Maruyama Shinichiro, Matsuzaki Motomichi, Misawa Kazuharu, Nozaki Hisayoshi
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
BMC Evol Biol. 2009 Aug 11;9:197. doi: 10.1186/1471-2148-9-197.
Eukaryotic genes with cyanobacterial ancestry in plastid-lacking protists have been regarded as important evolutionary markers implicating the presence of plastids in the early evolution of eukaryotes. Although recent genomic surveys demonstrated the presence of cyanobacterial and algal ancestry genes in the genomes of plastid-lacking protists, comparative analyses on the origin and distribution of those genes are still limited.
We identified 12 gene families with cyanobacterial ancestry in the genomes of a taxonomically wide range of plastid-lacking eukaryotes (Phytophthora [Chromalveolata], Naegleria [Excavata], Dictyostelium [Amoebozoa], Saccharomyces and Monosiga [Opisthokonta]) using a novel phylogenetic pipeline. The eukaryotic gene clades with cyanobacterial ancestry were mostly composed of genes from bikonts (Archaeplastida, Chromalveolata, Rhizaria and Excavata). We failed to find genes with cyanobacterial ancestry in Saccharomyces and Dictyostelium, except for a photorespiratory enzyme conserved among fungi. Meanwhile, we found several Monosiga genes with cyanobacterial ancestry, which were unrelated to other Opisthokonta genes.
Our data demonstrate that a considerable number of genes with cyanobacterial ancestry have contributed to the genome composition of the plastid-lacking protists, especially bikonts. The origins of those genes might be due to lateral gene transfer events, or an ancient primary or secondary endosymbiosis before the diversification of bikonts. Our data also show that all genes identified in this study constitute multi-gene families with punctate distribution among eukaryotes, suggesting that the transferred genes could have survived through rounds of gene family expansion and differential reduction.
在缺乏质体的原生生物中，具有蓝细菌祖先的真核基因被视为重要的进化标记，这暗示了质体在真核生物早期进化过程中的存在。尽管最近的基因组调查表明在缺乏质体的原生生物基因组中存在蓝细菌和藻类祖先基因，但对这些基因的起源和分布的比较分析仍然有限。
我们使用一种新颖的系统发育方法，在分类学范围广泛的缺乏质体的真核生物（疫霉属[色藻界]、纳格里亚属[古虫界]、盘基网柄菌属[变形虫界]、酿酒酵母属和单鞭滴虫属[后鞭毛生物界]）的基因组中鉴定出12个具有蓝细菌祖先的基因家族。具有蓝细菌祖先的真核基因分支大多由双鞭毛生物（古质体生物、色藻界、根足虫界和古虫界）的基因组成。除了一种在真菌中保守的光呼吸酶外，我们在酿酒酵母属和盘基网柄菌属中未发现具有蓝细菌祖先的基因。同时，我们发现了几个具有蓝细菌祖先的单鞭滴虫属基因，它们与其他后鞭毛生物界基因无关。
我们的数据表明，相当数量的具有蓝细菌祖先的基因对缺乏质体的原生生物，尤其是双鞭毛生物的基因组组成有贡献。这些基因的起源可能是由于横向基因转移事件，或者是在双鞭毛生物多样化之前发生的古老的一次或二次内共生。我们的数据还表明，本研究中鉴定的所有基因构成了在真核生物中呈点状分布的多基因家族，这表明转移的基因可能通过多轮基因家族扩展和差异减少而得以保留。
