the expression of auxin response factors expression in tomato by direct cleavage (Liu et al., 2014). [score:9]
In soybean, the miR167 modulates nodulation and lateral root development by targeting auxin response factors (Wang et al., 2015). [score:4]
MicroRNA167-directed regulation of the auxin response factors GmARF8a and GmARF8b is required for soybean nodulation and lateral root development. [score:3]
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7
[+] score: 15
miRNA Target Function References miR166 HD-ZIP TFs Leaf development[20] miR395 ATP Sulfurylase; Sulfate metabolism Environmental stress response[7, 23] miR167 ARF TFs Plant development and hormone signaling[50] miR164 NAC domain TFs; CUC1 and CUC2 Leaf development and hormone signaling[18, 21] miR399 Ubiquitin conjugating enzyme Phosphate metabolism[34] Figure 5Semi-quantitative reverse transcription Polymerase chain reaction (RT-PCR) of various pre-miRNAs in (A) leaves and (B) flower tissues of different plants viz. [score:6]
miRNA Target Function References miR166 HD-ZIP TFs Leaf development[20] miR395 ATP Sulfurylase; Sulfate metabolism Environmental stress response[7, 23] miR167 ARF TFs Plant development and hormone signaling[50] miR164 NAC domain TFs; CUC1 and CUC2 Leaf development and hormone signaling[18, 21] miR399 Ubiquitin conjugating enzyme Phosphate metabolism[34] Figure 5Semi-quantitative reverse transcription Polymerase chain reaction (RT-PCR) of various pre-miRNAs in (A) leaves and (B) flower tissues of different plants viz. [score:6]
, pre-miR166a, pre-miR166b, pre-miR167 and pre-miR395 (Table 2) in this study since the corresponding mature miRNAs are important in leaf development (miR166) and stress responses (miR167 and miR395). [score:2]
The precursors of miR162, miR172, miR395, miR397 and miR399 were induced to more than five folds in ToLCNDV infected leaves, while those of miR159, miR160, miR167 and miR319 showed almost 2-3 times increase in ToLCNDV infected leaves (Table 3). [score:1]
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8
[+] score: 13
In conclusion, we found that TRV vectors elicit the changes in the function of miR167, the abundance of phasiRNAs from two PHAS loci, expression patterns of over hundred protein-coding RNAs and twenty lncRNAs, as well as changes in alternative splicing patterns of 383 host transcripts. [score:3]
Interestingly, miR167 is a common target for a broad spectrum of plant pathogens including a viroid [16], viruses 25, 26, bacteria [27], and fungi [28]. [score:3]
In the meantime, the activity of miR167 in regulating other genes was not affected. [score:2]
MiR167 and target pairings are shown in the top panel. [score:2]
Thus, our data, together with the previous observations, further consolidate the ubiquitous role of miR167 -based regulation over ARF8 in plant-pathogen interactions. [score:2]
Interestingly, we found that the activities were significantly enhanced for miR167 -guided cleavage of transcripts encoding tomato auxin response factor 8/ARF8 (Solyc02g037530) when inoculated with TRV vectors. [score:1]
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[+] score: 9
org): miR156, miR156c, miR156kj and miR157d: Squamosa-promoter Binding Protein (SBP)-like transcription factors; miR166glmf: HD-Zip transcription factors, including Phabulosa (PHB) and Phavoluta (PHV) that regulate axillary meristem initiation and leaf development; miR167b, miR167d and miR167fijeghac: Auxin Response Factors (ARF transcription factors); miR396abcd: Growth Regulating Factor (GRF) transcription factors, rhodenase-like proteins, and kinesin-like protein B; miR394ab, F-box proteins; miR827abc: Unknown; miR403bdf: Virus defense; miR162 and miR162abc: Unknown; miR530: Unknown; miR398abc: copper superoxide dismutases and cytochrome C oxidase subunit V; miR482f: NB domain proteins; miR5300, Unknown. [score:4]
miR393, miR160 and miR167 are up-regulated in leaves challenged with the virulent bacterial pathogen Pseudomonas syringae pv. [score:4]
Similarly, miR393, miR319, miR158, miR160, miR167, miR165/166 and miR159 are induced, while miR390, miR408 and miR398 are repressed, in Arabidopsis thaliana (Arabidopsis) leaves infected with Pst DC3000 [20]. [score:1]
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10
[+] score: 9
The rest of 51 target genes were belonged to less significant categories 3 and 4. One of the stimulus response‐associated target PSII degraded by 16 miRNA families such as sly‐miR167, sly‐miR319, sly‐miR390, sly‐miR482, sly‐mir1919, sly‐miR5302 and sly‐miR9479. [score:5]
However, ARF was targeted by miR167 after selenium treatment in Astragalus (Cakir et al., 2015). [score:3]
Eleven miRNA families (sly‐miR156, sly‐miR157, sly‐miR164, sly‐miR166, sly‐miR167, sly‐miR168, sly‐miR4414, sly‐miR6022, sly‐miR6027, sly‐miR7822 and sly‐miR9471) were represented with the top read abundance above 10 000 at all libraries (Table S2). [score:1]
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11
[+] score: 8
These results indicate that expression of miR156 and miR167 in tomato plants is induced not only by exposure to acutely elevated temperatures (≥40 °C) but also by exposure to moderately elevated temperatures that were slightly higher than the optimum temperature for plant growth. [score:3]
In this study, spi-miR156f-5p_stu, spi-miR167a and spi-miR167b-3p_stu were significantly up-regulated (1.18, 1.19 and 1.65-fold, respectively) in the library from the plants held at 33 °C compared to the control library (Supplementary Table S3). [score:3]
For example, miR156 and miR167 were induced in Triticum aestivum and Brassica rapa by exposure to high temperatures (40 °C and 46 °C, respectively) 26 37. [score:1]
We found that some miRNAs (including miR156, miR167 and miR168) in tomato plants might respond when the plants are exposed to temperatures only slightly higher than the normal growing temperature, while others (miR160, miR398 and miR399) might only respond to acutely elevated temperatures. [score:1]
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[+] score: 8
Most of the conserved miRNAs (such as miR156, miR159, miR160, miR164, miR167, miR171, miR172, miR319, and some others) usually target a range of transcription factors like MYBs, ARFs, SBPs, NACs, AP2-like factors, GRFs, and GRASs, and their miRNAs -mediated regulations are important for plant growth and development and may act in the core gene expression networks (Liu et al., 2013). [score:7]
Micro RNA families MIR156, MIR172, and MIR5303 contained highest five members while 11 families viz, MIR162, MIR166, MIR167, MIR168, MIR171, MIR1919, MIR319, MIR398, MIR482, MIR6024, and MIR7997 contained several members (2–4). [score:1]
[1 to 20 of 2 sentences]
13
[+] score: 7
Nine miRNAs (sly-miR164a-3p, sly-miR166c-5p, sly-miR167b-3p, sly-miR168b-3p, sly-miR168b-5p, sly-miR394-3p, sly-miR396a-3p, sly-miR1919a and sly-miR9471a-5p) were down-regulated in M82, whereas they were up-regulated in IL9–1 (Fig. 5a). [score:7]
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[+] score: 7
Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. [score:3]
For conserved miRNA families, the miR167, miR396, and miR482 families were predominantly expressed in the range of 2000 transcripts per million (TPM) clean tags to 14,000 TPM in the stamen libraries, whereas the miR159, miR166, and miR482 families were predominantly in the range of 1500 TPM to 4500 TPM in the pistil libraries. [score:3]
In the stamen library, the miRNA167 and miRNA396 families were the most abundant, whereas in the pistil library, the miRNA159 and miRNA482 families were the most abundant (Fig.   4). [score:1]
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[+] score: 5
In Arabidopsis, ARF6 and ARF8, ARF16, and ARF17 were reported to be the targets of miR167 and miR160, respectively. [score:3]
In this study, ARF8 cleaved by miR167 was found via degradome sequencing. [score:1]
However, ARF6 was not identified for miR167, perhaps because the abundance of cleaved products was too low to be detected. [score:1]
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[+] score: 5
Other miRNAs from this paper: sly-MIR160a, sly-MIR167a, sly-MIR156a, sly-MIR156b, sly-MIR156c, sly-MIR172a, sly-MIR172b, sly-MIR399, mdm-MIR156a, mdm-MIR156b, mdm-MIR156c, mdm-MIR156d, mdm-MIR156e, mdm-MIR156f, mdm-MIR156g, mdm-MIR156h, mdm-MIR156i, mdm-MIR156j, mdm-MIR156k, mdm-MIR156l, mdm-MIR156m, mdm-MIR156n, mdm-MIR156o, mdm-MIR156p, mdm-MIR156q, mdm-MIR156r, mdm-MIR156s, mdm-MIR156t, mdm-MIR156u, mdm-MIR156v, mdm-MIR156w, mdm-MIR156x, mdm-MIR156y, mdm-MIR156z, mdm-MIR156aa, mdm-MIR156ab, mdm-MIR156ac, mdm-MIR156ad, mdm-MIR156ae, mdm-MIR160a, mdm-MIR160b, mdm-MIR160c, mdm-MIR160d, mdm-MIR160e, mdm-MIR167a, mdm-MIR167b, mdm-MIR167c, mdm-MIR167d, mdm-MIR167e, mdm-MIR167f, mdm-MIR167g, mdm-MIR167h, mdm-MIR167i, mdm-MIR167j, mdm-MIR168a, mdm-MIR168b, mdm-MIR172a, mdm-MIR172b, mdm-MIR172c, mdm-MIR172d, mdm-MIR172e, mdm-MIR172f, mdm-MIR172g, mdm-MIR172h, mdm-MIR172i, mdm-MIR172j, mdm-MIR172k, mdm-MIR172l, mdm-MIR172m, mdm-MIR172n, mdm-MIR172o, mdm-MIR399a, mdm-MIR399b, mdm-MIR399c, mdm-MIR399d, mdm-MIR399e, mdm-MIR399f, mdm-MIR399g, mdm-MIR399h, mdm-MIR399i, mdm-MIR399j, sly-MIR168a, sly-MIR168b, ppe-MIR156a, ppe-MIR156b, ppe-MIR156c, ppe-MIR156d, ppe-MIR156e, ppe-MIR156f, ppe-MIR156g, ppe-MIR156h, ppe-MIR156i, ppe-MIR160a, ppe-MIR160b, ppe-MIR167a, ppe-MIR167b, ppe-MIR167c, ppe-MIR167d, ppe-MIR168, ppe-MIR172a, ppe-MIR172b, ppe-MIR172c, ppe-MIR172d, ppe-MIR399a, ppe-MIR399b, ppe-MIR399c, ppe-MIR399d, ppe-MIR399e, ppe-MIR399f, ppe-MIR399g, ppe-MIR399h, ppe-MIR399i, ppe-MIR399j, ppe-MIR399k, ppe-MIR399l, ppe-MIR399m, ppe-MIR399n, sly-MIR156d, sly-MIR156e, sly-MIR172c, sly-MIR172d, mdm-MIR399k, mdm-MIR172p
In addition, several members of ARF family predicted to be targets of miR160, and in particular miR167 (whose target is the ARF8) (Mallory et al., 2005). [score:5]
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[+] score: 4
In the current study, auxin response factors genes were cleaved by decreased sha-miR160a and sha-miR167b_nta and more tag sequences were mainly detected in the NT library, while only miR167 -targeted auxin response factors genes were identified in the chilling response in rice [27]. [score:3]
In the CT and NT libraries, there were 153 miRNAs in common, while two miRNAs that were sha-miR169c-3p_stu and sha-miR408a-5p_stu were only found in the CT library; six miRNAs that were sha-miR156e-p3_stu, sha-miR156f-p5_stu, sha-miR162-p5_cme, sha-miR166g-p5_nta, sha-miR167-p3 and sha-miR171h-p5_vvi were specific to the NT library (Figure  3, Additional file 1: Table S1). [score:1]
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[+] score: 3
Moreover, miR167 and miR143 respond to exogenous ABA, and regulate abiotic stress adaptation in Oryza sativa [23]. [score:2]
In addition, some miRNAs such as miR160, miR167, miRNA172, miR158, miR159, miR165/166, miR319, and miR393 are involved in pathogen defense [5, 7]. [score:1]
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[+] score: 3
In contrast, a low digital expression was observed for miR1446, miR167, miR169, miR171, miR393, miR394, miR399, miR408, miR5304, miR9473 and miR9479 families (total TPM value < 100). [score:3]
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[+] score: 3
Other miRNAs from this paper: sly-MIR160a, sly-MIR167a
That is, Sl-ARF2A, Sl-ARF2B, Sl-ARF3 and Sl-ARF4 are predicted to be potentially targeted by TAS3; Sl-ARF6A, Sl-ARF8A and Sl-ARF8B by miR167; and Sl-ARF10A, Sl-ARF10B, Sl-ARF16A, Sl-ARF16B and Sl-ARF17 by miR160. [score:3]
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[+] score: 3
Additionally, CaARF13, 21 and 22, AtARF6 and 8 were clustered in class III, were a target for miRNA167. [score:3]
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[+] score: 2
Moreover, the balance between repressing (ARF17) and activating (ARF6 and ARF8) factors is post-transcriptionally regulated by miR160 and miR167 (Gutierrez et al., 2009). [score:2]
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[+] score: 1
Several miRNA families, including miR157, miR159, miR162, miR164, miR167, miR171, miR172, miR390, miR396, and miR482, were moderately abundant (Figure  2A). [score:1]
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[+] score: 1
The reads of four families (miR157, miR166, miR167 and miR168) were significantly higher than those of other families. [score:1]
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