Cyanidioschyzon merolae Genome. A Tool for Facilitating Comparable Studies on Organelle Biogenesis in Photosynthetic Eukaryotes  

Abstract

The ultrasmall unicellular red alga Cyanidioschyzon merolae lives in the extreme environment of acidic hot springs and is thought to retain primitive features of cellular and genome organization. We determined the 16.5-Mb nuclear genome sequence of C. merolae 10D as the first complete algal genome. BLASTs and annotation results showed that C. merolae has a mixed gene repertoire of plants and animals, also implying a relationship with prokaryotes, although its photosynthetic components were comparable to other phototrophs. The unicellular green alga Chlamydomonas reinhardtii has been used as a model system for molecular biology research on, for example, photosynthesis, motility, and sexual reproduction. Though both algae are unicellular, the genome size, number of organelles, and surface structures are remarkably different. Here, we report the characteristics of double membrane-and single membrane-bound organelles and their related genes in C. merolae and conduct comparative analyses of predicted protein sequences encoded by the genomes of C. merolae and C. reinhardtii. We examine the predicted proteins of both algae by reciprocal BLASTP analysis, KOG assignment, and gene annotation. The results suggest that most core biological functions are carried out by orthologous proteins that occur in comparable numbers. Although the fundamental gene organizations resembled each other, the genes for organization of chromatin, cytoskeletal components, and flagellar movement remarkably increased in C. reinhardtii. Molecular phylogenetic analyses suggested that the tubulin is close to plant tubulin rather than that of animals and fungi. These results reflect the increase in genome size, the acquisition of complicated cellular structures, and kinematic devices in C. reinhardtii.To date, the genomes of more than 200 prokaryotes and several eukaryotes, including an alga, fungi, plants, animals, and their parasites, are known. However, we have little insight into the genomes of photosynthetic eukaryotes, such as Chlamydomonas reinhardtii, which are evolutionary intermediate organisms between primitive alga (Cyanidioschyzon merolae) and higher plants (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), although such information would prove invaluable for investigations of the fundamental traits, origin, and evolution of eukaryotic and plant cells.The primitive red alga C. merolae is a small (1.5 mm in diameter) organism that lives in sulfate-rich hot springs (pH 1.5, 45°C;De Luca et al., 1978). It has many characteristics that make it an ideal organism for elucidating the function, biosynthesis, and multiplication of organelles in eukaryotic cells. Figure 1 summarizes the dynamic changes in fine structures during mitosis in C. merolae compared with typical eukaryotic cells. A detailed description of the behavior and genes of each organelle will be shown in ''Results and Discussion.'' Although a typical eukaryotic cell contains one nucleus, it has many double membranebound (nucleus, mitochondria, and plastids) and single membrane...

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