Wang Daryi, Wu Yu-Wei, Shih Arthur Chun-Chieh, Wu Chung-Shien, Wang Ya-Nan, Chaw Shu-Miaw
Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan.
Mol Biol Evol. 2007 Sep;24(9):2040-8. doi: 10.1093/molbev/msm133. Epub 2007 Jul 3.
With the completion of the first gymnosperm mitochondrial genome (mtDNA) from Cycas taitungensis and the availability of more mtDNA taxa in the past 5 years, we have conducted a systematic analysis of DNA transfer from chloroplast genomes (cpDNAs) to mtDNAs (mtpts) in 11 plants, including 2 algae, 1 liverwort, 1 moss, 1 gymnosperm, 3 monocots, and 3 eudicots. By using shared gene order and boundaries between different mtpts as the criterion, the timing of cpDNA transfer during plant evolution was estimated from the phylogenetic tree reconstructed independently from concatenated protein-coding genes of 11 available mtDNAs. Several interesting findings emerged. First, frequent DNA transfer from cpDNA to mtDNA occurred at least as far back as the common ancestor of extant gymnosperms and angiosperms, about 300 MYA. The oldest mtpt is trnV(uac)-trnM(cau)-atpE-atpB-rbcL. Three other mtpts--psaA-psaB, rps19-trnH(gug)-rpl2-rpl23, and psbE-psbF--were dated to the common ancestor of extant angiosperms, at least 150 MYA. However, all protein-coding genes of mtpts have degenerated since their first transfer. Therefore, mtpts contribute nothing to the functioning of mtDNA but junk sequences. We discovered that the cpDNA transfers have occurred randomly at any positions of the cpDNAs. We provide strong evidence that the cp-derived tRNA-trnM(cau) is the only mtpt (1 out of 3 cp-derived tRNA shared by seed plants) truly transferred from cpDNA to mtDNA since the time of the common ancestor of extant gymnosperms and angiosperms. Our observations support the proposition of Richly and Leister (2004) that "primary insertions of organellar DNAs are large and then diverge and fragment over evolutionary time."
随着台东苏铁首个裸子植物线粒体基因组（mtDNA）的完成以及过去5年中更多mtDNA分类群的可得，我们对11种植物中从叶绿体基因组（cpDNA）到线粒体DNA（mtpts）的DNA转移进行了系统分析，这11种植物包括2种藻类、1种苔类植物、1种藓类植物、1种裸子植物、3种单子叶植物和3种双子叶植物。以不同mtpts之间共享的基因顺序和边界为标准，根据从11个可用mtDNA的串联蛋白质编码基因独立重建的系统发育树，估计了植物进化过程中cpDNA转移的时间。出现了几个有趣的发现。首先，从cpDNA到mtDNA的频繁DNA转移至少可以追溯到现存裸子植物和被子植物的共同祖先，约3亿年前。最古老的mtpt是trnV（uac）-trnM（cau）-atpE-atpB-rbcL。另外三个mtpts——psaA-psaB、rps19-trnH（gug）-rpl2-rpl23和psbE-psbF——可追溯到现存被子植物的共同祖先，至少1.5亿年前。然而，mtpts的所有蛋白质编码基因自首次转移以来已经退化。因此，mtpts对mtDNA的功能没有贡献，只是垃圾序列。我们发现cpDNA转移在cpDNA的任何位置随机发生。我们提供了有力证据，表明自现存裸子植物和被子植物的共同祖先时期以来，cp衍生的tRNA-trnM（cau）是唯一真正从cpDNA转移到mtDNA的mtpt（种子植物共享的3个cp衍生tRNA中的1个）。我们的观察结果支持了Richly和Leister（2004年）的观点，即“细胞器DNA的初次插入很大，然后在进化过程中发生分歧和片段化”。
