Research article

A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae

Hisayoshi Nozaki¹ , Hiroyoshi Takano² , Osami Misumi^3,4 , Kimihiro Terasawa^5,6 , Motomichi Matsuzaki¹ , Shinichiro Maruyama^1,6 , Keiji Nishida^3,4 , Fumi Yagisawa^3,4 , Yamato Yoshida^7,4 , Takayuki Fujiwara^3,4 , Susumu Takio⁸ , Katsunori Tamura⁶ , Sung Jin Chung^2,10 , Soichi Nakamura⁹ , Haruko Kuroiwa^3,4 , Kan Tanaka⁶ , Naoki Sato⁵ and Tsuneyoshi Kuroiwa^3,4

¹Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan

²Graduate School of Science and Technology, Kumamoto University, Japan

³Department of Life Science, College of Science, Rikkyo (St. Paul's) University, Tokyo, Japan

⁴Research Information Center for Extremophile, Rikkyo (St. Paul's) University, Tokyo, Japan

⁵Department of Life Sciences, Graduate School of Arts and Sciences, the University of Tokyo, Tokyo, Japan

⁶Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo, Japan

⁷Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan

⁸Center for Marine Environment Studies, Kumamoto University, Kumamoto, Japan

⁹Laboratory of Cell and Functional Biology, Faculty of Science, University of the Ryukyus, Okinawa, Japan

¹⁰Radiation Research Center for Bio-Technology, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeollabuk-do, Korea

author email corresponding author email

BMC Biology 2007, 5:28doi:10.1186/1741-7007-5-28

Published:	10 July 2007

Abstract

Background

All previously reported eukaryotic nuclear genome sequences have been incomplete, especially in highly repeated units and chromosomal ends. Because repetitive DNA is important for many aspects of biology, complete chromosomal structures are fundamental for understanding eukaryotic cells. Our earlier, nearly complete genome sequence of the hot-spring red alga Cyanidioschyzon merolae revealed several unique features, including just three ribosomal DNA copies, very few introns, and a small total number of genes. However, because the exact structures of certain functionally important repeated elements remained ambiguous, that sequence was not complete. Obviously, those ambiguities needed to be resolved before the unique features of the C. merolae genome could be summarized, and the ambiguities could only be resolved by completing the sequence. Therefore, we aimed to complete all previous gaps and sequence all remaining chromosomal ends, and now report the first nuclear-genome sequence for any eukaryote that is 100% complete.

Results

Our present complete sequence consists of 16546747 nucleotides covering 100% of the 20 linear chromosomes from telomere to telomere, representing the simple and unique chromosomal structures of the eukaryotic cell. We have unambiguously established that the C. merolae genome contains the smallest known histone-gene cluster, a unique telomeric repeat for all chromosomal ends, and an extremely low number of transposons.

Conclusion

By virtue of these attributes and others that we had discovered previously, C. merolae appears to have the simplest nuclear genome of the non-symbiotic eukaryotes. These unusually simple genomic features in the 100% complete genome sequence of C. merolae are extremely useful for further studies of eukaryotic cells.