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Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L.

Zhao JP, Diao S, Zhang BY, Niu BQ, Wang QL, Wan XC, Luo YQ - PLoS ONE (2012)

Bottom Line: Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448.We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448.The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China. zhaojiaping@gmail.com

ABSTRACT
The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

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Related in: MedlinePlus

The stem-loop structure and thermodynamic stability of the pre-miR482 and pre-miR1448 in Populus.Free energy values are given in kcal/mole. Vertical bars indicate between-species variability calculated as the double standard error. The mature sequences of miR482.2 and miR1448 were highlighted in light blue.
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pone-0047811-g003: The stem-loop structure and thermodynamic stability of the pre-miR482 and pre-miR1448 in Populus.Free energy values are given in kcal/mole. Vertical bars indicate between-species variability calculated as the double standard error. The mature sequences of miR482.2 and miR1448 were highlighted in light blue.

Mentions: The precursor and mature sequences of miR482.2 and miR1448 were determined for the highly homologous MIR482-MIR1448 polycistron in Populus and Salix, according to the aligned results. The pre-miR482 and the pre-miR1448 in both Populus and Salix could form the classic stem-loop structures that closely resemble the secondary structures of pre-miR482 and pre-miR1448 in P. trichocarpa respectively [6], [13] (Figure 3). The minimum free energy (MFE) analysis indicated that the stability of the secondary structure of pre-miR1448 in both Populus and Salix was −42.6±1.75 kcal/mole and that of pre-miR482 was −45.3±2.12 kcal/mole (two-tailed t-test, not statistically significant at the 5% level).


Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L.

Zhao JP, Diao S, Zhang BY, Niu BQ, Wang QL, Wan XC, Luo YQ - PLoS ONE (2012)

The stem-loop structure and thermodynamic stability of the pre-miR482 and pre-miR1448 in Populus.Free energy values are given in kcal/mole. Vertical bars indicate between-species variability calculated as the double standard error. The mature sequences of miR482.2 and miR1448 were highlighted in light blue.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475693&req=5

pone-0047811-g003: The stem-loop structure and thermodynamic stability of the pre-miR482 and pre-miR1448 in Populus.Free energy values are given in kcal/mole. Vertical bars indicate between-species variability calculated as the double standard error. The mature sequences of miR482.2 and miR1448 were highlighted in light blue.
Mentions: The precursor and mature sequences of miR482.2 and miR1448 were determined for the highly homologous MIR482-MIR1448 polycistron in Populus and Salix, according to the aligned results. The pre-miR482 and the pre-miR1448 in both Populus and Salix could form the classic stem-loop structures that closely resemble the secondary structures of pre-miR482 and pre-miR1448 in P. trichocarpa respectively [6], [13] (Figure 3). The minimum free energy (MFE) analysis indicated that the stability of the secondary structure of pre-miR1448 in both Populus and Salix was −42.6±1.75 kcal/mole and that of pre-miR482 was −45.3±2.12 kcal/mole (two-tailed t-test, not statistically significant at the 5% level).

Bottom Line: Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448.We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448.The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China. zhaojiaping@gmail.com

ABSTRACT
The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.

Show MeSH
Related in: MedlinePlus