Chang Ching-Chun, Lin Hsien-Chia, Lin I-Pin, Chow Teh-Yuan, Chen Hong-Hwa, Chen Wen-Huei, Cheng Chia-Hsiung, Lin Chung-Yen, Liu Shu-Mei, Chang Chien-Chang, Chaw Shu-Miaw
Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan.
Mol Biol Evol. 2006 Feb;23(2):279-91. doi: 10.1093/molbev/msj029. Epub 2005 Oct 5.
Whether the Amborella/Amborella-Nymphaeales or the grass lineage diverged first within the angiosperms has recently been debated. Central to this issue has been focused on the artifacts that might result from sampling only grasses within the monocots. We therefore sequenced the entire chloroplast genome (cpDNA) of Phalaenopsis aphrodite, Taiwan moth orchid. The cpDNA is a circular molecule of 148,964 bp with a comparatively short single-copy region (11,543 bp) due to the unusual loss and truncation/scattered deletion of certain ndh subunits. An open reading frame, orf91, located in the complementary strand of the rrn23 was reported for the first time. A comparison of nucleotide substitutions between P. aphrodite and the grasses indicates that only the plastid expression genes have a strong positive correlation between nonsynonymous (Ka) and synonymous (Ks) substitutions per site, providing evidence for a generation time effect, mainly across these genes. Among the intron-containing protein-coding genes of the sampled monocots, the Ks of the genes are significantly correlated to transitional substitutions of their introns. We compiled a concatenated 61 protein-coding gene alignment for the available 20 cpDNAs of vascular plants and analyzed the data set using Bayesian inference, maximum parsimony, and neighbor-joining (NJ) methods. The analyses yielded robust support for the Amborella/Amborella-Nymphaeales-basal hypothesis and for the orchid and grasses together being a monophyletic group nested within the remaining angiosperms. However, the NJ analysis using Ka, the first two codon positions, or amino acid sequences, respectively, supports the monocots-basal hypothesis. We demonstrated that these conflicting angiosperm phylogenies are most probably linked to the transitional sites at all codon positions, especially at the third one where the strong base-composition bias and saturation effect take place.
在被子植物中，无油樟/无油樟 - 睡莲目或禾本科谱系哪个最先分化，这一问题近来备受争议。该问题的核心聚焦于仅对单子叶植物中的禾本科进行取样可能产生的假象。因此，我们对蝴蝶兰（台湾蝴蝶兰）的整个叶绿体基因组（cpDNA）进行了测序。该cpDNA是一个148,964 bp的环状分子，由于某些ndh亚基的异常缺失和截断/分散缺失，其单拷贝区域相对较短（11,543 bp）。首次报道了位于rrn23互补链上的一个开放阅读框orf91。蝴蝶兰与禾本科之间的核苷酸替换比较表明，只有质体表达基因在每个位点的非同义（Ka）和同义（Ks）替换之间具有很强的正相关性，这为世代时间效应提供了证据，主要体现在这些基因上。在取样的单子叶植物中含内含子的蛋白质编码基因中，这些基因的Ks与它们内含子的转换替换显著相关。我们为现有的20种维管植物cpDNA编制了一个串联的61个蛋白质编码基因比对，并使用贝叶斯推断、最大简约法和邻接法（NJ）对数据集进行了分析。分析结果有力地支持了无油樟/无油樟 - 睡莲目为基部类群的假说，以及兰花和禾本科共同构成一个嵌套在其余被子植物中的单系类群。然而，分别使用Ka、前两个密码子位置或氨基酸序列进行的NJ分析支持单子叶植物为基部类群的假说。我们证明，这些相互矛盾的被子植物系统发育关系很可能与所有密码子位置的转换位点有关，尤其是在第三个密码子位置，那里存在强烈的碱基组成偏差和饱和效应。
