Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of Rhizaria with Chromalveolates
Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of Rhizaria with Chromalveolates
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DOI：
10.1093/molbev/msm089
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发表时间：
2007-08-01
影响因子：
10.7
通讯作者：
Bhattacharya, Debashish
中科院分区：
文献类型：
--
作者：
Hackett, Jeremiah D.;Yoon, Hwan Su;Bhattacharya, Debashish
在这里，我们使用表达序列标签（EST）的数据从生态上重要的球石藻形成Emiliania huxleyi和缺乏质体的隐藻Goniomonascf。pacifica，以建立它们在真核生物树中的系统发育位置。附着植物和隐芽植物是假定的真核生物超组Chromalveolata（染色植物[隐芽植物，附着植物，层生植物]和肺泡[顶复门，纤毛虫和甲藻]）的成员。基于光合成员的质体色素沉着、质体基因与基因组的关系、某些染色质气孔谱系的核“宿主”遗传、这些类群所共有的独特基因复制和替换以及质体输入和易位系统组分的进化历史，推测染色质气孔是单系的。然而，隐芽植物和附着植物的系统发育位置以及整个显色脉状植物的单系性仍有待证实。在这里，我们评估chromalveolate单系使用多基因数据集的核基因，包括所有6个真核生物超组的成员。使用自动化的基因组学流水线，然后进行有针对性的数据库搜索，从46个分类群中组装16个蛋白质数据集（6，735 aa），用于树推断。这些数据的最大似然和贝叶斯分析支持单系性的附着植物和隐芽植物。这种关系是一致的，通过水平基因转移的质体编码的rp 136，这是独特的共享这些类群的基因置换。该haptophytes + cryptophytes是姐妹的一个分支，包括所有其他chromalveolates，令人惊讶的是，两个成员的Rhizaria，Reticulomyxa filosa和Bigelowiella natans。两个根瘤菌与chromalveolates的协会是支持的近似无偏（Au）-测试，当最快的演变氨基酸位点从16-蛋白质比对。
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 rp136 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.