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

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Presentation transcript:

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

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

Anabaena sp. PCC Mb(2001) Gloeobacter violaceus PCC Mb (2003) Synechocystis sp. PCC Mb (1996) Thermosynechococcus elongatus BP1 2.6 Mb (2002) Microbial genome sequencing project Cyanobacteria Rhizobia Bradyrhizobium japonicum USDA Mb (2002) Mesorhizobium loti MAFF Mb (2000)

August December % 25% 20% A. thaliana genome sequencing project

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

Sequencing of tomato Chromosome 8 Genetic length: 87 cM Length of the euchromatic regions: approxomately 17 Mb Number of the markers as seed points: 97 Estimated number of the clones to sequence: 175 Features Procedure Selection of clones to sequence by PCR Confirmation of integrity (Fingerprinting and PCR based on the end sequences) Shotgun libraries (sonication -> pBluescript) Template preparation (TempliPhi) Sequencing (ABI 3700, 3730)x6 coverage Assembly (Phrap) Manual editing and re-sequencing

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

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

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

Status

Chromosome 8

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

BT005 (0005L01)

BT020 (0165B06)

BT040 (0320P23)

Summary