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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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Neighbor-joining phylogenetic trees based on the MIR482-MIR1448 polycistron and rDNA-ITS combined dataset in Populus.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). Two Salix clones were treated as an outgroup.
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pone-0047811-g005: Neighbor-joining phylogenetic trees based on the MIR482-MIR1448 polycistron and rDNA-ITS combined dataset in Populus.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). Two Salix clones were treated as an outgroup.

Mentions: In addition, we found that the pre-miRNAs, rDNA-ITS1, and rDNA-ITS2 had similar substitution ratios. Nuclear rDNA-ITS sequences have been applied widely to the phylogenetic analysis of plants and fungi [16], [17]. This led to the question of whether the MIR482-MIR1448 polycistron (the single-copy in the poplar genome) would be beneficial for taxonomic purposes in poplars. We constructed three NJ trees based on the combined data from the MIR482-MIR1448 polycistron (not including the 5′ upstream sequence before −92 nt from the pre-miR482), rDNA-ITS and MIR482-MIR1448-ITS data, respectively. The results were similar to the results in the previous study [16]. The three phylogenetic trees could reveal the difference of the species in Populus sections Leuce, Turanga, and Leucoides, but could not distinguish the species in sections Tacamahaca and Aigeiros (the NJ phylogentic tree based on MIR482-MIR1448-ITS data see Figure 5).


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)

Neighbor-joining phylogenetic trees based on the MIR482-MIR1448 polycistron and rDNA-ITS combined dataset in Populus.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). Two Salix clones were treated as an outgroup.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047811-g005: Neighbor-joining phylogenetic trees based on the MIR482-MIR1448 polycistron and rDNA-ITS combined dataset in Populus.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). Two Salix clones were treated as an outgroup.
Mentions: In addition, we found that the pre-miRNAs, rDNA-ITS1, and rDNA-ITS2 had similar substitution ratios. Nuclear rDNA-ITS sequences have been applied widely to the phylogenetic analysis of plants and fungi [16], [17]. This led to the question of whether the MIR482-MIR1448 polycistron (the single-copy in the poplar genome) would be beneficial for taxonomic purposes in poplars. We constructed three NJ trees based on the combined data from the MIR482-MIR1448 polycistron (not including the 5′ upstream sequence before −92 nt from the pre-miR482), rDNA-ITS and MIR482-MIR1448-ITS data, respectively. The results were similar to the results in the previous study [16]. The three phylogenetic trees could reveal the difference of the species in Populus sections Leuce, Turanga, and Leucoides, but could not distinguish the species in sections Tacamahaca and Aigeiros (the NJ phylogentic tree based on MIR482-MIR1448-ITS data see Figure 5).

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