Oryza sativa
| 1. The MSU Rice Genome Annotation Project Database and Resource (Version 6.1, June 2009) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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The reference annotation layer consists in the 12 rice pseudo-chromosomes released by The MSU Rice Genome Annotation Project(TIGR) and most particularly by the division of the Rice Genome Annotation Database and Resource. The TIGR constructed pseudomolecules for each of rice 12 chromosomes by resolving discrepancies between overlapping BAC/PAC clones, trimming the overlap regions and linking the unique sequences to form a contigous sequence. A total of 3,450 rice BAC/PAC clones were included in the pseudomolecules. In the current release (Version 5.0, January 2007), there are 370,630,783 bp of non-overlapping rice genome sequence from the 12 rice chromosomes and 57,915 genes were identified. The Rice genome and its annotation were downloaded from the FTP site of the TIGR. |
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| Qiaoping Yuan , Shu Ouyang , Jia Liu , Bernard Suh , Foo Cheung , Razvan Sultana , Dan Lee , John Quackenbush , and C. Robin Buell. The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucl. Acids Res. 31: 229-233. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2. International Rice Genome Sequencing Project - IRGSP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| The International Rice Genome Sequencing Project (IRGSP), a consortium of publicly funded laboratories, was established in 1997 to obtain a high quality, map-based sequence of the rice genome using the cultivar Nipponbare of Oryza sativa ssp. japonica. It is currently comprised of ten members: Japan, the United States of America, China, Taiwan, Korea, India, Thailand, France, Brazil, and the United Kingdom. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. As of December 2002, the IRGSP has already published 367 Mb of non-overlapping nucleotide sequence of the rice genome in public databases. |
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| 3. Flanking Sequence Tag (FSTs) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| OryGenesDB contains data that our group is contributing to produce such as T-DNA and Ds flanking sequence tags deriving from the genomics initiative Genoplante (Oryza Tag Line) and the European consortium Cereal Gene Tags, respectively. Other public FST information from other groups is also displayed. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| The flanking sequence have been placed in the pseudo-chromosomes by finding the highest hit based on a 1e-10 cut-off. The mapped insertions were then assigned to clones and, when appropriate, to genes, based on the insertion map locations relative to the TIGR genome annotations. For our purposes, a gene was defined as beginning 800 bp 5' of the initiation codon and to the end of the 3'-UTR, where known. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 4. The Gene Index Databases | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The goal of The Gene Index Project is to use the available EST and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the fucntional roles played by these genes and their products.
 DFCI Sugarcane Gene Index - SOGI (Release 2.1, October 2004)
DFCI Rice Gene Index - OGI (Release 17.0, June 2006)
DFCI Sorghum Gene Index - SBGI (Release 8.0, May 2004)
DFCI Maize Gene Index - ZMGI (Release 17.0, November 2006)
DFCI Barley Gene Index - HVGI (Release 9.0, September 2004)
DFCI Wheat Gene Index - TAGI (Release 10.0, January 2005)
We used the GMAP alignment program to align the TC (Tentative Consensus) sequences against the pseudo-chromosomes. |
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| Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucl. Acids Res. 2000 28: 141-145. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 5. Gramene markers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ware, Doreen, Jaiswal, Pankaj, Ni, Junjian, Pan, Xiaokang, Chang, Kuan, Clark, Kenneth, Teytelman, Leonid, Schmidt, Steve, Zhao, Wei, Cartinhour, Samuel, McCouch, Susan, Stein, Lincoln. Gramene : a resource for comparative grass genomics, Nucl. Acids Res. 2002 30: 103-105. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 6. Knowledge-based Oryza Molecular biological Encyclopedia - KOME | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Kikuchi, Shoshi, Satoh, Kouji, Nagata, Toshifumi, Kawagashira, Nobuyuki, Doi, Koji, Kishimoto, Naoki, Yazaki, Junshi, Ishikawa, Masahiro, Yamada, Hitomi, Ooka, Hisako, Hotta, Isamu, Kojima, Keiichi, Namiki, Takahiro, Ohneda, Eisuke, Yahagi, Wataru, Suzuki, Kohji, Li, Chao Jie, Ohtsuki, Kenji, Shishiki, Toru, Otomo, Yasuhiro, Murakami, Kazuo, Iida, Yoshiharu, Sugano, Sumio, Fujimura, Tatsuto, Suzuki, Yutaka, Tsunoda, Yuki, Kurosaki, Takashi, Kodama, Takeko, Masuda, Hiromi, Kobayashi, Michie, Xie, Quihong, Lu, Min, Narikawa, Ryuya, Sugiyama, Akio, Mizuno, Kouichi, Yokomizo, Satoko, Niikura, Junko, Ikeda, Rieko, Ishibiki, Junya, Kawamata, Midori, Yoshimura, Akemi, Miura, Junichirou, Kusumegi, Takahiro, Oka, Mitsuru, Ryu, Risa, Ueda, Mariko, Matsubara, Kenichi, Kawai, Jun, Carninci, Piero, Adachi, Jun, Aizawa, Katsunori, Arakawa, Takahiro, Fukuda, Shiro, Hara, Ayako, Hashidume, Wataru, Hayatsu, Norihito, Imotani, Koichi, Ishii, Yoshiki, Itoh, Masayoshi, Kagawa, Ikuko, Kondo, Shinji, Konno, Hedeaki, Miyazaki, Ai, Osato, Naoki, Ota, Yoshimi, Saito, Rintaro, Sasaki, Daisuke, Sato, Kenjiro, Shibata, Kazuhiro, Shinagawa, Akira, Shiraki, Toshiyuki, Yoshino, Masayasu, Hayashizaki, Yoshihide. Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica, Rice Science 2003 301: 376-379. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 7. Rice / Arabidopsis orthologs | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Using the reciprocal top hit method strategy (BBMH), we have identified 11,170 genes orthologs between Oryza sativa and Arabidopsis thaliana. The in silico predicted Arabidopsis orthologous genes have been integrated into OryGenesDB allowing useful comparison between the rice and Arabidopsis genes annotations. Each Arabidopsis gene contain a link to the Gbrowse representation of the Arabidopsis genome with a track corresponding to the rice orthologous genes, linked in return to the rice genome. Thus the user can easily navigate between the two plant genomes. |
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Arabidopsis thaliana
| 1. The Arabidospsis Information Resource - TAIR (Version 9.0, June 2009) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| The TAIR9 release 27,379 protein coding genes, 4827 pseudogenes or transposable elements and 1312 ncRNAs (33,518 genes in all, 39,640 gene models). A total of 282 new loci and 739 new gene models were added.. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2. Flanking Sequence Tag (FSTs) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| The flanking sequence have been placed in the pseudo-chromosomes by finding the highest hit based on a 1e-10 cut-off. The mapped insertions were then assigned to clones and, when appropriate, to genes, based on the insertion map locations relative to the TAIR genome annotations. For our purposes, a gene was defined as beginning 800 bp 5' of the initiation codon and to the end of the 3'-UTR, where known. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 3. The Gene Index Databases | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| The goal of The Gene Index Project is to use the available EST and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these with information regarding the fucntional roles played by these genes and their products.
DFCI Arabidopsis Gene Index - AGI (Release 13.0, June 2006)
We used the GMAP alignment program to align the TC (Tentative Consensus) sequences against the pseudo-chromosomes. |
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| Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucl. Acids Res. 2000 28: 141-145. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 4. Arabidopsis / Rice orthologs | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Using the reciprocal top hit method strategy (BBMH), we have identified 11,170 genes orthologs between Oryza sativa and Arabidopsis thaliana. The in silico predicted Arabidopsis orthologous genes have been integrated into OryGenesDB allowing useful comparison between the rice and Arabidopsis genes annotations. Each Arabidopsis gene contain a link to the Gbrowse representation of the Arabidopsis genome with a track corresponding to the rice orthologous genes, linked in return to the rice genome. Thus the user can easily navigate between the two plant genomes. |
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