Plastid DNA insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis

Funct Integr Genomics. 2015 Mar;15(2):131-9. doi: 10.1007/s10142-014-0422-z. Epub 2014 Nov 30.

Abstract

The transfer of plastid DNA sequences into plant nuclear genomes plays an important role in the genomic evolution of plants. The abundance of nuclear-localized plastid DNA (nupDNA) correlates positively with nuclear genome size, but the genetic content of nupDNA remains unknown. In this mini review, we analyzed the number of nuclear-localized plastid gene fragments in known plant genomic data. Our analysis suggests that nupDNAs are abundant in plant nuclear genomes and can include multiple complete copies of protein-coding plastid genes. Mutated nuclear copies of plastid genes contained synonymous and nonsynonymous substitutions. We estimated the age of the nupDNAs based on the time when each integration occurred, which was calculated by comparing the nucleotide substitution rates of the nupDNAs and their respective plastid genes. These data suggest that there are two distinct age distribution patterns for nupDNAs in plants, and Oryza sativa and Zea mays were found to contain a very high proportion of young nupDNAs. Expressed sequence tags and predicted promoters of nupDNAs were identified, revealing that certain nuclear-localized plastid genes may be functional and that some have undergone positive natural selection pressure.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Cell Nucleus / genetics
  • DNA, Chloroplast / analysis
  • DNA, Chloroplast / chemistry*
  • DNA, Plant / analysis
  • DNA, Plant / chemistry*
  • Genes, Chloroplast
  • Genome, Plant*
  • Promoter Regions, Genetic*

Substances

  • DNA, Chloroplast
  • DNA, Plant