PoplarV1, Main, Exploration, bibRecord, 002960

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

Identifieur interne : 002960 ( Main/Exploration ); précédent : 002959; suivant : 002961

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

Auteurs : Jia-Ping Zhao [République populaire de Chine] ; Shu Diao ; Bing-Yu Zhang ; Bao-Qing Niu ; Qing-Ling Wang ; Xian-Chong Wan ; You-Qing Luo

Source :

PloS one [ 1932-6203 ] ; 2012.

RBID : pubmed:23094096

Descripteurs français

English descriptors

KwdEn :
- Arabidopsis (genetics), Base Sequence (MeSH), Cloning, Molecular (MeSH), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), MicroRNAs (MeSH), Molecular Sequence Data (MeSH), Multigene Family (MeSH), Oryza (genetics), Phylogeny (MeSH), Populus (classification), Populus (genetics), Populus (immunology), RNA Folding (MeSH), RNA, Plant (MeSH), Sequence Homology, Nucleic Acid (MeSH).
MESH :
- chemical : MicroRNAs, RNA, Plant.
- classification : Populus.
- genetics : Arabidopsis, Oryza, Populus.
- immunology : Populus.
- Base Sequence, Cloning, Molecular, Evolution, Molecular, Gene Duplication, Gene Expression Regulation, Plant, Genes, Plant, Molecular Sequence Data, Multigene Family, Phylogeny, RNA Folding, Sequence Homology, Nucleic Acid.

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.

DOI: 10.1371/journal.pone.0047811
PubMed: 23094096
PubMed Central: PMC3475693

Affiliations:

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Le document en format XML

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<term>Famille multigénique (MeSH)</term>
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<front><div type="abstract" xml:lang="en">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.</div>
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<Abstract><AbstractText>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.</AbstractText>
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<affiliations><list><country><li>République populaire de Chine</li>
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<name sortKey="Luo, You Qing" sort="Luo, You Qing" uniqKey="Luo Y" first="You-Qing" last="Luo">You-Qing Luo</name>
<name sortKey="Niu, Bao Qing" sort="Niu, Bao Qing" uniqKey="Niu B" first="Bao-Qing" last="Niu">Bao-Qing Niu</name>
<name sortKey="Wan, Xian Chong" sort="Wan, Xian Chong" uniqKey="Wan X" first="Xian-Chong" last="Wan">Xian-Chong Wan</name>
<name sortKey="Wang, Qing Ling" sort="Wang, Qing Ling" uniqKey="Wang Q" first="Qing-Ling" last="Wang">Qing-Ling Wang</name>
<name sortKey="Zhang, Bing Yu" sort="Zhang, Bing Yu" uniqKey="Zhang B" first="Bing-Yu" last="Zhang">Bing-Yu Zhang</name>
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Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L.

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

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