Nakamura Group • Genome Informatics Laboratory

Advancement of large-scale genome sequences and promotion of DDBJ

Faculty

 

Research Summary

Ultra high-throughput sequencing technologies allow biologists to obtain larger amounts of nucleotide sequence data. To facilitate for reuse such huge nucleotide data, it is necessary to create a high-quality sequence database as reference data. It is also important to equip automated annotation system that make it possible fast and accurate results for reliable sequencing analysis. Our laboratory is in charge of DNA Data Bank of Japan (DDBJ) and attempts to develop advanced database management systems, and to improve quality of annotations in genome databases. We have been constructing an automatic annotation system for prokaryotes:DDBJ Fast Annotation and Submission Tool (DFAST). We are also providing several high-quality annotated genome information for important plant species such as a liverwort Marchantia polymorpha and a japanese orange Citrus unshu.

(A)Screenshot of DDBJ Fast Annotation and Submission Tool (DFAST)

(B) Screenshot of Marpolbase: a liverwort Marchantia polymorpha genome database

Selected Publications

Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Curr Biol. 2020 Jan 24. pii: S0960-9822(19)31610-0. [Epub ahead of print]

Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018 Mar 15;34(6):1037-1039.

Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, et al., Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. Cell. 2017 Oct 5;171(2):287-304.e15.


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