Basu Malay Kumar, Rogozin Igor B, Deusch Oliver, Dagan Tal, Martin William, Koonin Eugene V
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Mol Biol Evol. 2008 Jan;25(1):111-9. doi: 10.1093/molbev/msm234. Epub 2007 Oct 31.
Some of the principal transitions in the evolution of eukaryotes are characterized by engulfment of prokaryotes by primitive eukaryotic cells. In particular, approximately 1.6 billion years ago, engulfment of a cyanobacterium that became the ancestor of chloroplasts and other plastids gave rise to Plantae, the major branch of eukaryotes comprised of glaucophytes, red algae, green algae, and green plants. After endosymbiosis, there was large-scale migration of genes from the endosymbiont to the nuclear genome of the host such that approximately 18% of the nuclear genes in Arabidopsis appear to be of chloroplast origin. To gain insights into the process of evolution of gene structure in these, originally, intronless genes, we compared the properties and the evolutionary dynamics of introns in genes of plastid origin and ancestral eukaryotic genes in Arabidopsis, poplar, and rice genomes. We found that intron densities in plastid-derived genes were slightly but significantly lower than those in ancestral eukaryotic genes. Although most of the introns in both categories of genes were conserved between monocots (rice) and dicots (Arabidopsis and poplar), lineage-specific intron gain was more pronounced in plastid-derived genes than in ancestral genes, whereas there was no significant difference in the intron loss rates between the 2 classes of genes. Thus, after the transfer to the nuclear genome, the plastid-derived genes have undergone a massive intron invasion that, by the time of the divergence of dicots and monocots (150-200 MYA), yielded intron densities only slightly lower than those in ancestral genes. Nevertheless, the accumulation of introns in plastid-derived genes appears not to have reached saturation and continues to this time, albeit at a low rate. The overall pattern of intron gain and loss in the plastid-derived genes is shaped by this continuing gain and the more general tendency for loss that is characteristic of the recent evolution of plant genes.
真核生物进化过程中的一些主要转变以原始真核细胞吞噬原核生物为特征。特别是，大约16亿年前，一种蓝细菌被吞噬，它成为了叶绿体和其他质体的祖先，从而产生了植物界，这是真核生物的主要分支，包括灰胞藻、红藻、绿藻和绿色植物。内共生之后，基因从内共生体大规模迁移到宿主的核基因组中，以至于拟南芥中约18%的核基因似乎起源于叶绿体。为了深入了解这些最初无内含子的基因的基因结构进化过程，我们比较了拟南芥、杨树和水稻基因组中质体起源基因和祖先真核基因内含子的特性和进化动态。我们发现，质体衍生基因中的内含子密度略低于祖先真核基因，但差异显著。尽管这两类基因中的大多数内含子在单子叶植物（水稻）和双子叶植物（拟南芥和杨树）之间是保守的，但质体衍生基因中的谱系特异性内含子获得比祖先基因更明显，而这两类基因的内含子丢失率没有显著差异。因此，转移到核基因组后，质体衍生基因经历了大规模的内含子入侵，到双子叶植物和单子叶植物分化时（1.5 - 2亿年前），其内含子密度仅略低于祖先基因。然而，质体衍生基因中内含子的积累似乎尚未达到饱和，并且一直持续到现在，尽管速率很低。质体衍生基因内含子得失的总体模式是由这种持续的获得以及植物基因近期进化中更普遍特征性丢失趋势所塑造的。
