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A Workflow for the Quantitative Assessment of the Endophytic and Epiphytic Bacterial Microbiomes of the Bark of Populus trichocarpa
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Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L

Jia-Ping Zhao1, Shu Diao, Bing-Yu Zhang

  • 1State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China. zhaojiaping@gmail.com

Plos One
|October 25, 2012
PubMed

Insights

MicroRNAs miR482 and miR1448 evolved in poplar via tandem duplication. Compensatory mutations and co-evolution with targets, including a novel frameshift mechanism, drove their diversification and distinct disease resistance roles.

Area of Science:

  • Plant molecular biology
  • Evolutionary genomics
  • Biochemistry

Background:

  • MicroRNAs (miRNAs) miR482 and miR1448 are implicated in plant disease resistance.
  • miR1448 is specific to Populus trichocarpa, while miR482 is widespread in seed plants.
  • Poplar miR1448 shares sequence homology with miR482 and is co-transcribed, suggesting a shared evolutionary origin.

Purpose of the Study:

  • To investigate the molecular evolution of the MIR1448 gene from the MIR482 gene in poplar.
  • To elucidate the mechanisms driving the evolution of these disease resistance-related miRNAs.
  • To understand the co-evolutionary dynamics between miRNAs and their targets.

Main Methods:

  • Cloning and BLAST analysis of NCBI ESTs and whole-genome shotgun (WGS) contigs.
  • Phylogenetic analysis to determine evolutionary relationships.
  • Nucleotide substitution analysis and comparison of miRNA-target complexes.
  • Identification of novel miRNA-target pairing patterns.

Main Results:

  • The MIR482-MIR1448 polycistron is a family-specific miRNA cluster in Salicaceae.
  • Phylogenetic analysis confirms MIR1448 arose from a tandem duplication of MIR482.
  • Both miRNAs evolve faster than rDNA genes, driven by compensatory mutations in stem regions.
  • Co-evolution with targets, including a novel 'frameshift targeted mechanism', facilitated MIR1448's target gene acquisition.
  • miR482 primarily targets NBS-LRR proteins for disease resistance, while miR1448 exhibits broader functions.

Conclusions:

  • MIR1448 evolved from MIR482 in poplar through tandem duplication and subsequent co-evolutionary processes.
  • Compensatory mutations and a novel frameshift targeted mechanism are key drivers of miRNA evolution and target expansion.
  • miR482 and miR1448 play distinct roles in plant defense, with miR1448 possessing a more diverse functional repertoire.

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