Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
Funct Integr Genomics. 2015 Mar;15(2):131-9. doi: 10.1007/s10142-014-0422-z. Epub 2014 Nov 30.
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.
质体 DNA 序列向植物核基因组的转移在植物基因组进化中起着重要作用。定位于核内的质体 DNA（nupDNA）的丰度与核基因组大小呈正相关，但 nupDNA 的遗传内容尚不清楚。在这篇迷你综述中，我们分析了已知植物基因组数据中定位于核内的质体基因片段的数量。我们的分析表明，nupDNA 在植物核基因组中很丰富，并且可以包含多个完整的蛋白编码质体基因拷贝。质体基因的突变核拷贝包含同义和非同义替换。我们根据每个整合发生的时间来估计 nupDNA 的年龄，这是通过比较 nupDNA 和其各自的质体基因的核苷酸替换率来计算的。这些数据表明，植物中 nupDNA 有两种不同的年龄分布模式，并且发现水稻和玉米含有非常高比例的年轻 nupDNA。鉴定了 nupDNA 的表达序列标签和预测启动子，揭示了某些定位于核内的质体基因可能是有功能的，并且有些基因经历了正向自然选择压力。
