Hackett Jeremiah D, Yoon Hwan Su, Li Shenglan, Reyes-Prieto Adrian, Rümmele Susanne E, Bhattacharya Debashish
Department of Biological Sciences and Roy J. Carver Center for Comparative Genomics, University of Iowa, IA, USA.
Mol Biol Evol. 2007 Aug;24(8):1702-13. doi: 10.1093/molbev/msm089. Epub 2007 May 7.
Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the putative eukaryotic supergroup Chromalveolata (chromists [cryptophytes, haptophytes, stramenopiles] and alveolates [apicomplexans, ciliates, and dinoflagellates]). The chromalveolates are postulated to be monophyletic on the basis of plastid pigmentation in photosynthetic members, plastid gene and genome relationships, nuclear "host" phylogenies of some chromalveolate lineages, unique gene duplication and replacements shared by these taxa, and the evolutionary history of components of the plastid import and translocation systems. However the phylogenetic position of cryptophytes and haptophytes and the monophyly of chromalveolates as a whole remain to be substantiated. Here we assess chromalveolate monophyly using a multigene dataset of nuclear genes that includes members of all 6 eukaryotic supergroups. An automated phylogenomics pipeline followed by targeted database searches was used to assemble a 16-protein dataset (6,735 aa) from 46 taxa for tree inference. Maximum likelihood and Bayesian analyses of these data support the monophyly of haptophytes and cryptophytes. This relationship is consistent with a gene replacement via horizontal gene transfer of plastid-encoded rpl36 that is uniquely shared by these taxa. The haptophytes + cryptophytes are sister to a clade that includes all other chromalveolates and, surprisingly, two members of the Rhizaria, Reticulomyxa filosa and Bigelowiella natans. The association of the two Rhizaria with chromalveolates is supported by the approximately unbiased (AU)-test and when the fastest evolving amino acid sites are removed from the 16-protein alignment.
在此，我们运用系统发育基因组学，结合来自具有重要生态意义的形成颗石藻的藻类——赫氏颗石藻以及缺乏质体的隐藻——太平洋拟角毛藻的表达序列标签（EST）数据，来确定它们在真核生物树中的系统发育位置。定鞭藻和隐藻是假定的真核生物超群——色藻界（色素体生物[隐藻、定鞭藻、不等鞭毛藻]和囊泡虫类[顶复门、纤毛虫和甲藻]）的成员。基于光合成员中的质体色素沉着、质体基因和基因组关系、一些色藻界谱系的核“宿主”系统发育、这些分类群共有的独特基因重复和替换，以及质体输入和转运系统成分的进化历史，推测色藻界是单系的。然而，隐藻和定鞭藻的系统发育位置以及色藻界作为一个整体的单系性仍有待证实。在此，我们使用一个包含所有6个真核生物超群成员的核基因多基因数据集来评估色藻界的单系性。采用自动化的系统发育基因组学流程，随后进行有针对性的数据库搜索，以从46个分类群中组装一个16蛋白数据集（6735个氨基酸）用于树推断。对这些数据进行的最大似然法和贝叶斯分析支持定鞭藻和隐藻的单系性。这种关系与通过水平基因转移对质体编码的rpl36进行基因替换一致，而这是这些分类群唯一共有的。定鞭藻 + 隐藻是一个分支的姐妹群，该分支包括所有其他色藻界以及令人惊讶的根足虫界的两个成员，丝状网柱黏菌和纳氏比格洛黏菌。根足虫界的这两个成员与色藻界的关联得到了近似无偏（AU）检验的支持，并且当从16蛋白比对中去除进化最快的氨基酸位点时也得到了支持。
