6 publications mentioning ptc-MIR167f

Open access articles that are associated with the species Populus trichocarpa and mention the gene name MIR167f. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1

Figure 5Microsynteny related to miR167 family across three eudicots species (Arabidopsis, Populus and grape) and the duplication events of miR167 family in these species.

We demonstrated the utility of this software in the case study of miR167, a miRNA gene family whose evolutionary relationship cannot be inferred based on the traditional phylogenetic tree analysis due to short conserved sequences of these miRNAs.

Evolution of miR167 gene family in plants.

The paralogs evolved from R3 duplication are located on different chromosomes (e. g., miR167f on chromosome 10, miR167g on chromosome 8), indicating that they likely arose from a whole-genome duplication event.

Figure 4Microsynteny related to miR167 families in a) Arabidopsis; c) Populus; e) grape; g) rice and reconstruction of the miRNA167 families evolution in b) Arabidopsis; d) Populus; f) grape; h) rice.

In rice, three pairs (miR167c/miR167d, miR167f/miR167g and miR167e/miR167i) appear to have evolved from a recent duplication event as these gene pairs all have a conservative region with miR167a (Figure 4h).

Click here for file Figure S1 - Microsynteny related to miR167 families between Arabidopsis and rice.

Here we found that the miR167 homologs appear to have arisen via gene duplication events, which are designated as R1, R2 and R3 in this study (Figure 5).

According to the extent of conservation within this gene family, miR167f/miR167g and miR167a/miR167b/miR167c/miR167d arose from a duplication event, and the common ancestor of miR167f/miR167g and miR167a/miR167b/miR167c/miR167d, might be evolved from duplication after the ancestor of miR167e/miR167h appeared (Figure 4d).

We applied MicroSyn to study the miR167 gene family in Arabidopsis, Populus, grape and rice, four of the plant species with available whole-genome sequence.

miR167a in Arabidopsis, miR167f and miR167g in Populus, and miR167e in grape have a conserved colinearity, and are classified into the group "A".

In grape, there are five members in the miR167 family.

miR167f and miR167g share conserved synteny and microsynteny was detected between miR167e and miR167h.

There are four miR167 genes in Arabidopsis.

b: The evolution relationship was generated to demonstrate the order of duplication events for the miR167 family in eudicots species.

From the orthologous group mo del across three lineages and the synteny relationship within species, we presume that miR167 duplication of group C and the common ancestor of group A and B occurred at R1 and group A and B evolved at R2.

In this study, it was also challenging to infer the contribution of this recent duplication to the miR167 duplication events, for that reason the orthologous correlation of miR167s in rice to group A, B or C in eudicots is unclear.

However, from our results based on microsynteny related to miR167, miR167e in grape obviously remains in an orthologous relationship with group A (Figure 5).

Microsynteny was detected between 1) miR167c and miR167d, 2) miR167f and miR167g and 3) miR167e and miR167i (Figure 4g).

Figure S2 - Microsynteny related to miR167 families between Populus and rice.

To demonstrate the utility and use of MicroSyn, we presented a case study of the evolution of miR167 gene family in Arabidopsis thaliana (Arabidopsis), Populus trichocarpa (Populus), Vitis vinifera (grape) and Oryza sativa (rice).

Eight miR167 genes were identified in Populus.

We first analyzed the relationship of miR167 genes within each species to infer gene duplication events.

The region of miR167a lacks significant colinear relations to all other miR167 genes; therefore, miR167a is placed close to miR167b as an outlier (Figure 4f).

b, d, f, h: These evolution relationship were generated to demonstrate the order of duplication events for the miR167 families in respective species.

To clarify the relationship of miR167s across eudicots, the microsynteny of miR167 genes across Arabidopsis, Populus and grape was then examined.

Ten miR167 genes were identified in rice.

Figure S1 - Microsynteny related to miR167 families between Arabidopsis and rice.

Based on the predicted syntenic relationships, Arabidopsis miR167a and miR167b appear to have evolved from a single duplication event, while miR167c existed prior to this duplication event and miR167d is an ancient gene that has no detected linkage with other miR167 genes (Figure 4b).

Figure S3 - Microsynteny related to miR167 families between grape and rice.

Interestingly, the region around miR167a lacks detectable colinear relationship to all other miR167 genes in grape.

Obviously, the microsynteny of a single miR167 family cannot be applied with confidence to validate either of these two hypotheses, though the microsynteny and the Ks values suggest that, during grape speciation, the grape miR167e might come from outside of grape species.

2

miRNA167 was up-regulated dramatically in male flower, indicating that it may play an important role in specifying male flower cell types.

MAINTENANCE OF METHYLATION1 (MET1) was negatively regulated by miRNA167, which had expression significant higher in male flower than in female.

miRNA Cleave sitesTarget Gene Mo del [a] Putative function [b] Accession number TAIR Gene Mo del miRNA167 392 POPTR_0013s00750 similar to MAINTENANCE OF METHYLATION KC477290 AT5G66750 Pto-F6 235 POPTR_0005s14640 similar to gibberellin-responsive protein 5 KC477281 AT3G02380 Pto-F6 305 POPTR_0004s18020 similar to myb family transcription factor (MYB4); KC477284 AT1G74670 Pto-F6 394 POPTR_0019s15030 similar to DECREASED DNA METHYLATION 1 KC297686 AT1G08060 Pto-F7 193 POPTR_0004s10800 similar to CONSTANS-like protein CO2.

miR167 and miR160 are thought to control transcription in response to the phytohormone auxin by targeting mRNAs coding for ARF DNA -binding proteins [30], [31].

Our study indicated that miRNA167, Pto-F6 and Pto-F56 might play a positive regulatory role in maintaining DNA methylation levels of female flower through regulation of MET 1 and DDM1.

miRNA159 and miRNA319 also have been reported to act with miRNA164 and miRNA167 in specifying particular cell types during the later stages of flower development [28].

3

Auxin signal transduction is related to bacterial disease resistance in Arabidopsis [14], and this study indicated that miR160, miR167, and miR164 are tightly related to plant disease resistance.

Plants always regulate disease defense through phytohormone signal transduction [54], and several miRNAs (miR159, miR160, miR164, and miR167) were induced by phytohormones [55], [56].

Moreover, an auxin signal transduction feedback regulatory network of miR167-ARF in rice [58], [59] and miR164-NAC in Arabidopsis [60] have also been described.

Using bioinformatics analysis, two feedback regulatory network of miR160-ARF (Auxin receptor factor) and miR167-ARF interaction was found in Arabidopsis [57].

4

The ten most highly expressed miRNAs (miR156, miR157, miR159, miR164, miR167, miR172, miR393, miR396, miR414, miR2275, and miR5021) in buds and leaves are miRNAs regulating genes involved in flower and leaf development processes such as integument development, leaf morphogenesis, meristem initiation, maintenance, and growth, bilateral symmetry determination, organ morphogenesis, plant phase transition, shoot apical meristem identity, flower and fruit development, and plant architecture.

Similar sets of miRNAs, with the exception of miR167 and miR395, were highly expressed in leaves.

5

Target sequences for miR160 have been detected in PoptrARF10.1- 10.2, PoptrARF16.1–16.5 and PoptrARF17.1–17.2 and miR167 targets have been found in PoptrARF6.1–6.3 and PoptrARF8.1–8.2.

AtARF 10, 16 and 17 are known to be regulated by miR160, a miRNA group that is highly conserved across the plant kingdom [45, 46] and AtARF6 and AtARF8 have shown to be regulated by miR167 [47].

6

In Arabidopsis, four drought-responsive miRNAs (miR396, miR168, miR167, and miR171) have been identified by microarray analysis [12].