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

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• 作者：Hongyu Chen (1)
  Ying Yu (2)
  Xiuling Chen (3)
  Zhenzhu Zhang (1)
  Chao Gong (1)
  Jingfu Li (3)
  Aoxue Wang (1)
  
  1. Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes ; College of Life Science ; Northeast Agricultural University ; Harbin ; 150030 ; China
  2. Institute of Industrial Crops ; Heilongjiang Academy of Agricultural Sciences ; Harbin ; 150086 ; China
  3. College of Horticulture ; Northeast Agricultural University ; Harbin ; 150030 ; China
  
• 关键词：Plastid DNA ; Genome ; Promoter ; Plant
• 刊名：Functional & Integrative Genomics
• 出版年：2015
• 出版时间：March 2015
• 年：2015
• 卷：15
• 期：2
• 页码：131-139
• 全文大小：890 KB
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• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Plant Genetics and Genomics
  Microbial Genetics and Genomics
  Biochemistry
  Bioinformatics
  Animal Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1438-7948

文摘

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.