Kazusa DNA Research Institute Established in 1994 Three

Kazusa DNA Research Institute Established in 1994 Three departments-6 laboratories 30 researchers, 40 technicians etc. Budget: 19 M$ (Local: Fed = 8: 2) Kazusa DNA Research Institute Chiba Prefecture

Plant Genomics team Libraries Sequencing Informatics Shusei Sato Takakazu Kaneko Yasukazu Nakamura Erika Asamizu Shigemi Sasamoto Tsunakazu Fujishiro Akiko Watanabe Shinobu Nakayama Chiaki Kiyokawa Akiko Muraki Mitsuyo Kohara Sayaka Shinpo Mizuho Ishikawa Manabu Yamada Naoko Torikai Yoshie Kishida Mayumi Iriguchi Naomi Nakazaki Midori Kato Kumiko Kawashima Ai Matsuno Yoshimi Shimizu Kyoko Hayashi Yoko Hasegawa

Microbial genome sequencing project Cyanobacteria Anabaena sp. PCC 7120 6. 4 Mb (2001) Gloeobacter violaceus PCC 7421 4. 6 Mb (2003) Synechocystis sp. PCC 6803 3. 6 Mb (1996) Thermosynechococcus elongatus BP 1 2. 6 Mb (2002) Rhizobia Mesorhizobium loti MAFF 303099 7. 6 Mb (2000) Bradyrhizobium japonicum USDA 110 9. 1 Mb (2002)

A. thaliana genome sequencing project August 1996 - December 2000 55% 20%

Ongoing sequencing projects Eucalyptus camaldulensis 660 Mbp 2004～ Lotus japonicus 470 Mbp 2000～

Sequencing of tomato Chromosome 8 Features Genetic length: 87 c. M Length of the euchromatic regions: approxomately 17 Mb Number of the markers as seed points: 97 Estimated number of the clones to sequence: 175 Procedure Selection of clones to sequence by PCR Confirmation of integrity (Fingerprinting and PCR based on the end sequences) Shotgun libraries (sonication -> p. Bluescript) Template preparation (Templi. Phi) Sequencing (ABI 3700, 3730) Assembly (Phrap) Manual editing and re-sequencing x 6 coverage

Confirmation – integrity and map position 1. Fingerprinting and PCR Selected clone PCR amplification FTC We need the genomic libraries and the end sequence data !

Confirmation – integrity and map position Probe or primers Selected clone FTC 2. Multiple positive (over-go hybridization and PCR) clones in a single FPC

Confirmation – map position Probe or primers FTC 2. Multiple positive (over-go hybridization and PCR) clones in a single FPC

Status

Chromosome 8

Pipeline for gene modeling and annotation 1. Similarity search 2. ab initio prediction Automatic modeling Manual modeling High-throughput Low-throughput Higher accuracy Annotation

BT 005 (0005 L 01)

BT 020 (0165 B 06)

BT 040 (0320 P 23)

Summary