Edgcomb V P, Roger A J, Simpson A G, Kysela D T, Sogin M L
Josephine Bay-Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA.
Mol Biol Evol. 2001 Apr;18(4):514-22. doi: 10.1093/oxfordjournals.molbev.a003830.
Jakobids are free-living, heterotrophic flagellates that might represent early-diverging mitochondrial protists. They share ultrastructural similarities with eukaryotes that occupy basal positions in molecular phylogenies, and their mitochondrial genome architecture is eubacterial-like, suggesting a close affinity with the ancestral alpha-proteobacterial symbiont that gave rise to mitochondria and hydrogenosomes. To elucidate relationships among jakobids and other early-diverging eukaryotic lineages, we characterized alpha- and beta-tubulin genes from four jakobids: Jakoba libera, Jakoba incarcerata, Reclinomonas americana (the "core jakobids"), and Malawimonas jakobiformis. These are the first reports of nuclear genes from these organisms. Phylogenies based on alpha-, beta-, and combined alpha- plus beta-tubulin protein data sets do not support the monophyly of the jakobids. While beta-tubulin and combined alpha- plus beta-tubulin phylogenies showed a sister group relationship between J. libera and R. americana, the two other jakobids, M. jakobiformis and J. incarcerata, had unclear affinities. In all three analyses, J. libera, R. americana, and M. jakobiformis emerged from within a well-supported large "plant-protist" clade that included plants, green algae, cryptophytes, stramenopiles, alveolates, Euglenozoa, Heterolobosea, and several other protist groups, but not animals, fungi, microsporidia, parabasalids, or diplomonads. A preferred branching order within the plant-protist clade was not identified, but there was a tendency for the J. libera-R. americana lineage to group with a clade made up of the heteroloboseid amoeboflagellates and euglenozoan protists. Jakoba incarcerata branched within the plant-protist clade in the beta- and the combined alpha- plus beta-tubulin phylogenies. In alpha- tubulin trees, J. incarcerata occupied an unresolved position, weakly grouping with the animal/fungal/microsporidian group or with amitochondriate parabasalid and diplomonad lineages, depending on the phylogenetic method employed. Tubulin gene phylogenies were in general agreement with mitochondrial gene phylogenies and ultrastructural data in indicating that the "jakobids" may be polyphyletic. Relationships with the putatively deep-branching amitochondriate diplomonads remain uncertain.
贾科比虫是自由生活的异养鞭毛虫，可能代表早期分化的线粒体原生生物。它们与在分子系统发育中处于基部位置的真核生物具有超微结构上的相似性，并且它们的线粒体基因组结构类似真细菌，这表明它们与产生线粒体和氢化酶体的祖先α-变形细菌共生体有密切的亲缘关系。为了阐明贾科比虫与其他早期分化的真核生物谱系之间的关系，我们对四种贾科比虫的α-和β-微管蛋白基因进行了表征：自由贾科比虫、囚禁贾科比虫、美洲隐滴虫（“核心贾科比虫”）和雅各布样马拉维虫。这些是关于这些生物核基因的首次报道。基于α-、β-以及α-加β-微管蛋白数据集的系统发育分析不支持贾科比虫的单系性。虽然β-微管蛋白以及α-加β-微管蛋白的系统发育分析显示自由贾科比虫和美洲隐滴虫之间存在姐妹群关系，但另外两种贾科比虫，雅各布样马拉维虫和囚禁贾科比虫的亲缘关系不明确。在所有这三种分析中，自由贾科比虫、美洲隐滴虫和雅各布样马拉维虫出现在一个得到充分支持的大型“植物 - 原生生物”分支中，该分支包括植物、绿藻、隐藻、不等鞭毛类、囊泡虫类、眼虫纲、异叶足虫类以及其他几个原生生物类群，但不包括动物、真菌、微孢子虫、副基体或双滴虫。在植物 - 原生生物分支中未确定一个优选的分支顺序，但自由贾科比虫 - 美洲隐滴虫谱系有与由异叶足虫类变形鞭毛虫和眼虫纲原生生物组成分支聚在一起的趋势。在β-微管蛋白以及α-加β-微管蛋白的系统发育分析中，囚禁贾科比虫在植物 - 原生生物分支内分支。在α-微管蛋白树中，囚禁贾科比虫处于一个未解决的位置，根据所采用的系统发育方法，它与动物/真菌/微孢子虫类群或与无线粒体的副基体和双滴虫谱系弱聚类。微管蛋白基因系统发育分析总体上与线粒体基因系统发育分析和超微结构数据一致，表明“贾科比虫”可能是多系的。与假定的深度分支的无线粒体双滴虫的关系仍然不确定。
