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.
Group Alias Publication Contact Vector Number of FST
CSIRO CSIRO [View] narayana.upadhyaya(@)csiro.au T-DNA 611
National Institute of Agrobiological Sciences NIAS [View] hirohiko(@)nias.affrc.go.jp Tos17 18,024
CerealGene Tags, European Union OSTID [View] andy.pereira(@)wur.nl Ds 1,380
CIRAD-INRA-IRD-CNRS,Genoplante OTL T-DNA [View] emmanuel.guiderdoni(@)cirad.fr T-DNA 27,555
CIRAD-Genoscope OTL Tos17   emmanuel.guiderdoni(@)cirad.fr Tos17 14,355
Gyeongsang National University PMBBRC [View] cdhan(@)nongae.gsnu.ac.kr Ds 1,072
Plant Functional Genomics Laboratory Postech [View] genean(@)postech.ac.kr T-DNA 107,171
National Center of Plant Gene Research (Wuhan) RMD [View] swang(@)mail.hzau.edu.cn T-DNA 33,197
Shanghai T-DNA Insertion Population SHIP   ship(@)sibs.ac.cn T-DNA 12,614
Taiwan Rice Insertional Mutant Program TRIM [View] bohsing(@)gate.sinica.edu.tw T-DNA 11,799
University of California at Davis UCD [View] sundar(@)ucdavis.edu Ds 17,730
Total 245,508
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.
  CSIRO NIAS OSTID OTL T-DNA OTL Tos17 PMBBRC Postech RMD SHIP TRIM UCD
Mapped 592 17,968 1,374 24,716 14,160 1,073 106,011 32,628 9,682 11,561 17,365
 
Promoter 75 1,259 174 3,541 760 139 16,394 3,911 1,697 2,197 1,916
5'UTR 34 546 53 892 389 38 4,604 1,161 492 606 392
Intron 83 5,022 200 3,205 3,773 163 16,766 5,022 1,211 1,624 1,716
Exon 157 5,576 342 2,261 4,573 279 12,819 4,044 900 1,639 2,098
3'UTR 18 527 52 948 345 38 4,575 1,237 557 523 522
Intergenic 224 5,037 552 13,869 4,320 415 50,852 17,253 4,824 4,971 10,721
 
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.

Arabidopsis thaliana

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)
Group Alias Publication Contact Vector Number of FST
Salk Institute Genomic Analysis Laboratory SALK   ecker(@)salk.edu T-DNA 175107
Syngenta Arabidopsis Insertion Library SAIL   allen.sessions(@)syngenta.com T-DNA 57429
Cold Spring Harbor Laboratory CSH [View] vivian.irish(@)yale.edu Ds 18308
GABI-Kat GABI-Kat [View] weisshaa(@)mpiz-koeln.mpg.de T-DNA 110353
Genoplante Genoplante [View] lecharny@ibp.u-psud.fr T-DNA 36287
University of California at Davis UCD   sundar(@)ucdavis.edu Ds 858
Plant Functional Genomics Research Group RIKEN   rarge-master(@)psc.riken.jp Ds 18622
Total 416964
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.
  CSH GABI-Kat Genoplante RIKEN SAIL SALK UCD
Mapped 18005 96442 28917 45219 148760 769 18187
 
Promoter 5019 29978 9578 5507 15864 47317 201
5'UTR 685 3305 815 827 1440 5212 44
Intron 2253 14309 3385 1843 5466 21662 82
Exon 6209 18359 4205 5836 12267 27985 301
3'UTR 615 4061 1228 523 1956 6429 33
Intergenic 3224 26430 9706 3651 8226 40155 108
 

Sorghum bicolor

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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