Nucleotide sequences are one of the most basic and reliable data that can be used to explain biological phenomena. The primary structure of DNA is written as an array of the combination of four nucleotides designated as A, G, C and T; in other words, it can be treated as a string of four characters in an electronic DNA database such as DDBJ. These nucleotide data, particularly after the publication of human genome structure, are often called as a treasure-trove and provide richest resources for biological researches.
However, it is also very difficult to uncover new findings if you only try to obtain them from your computer terminal. The comparative genomics laboratory was activated since April 2008 aiming at the understanding of basics and rules of biological phenomena based on active reading and analyses of genome structures of interest. Currently, we are planning to analyze genomes of organisms positioned on the branch point of the evolutionary tree of life, those living in the extreme environmental conditions, and deeper understanding of our genomes.

Todd D. Taylor, Hideki Noguchi, Yasushi Totoki, Atsushi Toyoda, Yoko Kuroki, KenDewar, Christine Lloyd, Takehiko Itoh, Tadayuki Takeda, Dae-Won Kim, Xinwei She, Karen F Barlow, Toby Bloom, Elspeth Bruford, Jean L. Chang, Christina A. Cuomo, Evan Eichler, Michael G. FitzGerald, David B. Jaffe, Kurt LaButti, Robert Nicol, Hong-Seog Park, Christopher Seaman, Carrie Sougnez, Xiaoping Yang, Andrew R. Zimmer, Michael C. Zody, Bruce W. Birren, Chad Nusbaum, Asao Fujiyama, Masahira Hattori, Jane Rogers, Eric S. Lander and Yoshiyuki Sakaki. (2006). Human chromosome 11 DNA sequence and analysis including novel gene identification. Nature 440, 497-500.

Yoko Kuroki, Atsushi Toyoda, Hideki Noguchi,, Todd D. Taylor, Takehiko Itoh, Dae-Soo Kim, Dae-Won Kim,, Sang-Haeng Choi, Il-Chul Kim, Han Ho Choi, Yong Sung Kim, Yoko Satta, Naruya Saitou, Tomoyuki Yamada, Shinichi Morishita, Masahira Hattori,, Yoshiyuki Sakaki, Hong-Seog Park, and Asao Fujiyama. (2006). Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway. NatureGenetics 38, 158-167.

Hongoh Y, Sharma VK, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M. (2008). Genome of an endosymbiont coupling N2 fixation to cellulolysis withinprotist cells in termite gut. Science 322, 1108-1109.

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutie´rrez EL, Dubchak I, Garcia-Ferna`ndez J, Gibson- Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. (2008). The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064-1071.

STAR Consortium; Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, ChenY, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, Guigo R, Guryev V, Heinig M, Hummel O, Jahn N, Klages S, Kren V, Kube M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee YA, Lopez-Bigas N, Lathrop GM, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet JA, Platzer M, Pravenec M, Reinhardt R, Sakaki Y, Schilhabel M, Schulz H, Serikawa T, Shikhagaie M, Tatsumoto S, Taudien S, Toyoda A, Voigt B, Zelenika D, Zimdahl H, Hubner N. (2008). SNP and haplotype mapping for genetic analysis in the rat. Nat. Genet. 40, 560-566.

Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H.(2008). Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539-543.

Stefan A. Rensing, Daniel Lang, Andreas D. Zimmer, Astrid Terry, Asaf Salamov, Harris Shapiro, Tomoaki Nishiyama, Pierre-Francois Perroud, Erika Lindquist, Yasuko Kamisugi, Takako Tanahashi,, Keiko Sakakibara, Tomomichi Fujita, Kazuko Oishi, Tadasu Shin-I, Yoko Kuroki, Atsushi Toyoda, Yutaka Suzuki, Shin-ichi Hashimoto, Kazuo Yamaguchi,, Sumio Sugano, Yuji Kohara,, Asao Fujiyama,,, Aldwin Anterola, Setsuyuki Aoki, Neil Ashton, W. Brad Barbazuk, Elizabeth Barker, Jeffrey L. Bennetzen, Robert Blankenship, Sung Hyun Cho, Susan K. Dutcher, Mark Estelle, Jeffrey A. Fawcett, Heidrun Gundlach, Kousuke Hanada,, Alexander Heyl, Karen A. Hicks, , Jon Hughes, Martin Lohr, Klaus Mayer, Alexander Melkozernov, Takashi Murata,, David Nelson, Birgit Pils, Michael Prigge, Bernd Reiss, Tanya Renner, Stephane Rombauts, Paul Rushton, Anton Sanderfoot, Gabriele Schween, Shin-Han Shiu, Kurt Stueber, Frederica L. Theodoulou, Hank Tu, Yves Van de Peer, Paul J. Verrier, Elizabeth Waters, Andrew Wood, Lixing Yang, David Cove,, Andrew C. Cuming, Mitsuyasu Hasebe,,, Susan Lucas, Brent D. Mishler, Ralf Reski, Igor V. Grigoriev, Ralph S. Quatrano*, Jeffrey L. Boore. (2008) The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants, Science 319, 64-69.