Zhang Z, Green B R, Cavalier-Smith T
Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
J Mol Evol. 2000 Jul;51(1):26-40. doi: 10.1007/s002390010064.
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
通过聚合酶链式反应（PCR）扩增并测序了五种含多甲藻素的甲藻（矮小异帽藻、尼氏异帽藻、圆异帽藻、卡氏扁藻和网状原角藻）的完整叶绿体23S rRNA和psbA基因；从赫氏胸球藻和旋链角毛藻获得了部分序列。与其他生物的叶绿体23S rRNA和psbA基因比较表明，甲藻叶绿体基因是所有基因中分歧最大且进化最快的。构建了四重谜、最大似然法、最大简约法、邻接法和对数行列式树。四重谜和邻接法考虑了位点间速率变化和不变位点。所有psbA和23S rRNA树都显示含多甲藻素的甲藻叶绿体是单系的。在psbA树中，它们与色素界生物和红藻的叶绿体相关。在23S rRNA树中，甲藻总是孢子虫（顶复门）的姐妹群；对三角异帽藻16S rRNA的最大似然分析也将甲藻和孢子虫序列归为一类，但其他方法结果不一致。因此，甲藻叶绿体可能实际上与孢子虫质体有关，但不能完全排除可重复的长枝假象的可能性。所有三个基因的结果都符合甲藻叶绿体通过次生内共生起源于红藻的观点，可能与色素界生物和孢子虫的次生内共生相同。使用不同系统发育算法构建的16S rRNA树之间存在明显分歧，表明这是一个用于阐明叶绿体整体系统发育的较差分子。我们讨论了为什么囊泡藻界（恐龙亚纲、孢子虫和纤毛虫纲）的质体和线粒体基因组都有超快的替换率以及倾向于独特的基因组重排的可能原因。
