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Comparative Genomics Laboratory • Fujiyama Group

Comparative Genomics Research toward Understanding
Diversity and Idiosyncrasy of Life Systems

Professor FUJIYAMA, Asao afujiyam
Project Associate Professor TOYODA, Atsushi atoyoda

　Genomic information is one of the most basic and reliable data that can be used to conduct basic research to explain various biological phenomena as well as many applied sciences such as medicine, pharmaco-genomics, agriculture, ecology or production of bio-materials.
　The genomic information, particularly after the publication of human genome paper in 2001 and 2004, are often referred to as a treasure-trove and has been providing richest resources to the community.
　The Comparative Genomics Laboratory was established in April 2008 with the task to understand basic rules of biological systems based on actively reading and analyzing various genomes of interest using cutting-edge DNA sequencing and analysis technology. Currently, we are analyzing personalized genomes of primates in addition to the organisms those living in the extreme environmental conditions. The figures in the left column show examples of such activities.

Left: FISH analysis of gorilla chromosomes using human chr-21 telomeric probe
Right: Water bear bearing eggs in its belly

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

Putnam, N.H., Butts, T., Ferrier, D.E., Furlong, R.F., Hellsten, U., Kawashima, T., Robinson-Rechavi, M., Shoguchi, E., Terry, A., Yu, J.K., Benito-Gutierrez, E.L., Dubchak, I., Garcia-Fernandez, J., Gibson- Brown, J.J., Grigoriev, I.V., Horton, A.C., de Jong, P.J., Jurka, J., Kapitonov, V.V., Kohara, Y., Kuroki, Y., Lindquist, E., Lucas, S., Osoegawa, K., Pennacchio, L.A., Salamov, A.A., Satou, Y., Sauka-Spengler, T., Schmutz, J., Shin-I, T., Toyoda, A., Bronner-Fraser, M., Fujiyama, A., Holland, L.Z., Holland, P.W., Satoh, N., Rokhsar, D.S. (2008). The amphioxus genome and the evolution of the chordate karyotype. Nature 453, 1064-1071.

STAR Consortium; including Fujiyama, A. Kuroki, Y., Sakaki, Y., Serikawa, T., Tatsumoto, S., and Toyoda, A. (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, M.A., Sakaki, Y., and Sasaki, H.(2008). Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539-543.

Sato, S., Hirakawa, H., Isobe, S., Fukai, E., Watanabe, A., Kato, M., Kawashima, K., Minami, C., Muraki, A., Nakazaki, N., Takahashi, C., Nakayama, S., Kishida, Y., Kohara, M., Yamada, M., Tsuruoka, H., Sasamoto, S., Tabata, S., Aizu, T., Toyoda, A., Shin-I, T., Minakuchi, Y., Kohara, Y., Fujiyama, A., Tsuchimoto, S., Kajiyama, S., Makigano, E., Ohmido, N., Shibagaki, N., Cartagena, J.A., Wada, N., Kohinata, T., Atefeh, A., Yuasa, S., Matsunaga, S., and Fukui, K. (2010). Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L. DNA Res. [Epub ahead of print].

Shang, W.H., Hori, T., Toyoda, A., Kato, J., Popendorf, K., Sakakibara, Y., Fujiyama, A., and Fukagawa, T. (2010). Chickens possess centromeres with both extended tandem repeats and short non-tandemrepetitive sequences. Genome Res. 9, 1219-28.

Nishito, Y., Osana, Y., Hachiya, T., Popendorf, K., Toyoda, A., Fujiyama, A., Itaya, M., and Sakakibara, Y. (2010). Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics. 11, 243.


Professor FUJIYAMA, Asao afujiyam	Associate Professor TOYODA, Atsushi 　 atoyoda

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