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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 tree of pre-miR482 sequences in seed plants obtained from MEGA 5.0.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). The phylogeny of pre-miR1448 of P. trichocarpa is also compared to pre-miR482 sequences in other plants.
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pone-0047811-g001: Neighbor-joining phylogenetic tree of pre-miR482 sequences in seed plants obtained from MEGA 5.0.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). The phylogeny of pre-miR1448 of P. trichocarpa is also compared to pre-miR482 sequences in other plants.

Mentions: The results of the phylogenetic analysis (Figure 1) indicate that MIR482 is an “old miRNA” gene [7], and its formation in plants predates the split of gymnosperms and angiosperms (∼300 million years ago) [11]. In addition, the paralog genes of MIR482 in some specific species (such as MIR482a, −b, −c and −d in loblolly pine) are the products of one or two gene duplication events after the species formed.


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 tree of pre-miR482 sequences in seed plants obtained from MEGA 5.0.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). The phylogeny of pre-miR1448 of P. trichocarpa is also compared to pre-miR482 sequences in other plants.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0047811-g001: Neighbor-joining phylogenetic tree of pre-miR482 sequences in seed plants obtained from MEGA 5.0.Numbers in the tree represent the bootstrap value (bootstrap values below 50% are not shown at the nodes). The phylogeny of pre-miR1448 of P. trichocarpa is also compared to pre-miR482 sequences in other plants.
Mentions: The results of the phylogenetic analysis (Figure 1) indicate that MIR482 is an “old miRNA” gene [7], and its formation in plants predates the split of gymnosperms and angiosperms (∼300 million years ago) [11]. In addition, the paralog genes of MIR482 in some specific species (such as MIR482a, −b, −c and −d in loblolly pine) are the products of one or two gene duplication events after the species formed.

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