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

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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.

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Acknowledgments

This work was supported by grants from the Trans-Century Training Program’s Foundation for the Talents by Heilongjiang Provincial Education Department (1251–NCET—004) and the Innovation Team Project by Heilongjiang Provincial Education Department to A. X. Wang, the Returned Oversea Scholar Foundation by Heilongjiang Provincial Education Department (1252HQ011), and the National Science Foundation of China (31301780) to X. L. Chen.

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Authors and Affiliations

  1. Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin, 150030, China

    Hongyu Chen, Zhenzhu Zhang, Chao Gong & Aoxue Wang

  2. Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China

    Ying Yu

  3. College of Horticulture, Northeast Agricultural University, Harbin, 150030, China

    Xiuling Chen & Jingfu Li

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  1. Hongyu Chen
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  2. Ying Yu
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  3. Xiuling Chen
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Correspondence to Aoxue Wang.

Supplementary material

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Online Resource 1

Homologs of plastid genes in plant nuclear DNA. (PDF 728 kb)

Online Resource 2

Homologs of intact coding DNA sequences (CDSs) of plastid genes in plant nuclear DNA. (PDF 257 kb)

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Sequence alignment of predicted plant gene promoter regions. (PDF 384 kb)

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Chen, H., Yu, Y., Chen, X. et al. Plastid DNA insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis. Funct Integr Genomics 15, 131–139 (2015). https://doi.org/10.1007/s10142-014-0422-z

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