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13 publications mentioning sly-MIR6024

Open access articles that are associated with the species Solanum lycopersicum and mention the gene name MIR6024. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

[+] score: 75
Therefore, the collective regulation by miR482, miR6024 as well as tasiRNAs triggered by them may control the expression level of I2 homologues in Solanaceae, and the down-regulation of the I2 homologues by these miRNAs may make the expansion of I2 homologues less costly in fitness. [score:7]
The miR482 family has high expression level in three tissues of potato (leaf, flower and stolon) (five members, with an average of 35,760 reads per million), while miR6024 family has a much lower expression in tomato (leaf, flower and fruit) (2,540 reads per million). [score:5]
Therefore, the I2 homologues from tomato are targeted by miR6024 and may not be targeted by miR482. [score:5]
In addition to the miR482 family targeting I2 homologues in potato [33], we identified and confirmed that miR6024 targets I2 family in tomato. [score:5]
Sly-miR6024 was previously shown to regulate the expression of R-gene Tm-2 in tomato [33]. [score:4]
We hypothesize that miR6024 regulate expression of most, if not all I2 homologues in tomato, which may facilitate its expansion in a genome. [score:4]
We hypothesized that miR6024 and miR482 might have facilitated the expansion of the I2 family in Solanaceae species, since they can minimize their potential toxic effects by down -regulating their expression. [score:4]
Sequencing the PCR products showed that the mRNAs of at least one I2 homologue from cultivar Hongxiaoli were cleaved at the predicted targeting site of miR6024 (Figure 5 and Additional file 2: Figure S5). [score:3]
The targeting site of sly-miR6024 encodes the 206 [th] – 213 [th] amino acids in the I2 protein, partially overlapping with the conserved P loop. [score:3]
However, point mutations were observed in the miR6024 [*] region of N. sylvestris and N. benthemiana, and it remains unclear if these mutations affect the biogenesis of miR6024 in the two species (Figure 6). [score:3]
However, our data showed that I2 homologues in tomato were targeted by miR6024 rather than miR482. [score:3]
The miR6024 gene has no similarity with I2 homologues except that the miR6024/miR6024* can match the target site in I2 homologues. [score:3]
showed that miR6024 was originated after the divergence of Solanaceae. [score:1]
Therefore, the miR6024 was not originated from duplication and inversion of I2 sequences [33]. [score:1]
However, the flanking sequences of the significant hits in M. guttatus and V. vinifera could not form hairpin structure, and therefore these two species do not have miR6024. [score:1]
Three miR6024 hairpin sequences (tomato, potato and tobacco) were downloaded from miRbase (release 20). [score:1]
MiR6024 triggers 21-nt phased siRNA from I2homologuesIt was shown that 22-nt miRNAs often trigger the biogenesis of secondary phased siRNA [55, 56]. [score:1]
Consequently, a total of 1,439 distinct sRNAs, including the 22-nt sly-miR6024, were found in the sRNA database when five mismatches were allowed. [score:1]
The arrow in T-I2-3 matching the miR6024 sequence shows the cleavage site of miR6024, evidenced by RACE-PCR and degradome analysis. [score:1]
The cleavage of miR6024 on I2 homologues was also confirmed in a degradome database of tomato. [score:1]
Search of the tomato degradome confirmed the cleavage function of miR6024 and also suggest the cleavage function of tasiRNAs triggered by miRNAs (see section). [score:1]
Underlines in the consensus sequences represent miR6024, while dash lines under the consensus sequence represent miR6024*. [score:1]
C. Cleavage sites of two tasiRNAs triggered by miR6024. [score:1]
These two degraded mRNA were most likely the cleavage products of tasiRNAs (3′S5 and 3′S3, respectively) since their cleavage points are located in the middle of a tasiRNA triggered by the miRNA6024 (Figure 5). [score:1]
The miR6024 sequences were used to BLAST search the ten genomes, and significant hits were found in eight of the ten plant species except in C. papaya and A. lyrata. [score:1]
The structure of these sRNAs and their phasing with the miR6024 cleavage site indicated that they were tasiRNAs triggered by the 22-nt miRNA6024. [score:1]
To gain insight into the evolution of miR6024 in plants, four members of the miR6024 family were downloaded from miRbase (release 20) including sly-miR6024 from tomato, nta-miR6024 from tobacco, stu-miR6024-3p and stu-miR6024-5p from potato. [score:1]
One of partial ones starts from the 485 [th] nucleotide of gene T-I2-3, confirming the cleavage function of miR6024 (Additional file 1: Figure S6A). [score:1]
All the six Solanaceae species have the miR6024 sequence and its flanking sequences (miR6024 gene) can form a predicted hairpin structure. [score:1]
Furthermore, miR6024 triggers phasiRNAs from I2 homologues in tomato. [score:1]
The 22-nt mature miR6024 was confirmed in a pepper sRNA database (Dr. [score:1]
Figure 5 Cleavage sites of miR6024 and two tasiRNAs in gene T-I2-3. [score:1]
Since miR6024 is present in distantly related species in Solanaceae, we hypothesize that the miR6024 was originated in the common ancestor of the Solanaceae family. [score:1]
To investigate if sly-miR6024 also target the I2 homologues, modified RNA ligase -mediated 5′-RACE was performed [50, 51]. [score:1]
The cleavage site of miR6024 obtained through sequencing RACE-PCR products. [score:1]
Figure 6 Alignment of the miR6024 genes in Solanaceae. [score:1]
In addition, whole genome sequences of ten plant species were chosen to identify miR6024 genes using bioinformatic approach (see MM section). [score:1]
The 22 nt miR6024 has three mismatches with gene T-I2-3. The blocks of 21 nt (marked by underlines) show the tasiRNAs triggered by miR6024, and the 6 [th]-14 [th] tasiRNAs were omitted as indicated by “//”. [score:1]
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[+] score: 40
Among them, 12 ABA-responsive miRNAs with differential expression were identified, containing eight up-regulated miRNAs (miR6024-3p, miR7997a, miR172a, miR5658, sly-miR5301, miR169b, sly-miR159 and miR165a-3p), and four down-regulated miRNAs (miR7997c, novel_mir_392, novel_mir_191 and sly-miR171d). [score:9]
These four miRNAs were predicted to act together with miR6024-3p, and most of their target NBS-LRR showed an increased expression. [score:5]
The targets of miR6024-3p comprise two RLK genes, and both showed an increase in expression in the transcriptome upon ABA treatment. [score:5]
Here, we predicted four differentially expressed miRNAs that target STK genes, including miR5813, miR6024-3p, miR4376a-3p and miR319b (Table  2). [score:5]
The miR6024-3p was predicted to target 27 members of NBS-LRR resistance genes. [score:3]
For example, miR6024-3p, showed a fall in expressed counts from 132.63 to 0.01 TPM following the ABA treatment, and was predicted to act on 71 genes corresponding to 95 transcripts in our ABA-responsive transcriptome. [score:3]
For instance, miR6024-3p, miR5658, miR5139, sly-miR156, novel_mir_156, and novel_mir_447 had 71, 45, 15, 11, 6 and 2 predicted target genes, respectively. [score:3]
Analysis of miR6024-3p showed a decrease in expression from 132.63 to 0.01 TPM following ABA treatment, although the abundance of other four miRNAs were elevated from 33.5 to 41.77, 3.58 to 7.43, 3.58 to 7.43 and 12.82 to 18.13 TPM. [score:3]
Here, one NAC gene, no apical meristem (NAM) protein, was targeted by miR6024-3p, and showed no change at transcript level. [score:3]
Here, we predicted that seven miRNAs act on NBS-LRR gene members, such as miR6024-3p, miR482a, sly-miR482a, sly-miR482c, and miR5083, miR6026-3p and novel_mir_674. [score:1]
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[+] score: 21
Sly-miR6024 targets six different transcripts: three (a 24 kDa vacuolar protein, a chlorophyll a oxygenase, and a chitinase A) were up-regulated (FC =  1.35, 1.57 and 1.70 respectively) in infected plants and three (an ATP binding protein, an auxin-independent growth promoter protein and a pectinesterase) were down-regulated (FC = 0.55, 0.77 and 0.25 respectively). [score:9]
In our work, we identified eleven target transcripts for Sly-miR6022, -miR6023, -miR6024 and -miR6027, all belonging to R genes -targeting miRNAs families (Table 2). [score:5]
A total of 29 DE genes were predicted targets of 11 tomato miRNAs (Table 2): four of them (miR156, miR159, miR171, miR172) were developmental miRNAs, conserved between plant families, and seven were family- (miR6022, miR6023, miR6024, miR6027, miR5303) or species-specific (miR1917, miR1918) miRNAs. [score:4]
Sly-miR6022, Sly-miR6023, Sly-miR6024 and Sly-miR6027 belong to miRNA families up to date identified only in solanaceous species, and able to target resistance (R) genes [41]. [score:3]
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[+] score: 14
In the network, it could be clearly seen that miR6024 had 11 targets and among the targets two of them were also the targets of miR482 (Figure 5). [score:7]
In addition, miR6024 and miR6027-3p shared one common targets. [score:3]
Moreover, another TAS5 (TAS5e) with the target sly-miR482b and two more TAS genes (Named TAS11a and TAS11b) triggered by sly-miR6024 were also found in our libraries (Table 4). [score:3]
Surprisingly, one more TAS5 family member (TAS5e) and two more TAS genes (TAS11a and TAS11b), triggered by sly-miR6024, are reported in our results (Table 4). [score:1]
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[+] score: 13
Similarly, some miRNAs showed expression only in upground tissues of sensitive genotype and the expression level was decreased or repressed after drought stress such as sly‐miR171a‐3p, sly‐miR1426, sly‐miR5239, sly‐miR6024‐3p and sly‐miR7997a (Table S2). [score:5]
In tomato degradome results, 15 target genes were related to stimulus response such as ARF and disease resistance proteins were identified in category 0 cleaved by sly‐miR160, sly‐miR168, sly‐miR172, sly‐miR396, sly‐miR482, sly‐miR6023 and sly‐miR6024 families (Figure  6, Table S4). [score:5]
Additionally, in control and drought‐treated samples, 37 miRNAs such as sly‐miR171a‐3p, sly‐miR6024‐3p and sly‐miR7997a were expressed specifically in control conditions, while 44 miRNAs such as sly‐miR845a, sly‐miR5797 and sly‐miR8762d were specific to drought‐treated upground tissues in sensitive genotype (Table S2, Figure  2b). [score:3]
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[+] score: 11
Some targets of miRNAs have been documented to be involved in plant disease resistance, such as the targets of sly-miR477-3p, sly-miR5300 and sly-miR6024 (Additional file 10: Table S10). [score:7]
The targets of sly-miR172a, sly-miR390b-5p, and sly-miR6024 encode AP2-like ethylene-responsive transcription factor, protein phosphatase 2C, and auxin-independent growth promoter protein-like protein, respectively; these genes function in hormone signal transduction pathways (Additional file 10: Table S10). [score:3]
Seven conserved miRNAs (sly-miR166c-5p, sly-miR168b-3p, sly-miR168b-5p, sly-miR396a-3p, sly- miR482e-5p, sly-miR6024 and sly-miR6027-5p) and three novel miRNAs (sly_miN_294, sly_miN_526 and sly_miN_1009) were selected in the validation. [score:1]
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[+] score: 10
Interestingly, in the case of sly-miR6024, it not only targeted lncRNA504 but also was targeted by the eTM of lncRNA3444 (Fig. 4). [score:5]
Of these three miRNA targets, lncRNA504 was the target of sly-miR6024 that was involved in plant immunity (F. Li et al., 2012). [score:5]
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[+] score: 5
Indeed, in 35S>>SlDCL1IR seedlings, sly-miR6024 was down-regulated 4-fold and Solyc11g071430-derived 21-nt phased siRNA numbers decreased by 2.6-fold. [score:4]
An example of an NBS–LRR gene-derived DEcluster (Cluster_146573), which is predicted to be triggered by sly-miR6024 -mediated cleavage, is shown in Fig. 4D. [score:1]
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[+] score: 5
Three miRNA-PHAS regulation cascades (miR482d-PHAS, miR482e-tasLRR, and miR6024-tasLRR) were also identified and confirmed in response to B. cinerea infection. [score:2]
Otherwise, the remaining four phasiRNAs triggered by conserved miRNAs (siR07-2 triggered by miR482e, siR71-2 triggered by miR482d, and both siR23-4 and siR43-7 triggered by miR6024) had increased abundance in both B. cinerea-infected leaves and B. cinerea-infected fruits (Fig.   4). [score:1]
From the analysis of phasiRNAs responsive to B. cinerea infection, five phasiRNAs triggered by four conserved miRNAs (miR6024, miR482d, miR482e, and miR390a) were also found. [score:1]
In addition, miR6024 may also trigger the production of phasiRNAs at NB-LRR loci in Solanaceae plants [12]. [score:1]
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[+] score: 5
2 was also found to have been cleaved by miR6024, which might be the reason why there was no correlation between the expression of miR482b and Solyc05g008070. [score:3]
Various letters indicate significant difference among samples, and letters shared in common between or among the groups indicate no significant difference (P < 0.05) To gain insight into the molecular mechanisms responsible for the late blight resistance, we previously used high-throughput sequencing to identify P. infestans -induced miRNAs in tomato, including miR169, miR398, miR482, miR6024, miR6026, and miR6027 25, 47, 48. [score:1]
Using high-throughput sequencing and homology -based computational research, we have previously identified a number of tomato miRNAs involved in tomato– P. infestans interaction including miR482, miR172, miR6024, miR6026, miR6027, etc. [score:1]
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[+] score: 2
Moreover, miR6022, miR166a-5p, and miR6024 were found as the most abundant families with 191,474.2, 4,180.5, and 2,990.12 transcripts, respectively. [score:1]
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]
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[+] score: 1
1, Solyc01g009700.1.1, Solyc03g082780.1.1, Solyc12g100020.1.1 miR6023 –1.2612632 Solyc01g005780.1.1, Solyc01g009690.1.1, Solyc03g082780.1.1, Solyc01g005710.2.1, Solyc01g014160.1.1, Solyc01g014930.1.1 miR6024 –3.44754718 Solyc02g070410.1.1, Solyc02g084890.1.1, Solyc03g006750.1.1, Solyc04g015220.2.1, Solyc05g005330.2.1, Solyc05g008070.2. [score:1]
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[+] score: 1
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, 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-MIR167b, 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
In contrast, several miRNA families such as miR403, miR408, miR6284, miR6025, and miR6024 have only one member. [score:1]
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