Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera)

PLoS One. 2013 Aug 8;8(8):e71435. doi: 10.1371/journal.pone.0071435. eCollection 2013.

Abstract

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arecaceae / genetics*
  • Base Sequence
  • Evolution, Molecular*
  • Genes, Plant
  • Genome, Plant
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Phylogeny
  • RNA, Plant / genetics*
  • Segmental Duplications, Genomic
  • Sequence Alignment

Substances

  • MicroRNAs
  • RNA, Plant

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (No. 31101179), the Project for High-Level Returned Scholar of Ministry of Human Resources and Social Security of P.R. China (2011), the National Nonprofit Institute Research Grant of CATAS- ITBB120506, and Australian Research Council Early Career Researcher Award (DE120100668). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.