Analyses of RNA polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang
Analyses of RNA polymerase II genes from free-living protists: Phylogeny, long branch attraction, and the eukaryotic big bang
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DOI：
10.1093/oxfordjournals.molbev.a004140
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发表时间：
2002-06-01
影响因子：
10.7
通讯作者：
Logsdon, JM
中科院分区：
文献类型：
--
作者：
Dacks, JB;Marinets, A;Logsdon, JM
主要真核原生生物谱系之间的系统发育关系在很大程度上是不确定的。长枝吸引（LBA）效应是重建真核生物系统发育的两个重要障碍，自由生活原生生物的分类单元取样质量差。我们获得并分析了来自Naeglcriagruberi（一种异裂体生物）和CercomonasATCC 50319（一种尾虫）的RNA聚合酶II（RPB 1）最大亚基的基因序列。和丹麦苍白单胞菌（一种异形体）：我们还分析了\ Guillardia theta（一种隐单胞菌）的核形（nm）基因组中的RPBI基因。利用各种系统发育学方法，我们的分析表明，来自贾第鞭毛虫和阴道毛滴虫的RPB 1，，可能受到强烈的LBA。这些分类群在RPBI树上的深分支是值得怀疑的，不应该被解释为支持它们早期分歧的证据。类似的影响也是显而易见的。在较小的程度上。反转鞭毛虫RPB 1序列一旦排除了外群和这些有问题的序列。对剩余RPBIs的分析表明在主要真核生物群中存在一些分辨率。最强大的更高级别的分支是后囊动物（动物加上真菌）和红藻加上隐藻nm-内部的结果提供了额外的支持隐藻叶绿体的红藻起源。包括Dictyosteelium discoideum Plus Castellaii（Amoebozoa）和Ochromonas plus（chromalveolates）的分支一直被观察到，并得到了适度的支持。我们的RPB 1分析支持的分支与其他数据一致。表明真正的系统发育关系正在被解决，因此。RPB 1基因显然保留了一些遗传学上有意义的信号，这使得从更多样的原生生物分类群中获得序列是值得的。其他RPB 1数据。特别是与其他基因的组合，应该提供进一步的分辨率的分支顺序之间的原生生物群体内的真核生物的明显快速早期分歧。
The phylogenetic relationships among major eukaryotic protist lineage,, are largely uncertain. Two significant obstacles in reconstructing eukaryotic phylogeny are long-branch attraction (LBA) effect,, quid poor taxon sampling of free-living protists, We have obtained and analyzed gene sequences encoding the largest subunit of RNA Polymerase II (RPB1) from Naeglcria gruberi (a heterolobusean), Cercomonas ATCC 50319 (a cercozoan). and Ochromonas danica (a heterokont): we have also analyzed the RPBI gene from the nucleomorph (nm) genome of\ Guillardia theta (a cryptomonad). Using a variety of phylogenetic methods Our analysis shows that RPB1,, from Giardia intestinalis and Trichomonas vaginalis are probably subject to intense LBA Thus. the deep branching of these taxa on RPBI trees is questionable and should not be interpreted as evidence favoring their early, divergence. Similar effects are discernable. to a lesser extent. with the Mastigamoeba invertens RPB1 sequence. Upon removal of the outgroup and these problematic sequences. analyses of the remaining RPBIs indicate some resolution among major eukaryotic groups. The most robustly higher-level clades are the opisthokonts (animals Plus fungi) and the red algae plus the cryptomonad nm-the Inner result gives added support to the red algal origin of cryptomonad chloroplasts. Clades comprising Dictyostelium discoideum Plus Acanthomoeba castellaii (Amoebozoa) and Ochromonas plus (chromalveolates) are consistently observed and moderately supported. The clades supported by our RPB1 analyses are congruent With other data. suggesting that bona fide phylogenetic relationships are being resolved, Thus. the RPB1 gene has apparently retained some phylogenetically meaningful signal, making it worthwhile to obtain sequences from more diverse protist taxa. Additional RPB1 data. especially in combination with other genes, should provide further resolution of branching order among protist groups within the apparently rapid early divergence of eukaryotes.