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 provide a high-quality genome annotation and versatile 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 and animal species such as a liverwort Marchantia polymorpha, a japanese orange Citrus unshu and a domestic cat Felis catus.
Selected Publications
Tanizawa Y, Fujisawa T, Kodama Y, Kosuge T, Mashima J, Tanjo T, Nakamura Y. DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic Acids Res. 2023 Jan 6;51(D1):D101-D105.
Kawamura S, Romani F, Yagura M, Mochizuki T, Sakamoto M, Yamaoka S, Nishihama R, Nakamura Y, Yamato KT, Bowman JL, Kohchi T, Tanizawa Y. MarpolBase Expression: A Web-Based, Comprehensive Platform for Visualization and Analysis of Transcriptomes in the Liverwort Marchantia polymorpha. Plant Cell Physiol. 2022 Nov 22;63(11):1745-1755.
Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DNA Res. 2023 Feb 1;30(1):dsac044.
Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. Sci Adv. 2022 Apr 29;8(17):eabi5075.
