The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids
The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids
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DOI：
10.1007/s00239-002-2419-9
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发表时间：
2003-04-01
影响因子：
3.9
通讯作者：
Kuroiwa, T
中科院分区：
文献类型：
--
作者：
Nozaki, H;Matsuzaki, M;Kuroiwa, T
红藻是一种主要的光合真核生物，具有原始的特征，如缺乏鞭毛和叶绿体中存在藻胆蛋白。最近的分子系统发育研究使用核基因序列提出了两个相互矛盾的假说（单系与非单系）之间的关系红藻和绿色植物。虽然王国级别的系统发育分析使用多个核基因从广泛的真核生物谱系最近进行，他们使用的隐藻核形（作为红藻类群）或不完整的红藻基因序列的高度分歧的基因序列。此外，先前基于核基因的真核生物的遗传学通常包括非常遥远的古细菌序列（指定为外群）和/或无线粒体生物，其可能由于寄生或线粒体的缺乏而携带不寻常的基因替换。在这里，我们进行了系统发育分析的各种血统的含核多基因序列的真核生物，包括完整的序列，从原始的红色Cyanidioschyzon merolae。氨基酸序列数据的两个级联旁系同源基因（α-和β-微管蛋白）从含藻的生物体有力地解决了基础位置的细胞黏菌，这被指定为外群在我们的系统发育分析。基于4个串联核基因的1525个氨基酸序列的53个操作分类单位（OTU）的系统发育分析（肌动蛋白、延伸因子-lot、α-微管蛋白和β-微管蛋白）仅在最大简约（MP）分析中可靠地解决了同源性，这表明存在两个大的稳健的单系群（A和B组）和基础真核谱系（红藻、真黏菌和阿米巴）。A组对应于后鞭毛门（后生动物和真菌），而B组包括各种含质体的初级和次级谱系（绿色植物、蓝绿藻、裸藻、异鞭毛类和顶复门）、纤毛门、动质体门和异叶目。红藻代表了B类的姐妹谱系。使用34个OTU，其中基本上四个基因的整个氨基酸序列是已知的，MP，距离，四重困惑，和两种类型的最大似然（ML）的计算都鲁棒解决了单系性的组B，以及真核生物中的基础位置的红藻。此外，还对12个含α-葡聚糖的OTU（包括C. merolae）解决了由红藻和属于组B的真核生物组成的稳健单系群内的绿色植物和红藻之间的稳健非姐妹关系。基于红藻在大分支（B组加红藻）中的基本系统发育位置，提出了一种新的质体起源和进化的设想。原生质体内共生可能发生在：这个大分支的共同祖先中，并且原生质体随后在盘嵴动物（裸藻目、动质体目和异叶目）、异鞭毛植物门和泡孔动物门（顶复门和纤毛门）的祖先中丢失。此外，根据原生质体内共生的共同历史，提出了B组光养生物和非光养生物以及红藻的“植物群”的新概念，包括原生含质体的光养生物和非光养的真核生物，它们可能含有在原生内共生中获得的蓝藻起源基因。
Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (alpha- and beta-tubulin) from mitochondria-containing organisms robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated nuclear genes (actin, elongation factor-lot, alpha-tubulin, and beta-tubulin) reliably resolved the phylogeny only in the maximum parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance, quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated 4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The primary plastid endosymbiosis likely occurred once in the: common ancestor of this large clade, and the primary plastids were subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta, and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of "Plantae" is proposed for phototrophic and nonphototrophic organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis.The Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial origin acquired in the primary endosymbiosis.