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3 publications mentioning ptc-MIR1444c

Open access articles that are associated with the species Populus trichocarpa and mention the gene name MIR1444c. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 105
Other miRNAs from this paper: ptc-MIR1444a, ptc-MIR1444b, ptc-MIR1444d, ptc-MIR1444e
miR1444 -mediated cleavage of PPO transcriptsPlant miRNAs have perfect or near-perfect complementarities to their targets, allowing an effective prediction of target sequence through computational approaches like psRNATarget 44 45. [score:7]
MIR1444 genes show extensive similarity to PPO targetsIn Arabidopsis, several MIRs, such as MIR161 and MIR163, were generated from inverted gene duplication events of target genes 49 50. [score:5]
psRNATarget analysis of miR1444 targets. [score:5]
Targets of ptr-miR1444a, ptr-miR1444b, peu-miR1444a, peu-miR1444b, spu-miR1444 and ssu-miR1444 were predicted using psRNATarget with the default parameters 45. [score:5]
Multiple sequence alignment of MIR1444 precursors and miR1444 -targeted PPOs in Populus and Salix. [score:3]
Using similar strategies, we identified two expressed MIR1444 genes from each of the other Populus species without whole genome sequences, including P. tomentosa, P. deltoids, P. balsamifera, P. tremula, P. tremuloides, P. simonii, and P. pruinosa (Fig. 1; Table S1). [score:3]
Blast analysis of MIR1444 sequences against RNA-seq data of S. matsudana showed the existence of an expressed MIR1444 gene, termed sma-MIR1444, in S. matsudana (Fig. 1). [score:3]
The results showed that spu-MIR1444 and ssu-MIR1444 were the expressed MIR1444 genes in S. purpurea and S. suchowensis, respectively. [score:3]
Thus, the origination of conserved CuB domain -targeted MIR1444 genes could be under strong negative selection. [score:3]
To elucidate the origin of MIR1444 genes, we aligned foldback arms and their flanking sequences of MIR1444 precursors with PPO targets. [score:3]
Mature miRNAs of the MIR1444 gene family target to the cDNA region encoding CuB domain. [score:3]
This hypothesis is supported by the fact that MIR1444 genes show extensive similarity to their PPO targets, and the existence of many partial PPO sequences in plant genomes. [score:3]
MIR1444 genes show extensive similarity to PPO targets. [score:3]
After duplication, the sequence of MIR1444 genes was further diversified through mutation as evidenced by precursors and mature miR1444 sequences in Populus and Idesia or lost through DNA segment deletion during chromosome rearrangement in Salix (Fig. 7). [score:2]
5′ RLM-RACE validation of miR1444-directed cleavage. [score:2]
miR1444-directed cleavage of PPO genes were validated using the modified RNA ligase -mediated rapid amplification of 5′ cDNA ends method (5′ RLM-RACE) as described previously 48. [score:2]
MIR1444 genes were expanded through the Salicoid genome duplication event and then further diversified through sequence mutation. [score:2]
Continuous mutation generates MIR1444 genes with sequences and mismatch patterns in and surrounding the miR1444:miR1444* region. [score:2]
Populus and Salix MIR1444 gene identification P. trichocarpa MIR1444 precursors were downloaded from miRBase 23. [score:1]
Ptr- MIR1444c shows 100% identities with the assembled genome sequence, while ptr- MIR1444b has one nucleotide mismatch located in the loop region of fold-back structure. [score:1]
Only one MIR1444 gene in S. Purpurea, S. Suchowensis and S. Matsudana. [score:1]
The results suggest that I. polycarpa contains two MIR1444 genes, termed ipo-MIR1444a and ipo-MIR1444b, respectively (Fig. 1). [score:1]
Transcriptome-wide identification of MIR1444 genes was carried out through BLAST analysis of ptr- MIR1444s against the Nt and EST databases and/or RNA-seq reads from illumina and 454 runs using BLASTn 65. [score:1]
In this study, we found two MIR1444 genes in various Populus species and one in Salix. [score:1]
Expansion of MIR1444 genes through the salicoid genome duplication event. [score:1]
cgi) and 318.6 million of RNA-seq reads from five illumina runs for ptr- MIR1444a– ptr- MIR1444c (Table S1) 27 28. [score:1]
Only one MIR1444 gene in S. Purpurea, S. Suchowensis and S. Matsudana Salix, comprising more than 300 species, is the genus phylogenetically most closely related to Populus 36. [score:1]
Supplementary Dataset 1. Supplementary Dataset 2. Hairpin structures of MIR1444 precursors in Populus, Salix and Idesia. [score:1]
A MIR1444 gene was identified from each of the two Salix genomes (Fig. 1). [score:1]
Duplication and divergence of MIR1444 genes in Populus. [score:1]
This brings the number of authentic MIR1444 precursors to 23, including 18 from Populus, 3 from Salix and 2 from Idesia. [score:1]
spu-MIR1444 showed the greatest similarity with SpuPPO1 and SpuPPO2 in S. purpurea. [score:1]
No sequence identical to ptr- MIR1444c was retrieved, although ptr- MIR1444c exhibited 100% identities with the assembled P. trichocarpa genome sequence. [score:1]
The mature ptr-miR1444b and ptr-miR1444c sequences are identical. [score:1]
Among the four P. trichocarpa and P. euphratica MIR1444 genes, MIR1444b showed greater similarity with PPO genes than MIR1444a in P. trichocarpa and P. euphratica, respectively. [score:1]
In order to test whether all of the five ptr- MIR1444 genes are authentic, we performed blast analysis of ptr- MIR1444 precursors against the P. trichocarpa genome database (v3.0, https://phytozome. [score:1]
Through the comparative analysis of MIR1444 genes in Populus and Idesia, we found that Idesia could also share the Salicoid genome duplication event and Populus and Idesia MIR1444 genes were all expanded through the event (Fig. 7). [score:1]
miR1444 -mediated cleavage of PPOs in Populus and Salix. [score:1]
It is consistent with the results from P. trichocarpa and P. euphratica, suggesting the existence of two MIR1444 genes in a genome of Populus species. [score:1]
Genome- and transcriptome-wide identification of MIR1444 genes in Populus. [score:1]
Sequence divergence between ptr-miR1444a and ptr-miR1444b was confirmed by mapping sequence reads from three previously reported small RNA libraries 40 (GSM717875, GSM717876 and GSM717877) to ptr-MIR1444 precursors (Fig. S2). [score:1]
Through genome- and transcriptome-wide analysis and molecular cloning, we identified a total of 23 MIR1444 genes in Populus, Salix and Idesia (Fig. 1). [score:1]
Proposed mo del for MIR1444 origin and evolution. [score:1]
Taken together, the results suggest that there is only one MIR1444 gene in a genome of Salix species, such as S. suchowensis, S. purpurea, and S. matsudana. [score:1]
Two P. euphratica peu- MIR1444 genes were identified (Fig. 1). [score:1]
miR1444 -mediated cleavage of PPO transcripts. [score:1]
Populus and Salix MIR1444 gene identification. [score:1]
A copy of the duplicated MIR1444 genes was lost through DNA segment deletion during chromosome rearrangement in Salix. [score:1]
Ptr- MIR1444d is an anti-sense sequence of ptr- MIR1444c, while ptr- MIR1444e is an anti-sense sequence of ptr- MIR1444b. [score:1]
Molecular cloning of Idesia Polycarpa MIR1444 precursors and phylogenetic analysis of Salicaceae MIR1444s Idesia is a genus formerly placed in the family Flacourtiaceae, but now included in the family Salicaceae 21. [score:1]
Taken together, we conclude that the P. trichocarpa genome contains two ptr- MIR1444 genes, ptr- MIR1444a in chromosome 8 and ptr- MIR1444b in chromosome 10. [score:1]
MIR1444 genes were originated from PPOs through an inverted gene duplication event. [score:1]
Molecular cloning of Idesia Polycarpa MIR1444 precursors and phylogenetic analysis of Salicaceae MIR1444s. [score:1]
Blast analysis of Populus and Salix MIR1444 genes against RNA-seq data of Idesia polycarpa flower buds was carried out using BLASTn 65. [score:1]
Molecular cloning of ipo-MIR1444a and ipo-MIR1444b genesBlast analysis of Populus and Salix MIR1444 genes against RNA-seq data of Idesia polycarpa flower buds was carried out using BLASTn 65. [score:1]
The results indicate the expansion of MIR1444 genes through the Salicoid duplication event. [score:1]
We next carried out blast analysis of the identified spu- and ssu-MIR1444 sequences against the high-throughput illumina and 454 sequencing data of S. purpurea and S. suchowensis (Table S1). [score:1]
P. trichocarpa MIR1444 precursors were downloaded from miRBase 23. [score:1]
Expansion of MIR1444 genes through the salicoid genome duplication eventAnalysis of the fourfold synonymous third-codon transversion position (4DTV) values in P. trichocarpa and P. euphratica has shown that two ancient whole-genome duplication (WGD) events occurred in the Populus lineage 2 22. [score:1]
ssu-MIR1444 showed the greatest similarity with SsuPPO2 and SsuPPO3 in S. suchowensis. [score:1]
Through the analysis of MIR1444 genes in Populus, Salix and Idesia, we proposed that MIR1444 genes were originated from PPOs through an inverted gene duplication event (Fig. 7). [score:1]
How to cite this article: Wang, M. et al. Origin and evolution of MIR1444 genes in Salicaceae. [score:1]
Blast analysis of Populus and Salix MIR1444 genes against RNA-seq data of I. polycarpa flower buds identified partial sequences of two ipo-MIR1444 genes. [score:1]
Since no Salix MIR1444 gene had been reported previously, we first searched current assemblies of the S. purpurea and the S. suchowensis genomes. [score:1]
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2
[+] score: 13
Other miRNAs from this paper: ptc-MIR1444a, ptc-MIR1444b, ptc-MIR1444d, ptc-MIR1444e, smi-MIR12112
MiR1444 -mediated regulation of PtPPOs is significant in copper homeostasis and stress responses in P. trichocarpa 7. In order to examine whether SmPPOs are regulated by miR1444, we analyzed published and our own high throughput sequencing data of small RNAs from roots, stems, leaves and flowers of S. miltiorrhiza 26 27. [score:3]
In P. trichocarpa, at least 13 PtPPOs are regulated by miR1444 7. In grapevine, VvPPO is regulated by miR058 51. [score:3]
Taken together, we conclude that miR1444 does not exist in S. miltiorrhiza and SmPPOs are not regulated by miR1444. [score:2]
SmPPOs are not regulated by miR1444 in S. miltiorrhiza. [score:2]
Consistently, no MIR1444 precursor sequence was identified. [score:1]
Analysis of small RNA data revealed the loss of miR1444 in S. miltiorrhiza. [score:1]
No miR1444 sequence was found. [score:1]
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3
[+] score: 12
Other miRNAs from this paper: ptc-MIR159a, ptc-MIR159b, ptc-MIR159d, ptc-MIR159e, ptc-MIR159c, ptc-MIR160a, ptc-MIR160b, ptc-MIR160c, ptc-MIR160d, ptc-MIR160e, ptc-MIR160f, ptc-MIR160g, ptc-MIR160h, ptc-MIR164a, ptc-MIR164b, ptc-MIR164c, ptc-MIR164d, ptc-MIR164e, ptc-MIR164f, ptc-MIR167a, ptc-MIR167b, ptc-MIR167c, ptc-MIR167d, ptc-MIR167e, ptc-MIR167f, ptc-MIR167g, ptc-MIR167h, ptc-MIR168a, ptc-MIR168b, ptc-MIR169a, ptc-MIR169aa, ptc-MIR169ab, ptc-MIR169ac, ptc-MIR169ad, ptc-MIR169ae, ptc-MIR169af, ptc-MIR169b, ptc-MIR169c, ptc-MIR169d, ptc-MIR169e, ptc-MIR169f, ptc-MIR169g, ptc-MIR169h, ptc-MIR169i, ptc-MIR169j, ptc-MIR169k, ptc-MIR169l, ptc-MIR169m, ptc-MIR169n, ptc-MIR169o, ptc-MIR169p, ptc-MIR169q, ptc-MIR169r, ptc-MIR169s, ptc-MIR169t, ptc-MIR169u, ptc-MIR169v, ptc-MIR169w, ptc-MIR169x, ptc-MIR169y, ptc-MIR169z, ptc-MIR171a, ptc-MIR171b, ptc-MIR171c, ptc-MIR171d, ptc-MIR171e, ptc-MIR171f, ptc-MIR171g, ptc-MIR171h, ptc-MIR171i, ptc-MIR390a, ptc-MIR390b, ptc-MIR390c, ptc-MIR390d, ptc-MIR394a, ptc-MIR394b, ptc-MIR395a, ptc-MIR395b, ptc-MIR395c, ptc-MIR395d, ptc-MIR395e, ptc-MIR395f, ptc-MIR395g, ptc-MIR395h, ptc-MIR395i, ptc-MIR395j, ptc-MIR396a, ptc-MIR396b, ptc-MIR396c, ptc-MIR396d, ptc-MIR396e, ptc-MIR396f, ptc-MIR396g, ptc-MIR398a, ptc-MIR403a, ptc-MIR408, ptc-MIR472a, ptc-MIR472b, ptc-MIR482a, ptc-MIR171k, ptc-MIR171l, ptc-MIR171m, ptc-MIR171j, ptc-MIR1444a, ptc-MIR1444b, ptc-MIR1446a, ptc-MIR482d, ptc-MIR169ag, ptc-MIR482b, ptc-MIR395k, ptc-MIR482c, ptc-MIR1444d, ptc-MIR1444e
Their targets include miR408 -targeted plastocyanin-like proteins and miR1444 -targeted all plastid polyphenol oxidases [60, 61]. [score:7]
Two downregulated miRNAs (Ptc-miR408 and Ptc-miR1444) have been reported to be Cu-responsive miRNAs in P. trichocarpa. [score:4]
In addition, miR472, miR473, and miR1444 were found to be drought-responsive only in Populus plants, including in this study. [score:1]
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