1. Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
2. Department of Life Science, College of Science, Rikkyo (St Paul's) University, 3-34-1 Nishiikebukuro, Toshima-ku, Tokyo 171-8501, Japan
3. Center for Genetic Resource Information, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
4. Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
5. National Institute of Livestock and Grassland Science, 2 Ikenodai, Tsukuba, Ibaraki 305-0901, Japan
6. Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
7. Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, 255 Shimo-Ohkubo, Sakura-ku, Saitama, Saitama 338-8570, Japan
8. Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
9. Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjyuku-ku, Tokyo 160-8582, Japan
10. Department of Biological Science, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
11. Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan

Correspondence to: Motomichi Matsuzaki¹Tsuneyoshi Kuroiwa² Email: tsune@rikkyo.ne.jp
Email: mzaki@biol.s.u-tokyo.ac.jp
Chromosome sequences were submitted to DDBJ with accession numbers AP006483–AP006502 (chromosome 1–20) and AP006600–AP006614 (unassigned contigs). Sequences and annotation are available at http://merolae.biol.s.u-tokyo.ac.jp/ or http://dolphin.lab.nig.ac.jp/publish/.

Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants^{1, 2}. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.

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