Centre de cooperation internationale en recherche agronomique pour le developpement
CIRAD 2008 - orygenesdb(at)cirad.fr - Last update: November 13, 2012
Oryza sativa ssp. japonica
|1. Unified Rice Pseudomolecules(Version 7.0, October 2011)|
The 12 rice pseudomolecule sequences are now common to both the MSU Rice Genome Annotation Project and the Rice Annotation Project Database (RAP-DB)/International Rice Genome Sequencing Project. This effort was undertaken in order to allow researchers to easily compare annotations from both the MSU and RAP-DB projects. Gene loci, gene models and associated annotations created by MSU-RAP and RAP-DB were independently derived, but the pseudomolecules used by the two rice annotation projects to generated those annotations are now identical and can be easily compared.
Note that while the MSU Rice Genome Annotation Project and the International Rice Annotation Project Database (RAP-DB) have different annotation efforts, these parallel annotation efforts utilize the same underlying pseudomolecule sequence.
In release 7, there were 373,245,519 bp of non-overlapping rice genome sequence from the 12 rice chromosomes. The genes that had been identified from release 6.1 were remapped and transfered to release 7. This process resulted in 55,986 genes (loci) had been identified, of which 6,457 had 10,352 additional alternative splicing isoforms resulting in a total of 66,338 transcripts (or gene models) in the rice genome.
| The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.
Qiaoping Yuan , Shu Ouyang , Jia Liu , Bernard Suh , Foo Cheung , Razvan Sultana , Dan Lee , John Quackenbush , and C. Robin Buell.
Nucl. Acids Res. 31: 229-233.
|2. 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.|
|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.|
|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 Sugarcane Gene Index - SOGI (Release 3.0, April 2010)
DFCI Rice Gene Index - OGI (Release 18.0, April 2010)
DFCI Sorghum Gene Index - SBGI (Release 9.0, July 2009)
DFCI Maize Gene Index - ZMGI (Release 19.0, June 2009)
DFCI Barley Gene Index - HVGI (Release 11.0, April 2010)
DFCI Wheat Gene Index - TAGI (Release 12.0, April 2010)
We used the GMAP alignment program to align the TC (Tentative Consensus) sequences against the pseudo-chromosomes.
| The TIGR Gene Indices: reconstruction and representation of expressed gene sequences.
Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan.
Nucl. Acids Res. 2000 28: 141-145.
|4. Gramene markers|
|Gramene : a resource for comparative grass genomics.
Ware, Doreen, Jaiswal, Pankaj, Ni, Junjian, Pan, Xiaokang, Chang, Kuan, Clark, Kenneth, Teytelman, Leonid, Schmidt, Steve, Zhao, Wei, Cartinhour, Samuel, McCouch, Susan, Stein, Lincoln.
Nucl. Acids Res. 2002 30: 103-105.
|5. Knowledge-based Oryza Molecular biological Encyclopedia - KOME|
|Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica rice
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.
Science 2003 301: 376-379.
Oryza sativa ssp. indica
|1. The Beijing Genomics Institute - BGI-RIS (December 2009)|
|BGI-RIS release contains 40,745 Glean predicted genes of 93-11|
|BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka - Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, and Jun Wang.
Nucl. Acids Res. (2004) 32(suppl 1): D377-D382.
|1. The Arabidospsis Information Resource - TAIR (Version 10.0, November 2010)|
|The TAIR10 release contains 27,416 protein coding genes, 4827 pseudogenes or transposable element genes and 1359 ncRNAs (33,602 genes in all, 41,671 gene models). A total of 126 new loci and 2099 new gene models were added.|
|2. Flanking Sequence Tag (FSTs)|
|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.|
|DOE Joint Genome Institute|
| The Sorghum bicolor genome and the diversification of grasses.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman , Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS.
Nature. 2009 Jan 29; 457(7229):551-6.
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