Understanding of the diversity and specificity by comparative genomic analysis using advanced sequencing technologies

Faculty

Research Summary

The Comparative Genomics Laboratory was established in April 2008 with the task to understand basic rules of biological systems using cutting-edge DNA sequencing and analysis technologies. Currently, we are analyzing personalized genomes of primates in addition to the organisms those living in the extreme environmental conditions. Furthermore, we have started supporting and developing metagenomic and bioinformatic analyses to promote human microbiome research. Figures show examples of such activities.

Selected Publications

Terao M, Ogawa Y, Takada S, Kajitani R, Okuno M, Mochimaru Y, Matsuoka K, Itoh T, Toyoda A, Kono T, Jogahara T, Mizushima S, Kuroiwa A. Turnover of mammal sex chromosomes in the Sry-deficient Amami spiny rat is due to male-specific upregulation of Sox9. Proc Natl Acad Sci U S A. 2022 Dec 6;119(49):e2211574119.

Rai A, Hirakawa H, Nakabayashi R, Kikuchi S, Hayashi K, Rai M, Tsugawa H, Nakaya T, Mori T, Nagasaki H, Fukushi R, Kusuya Y, Takahashi H, Uchiyama H, Toyoda A, Hikosaka S, Goto E, Saito K, Yamazaki M. Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat Commun. 2021 Jan 15;12(1):405.

Koiwai K, Koyama T, Tsuda S, Toyoda A, Kikuchi K, Suzuki H, Kawano R. Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process. Elife. 2021 Jun 16;10:e66954.

Nishiyama T, Sakayama H, de Vries J, Buschmann H, Saint-Marcoux D, Ullrich KK, Haas FB, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson PKI, Janitza P, Kern R, Heyl A, Rümpler F, Villalobos LIAC, Clay JM, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington AJ, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan GV, Van Nieuwerburgh F, Deforce D, Chang C, Karol KG, Hedrich R, Ulvskov P, Glöckner G, Delwiche CF, Petrášek J, Van de Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theißen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing SA. The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization. Cell. 2018 Jul 12;174(2):448-464.e24.