The TIGR Rice Genome Annotation Resource: Improvements and new features

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Ouyang, Shu ^a   Zhu, Wei ^a   Hamilton, John ^a   Lin, Haining ^a   Campbell, Matthew ^a   Childs, Kevin ^a   Thibaud Nissen, Françoise ^a   Malek, Renae L ^a   Lee, Yuandan ^a   Zheng, Li ^a   Orvis, Joshua ^a   Haas, Brian ^a   Wortman, Jennifer ^a   Buell, Robin C ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC DATABASE; GENETIC MODEL; GENOME; INFORMATION RETRIEVAL; INTERNET; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; PROTEOMICS; RICE; TIGR RICE GENOME ANNOTATION RESOURCE; TRANSCRIPTOMICS; TRANSPOSON; WEB BROWSER;

DATABASES, GENETIC; DNA TRANSPOSABLE ELEMENTS; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION; GENOME, PLANT; INTERNET; ORYZA SATIVA; PROTEOMICS; USER-COMPUTER INTERFACE;

EID: 33846101405     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl976     Document Type: Article

References (32)

1. Gale,M.D. and Devos,K.M. (1998) Comparative genetics in the grasses. Proc. Natl Acad. Sci. USA, 95, 1971-1974.
2. Goff,S.A., Ricke,D., Lan,T.H., Presting,G., Wang,R., Dunn,M., Glazebrook,J., Sessions,A., Oeller,P., Varma,H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100.
3. Sorrells,M.E., La Rota,M., Bermudez-Kandianis,C.E., Greene,R.A., Kantety,R., Munkvold,J.D., Miftahudin Mahmoud,A., Ma,X., Gustafson,P.J. et al. (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res., 13, 1818-1827.
4. Ware,D. and Stein,L. (2003) Comparison of genes among cereals. Curr. Opin. Plant Biol., 6, 121-127.
5. The Rice Chromosome3 Sequencing Consortium (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res., 15, 1284-1291.
6. The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science, 300, 1566-1569.
7. The Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol., 3, 20.
8. Barry,G.F. (2001) The use of the Monsanto draft rice genome sequence in research. Plant Physiol., 125, 1164-1165.
9. Yu,J., Hu,S., Wang,J., Wong,G.K., Li,S., Liu,B., Deng,Y., Dai,L., Zhou,Y., Zhang,X. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79-92.
10. Yu,J., Wang,J., Lin,W., Li,S., Li,H., Zhou,J., Ni,P., Dong,W., Hu,S., Zeng,C. et al. (2005) The Genomes of Oryza sativa: A history of duplications. PLoS Biol., 3, e38.
11. The International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
12. Goff,S.A. (1999) Rice as a model for cereal genomics. Curr. Opin. Plant Biol., 2, 86-89.
13. Yuan,Q., Ouyang,S., Liu,J., Suh,B., Cheung,F., Sultana,R., Lee,D., Quackenbush,J. and Buell,C.R. (2003) The TIGR rice genome annotation resource: Annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res., 31, 229-233.
14. Yuan,Q., Ouyang,S., Wang,A., Zhu,W., Maiti,R., Lin,H., Hamilton,J., Haas,B., Sultana,R., Cheung,F. et al. (2005) The Institute for Genomic Research Osal rice genome annotation database. Plant Physiol., 138, 18-26.
15. Ito,Y., Arikawa,K., Antonio,B.A., Ohta,I., Naito,S., Mukai,Y., Shimano,A., Masukawa,M., Shibata,M., Yamamoto,M. et al. (2005) Rice Annotation Database (RAD): A contig-oriented database for map-based rice genomics. Nucleic Acids Res., 33, D651-D655.
16. Ohyanagi,H., Tanaka,T., Sakai,H., Shigemoto,Y., Yamaguchi,K., Habara,T., Fujii,Y., Antonio,B.A., Nagamura,Y., Imanishi,T, et al. (2006) The Rice Annotation Project Database (RAP-DB): Hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res., 34, D741-D744.
17. Haas,B.J., Delcher,A.L., Mount,S.M., Wortman,J.R., Smith,R.K., Jr, Hannick,L.I., Maiti,R., Ronning,C.M., Rusch,D.B., Town,C.D. et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res., 31, 5654-5666.
18. Ouyang,S. and Buell,C.R. (2004) The TIGR Plant Repeat Databases: A collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res., 32, D360-D363.
19. Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H. et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 301, 376-379.
20. Nakano,M., Nobuta,K., Vemaraju,K., Tej,S.S., Skogen,J.W. and Meyers,B.C. (2006) Plant MPSS databases: Signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res., 34, D731-D735.
21. Gowda,M., Jantasuriyarat,C., Dean,R.A. and Wang,G.L. (2004) Robust-LongSAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol., 134, 890-897.
22. Koller,A., Washburn,M.P., Lange,B.M., Andon,N.L., Deciu,C., Haynes,P.A., Hays,L., Schieltz,D., Ulaszek,R., Wei,J. et al. (2002) Proteomic survey of metabolic pathways in rice. Proc. Natl Acad. Sci. USA, 99, 11969-11974.
23. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
24. Quackenbush,J., Cho,J., Lee,D., Liang,F., Holt,I., Karamycheva,S., Parvizi,B., Pertea,G., Sultana,R. and White,J. (2001) The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res., 29, 159-164.
25. Childs,K., Hamilton,J., Zhu,W., Ly,E., Cheung,F., Wu,H., Rabinowicz,P.D., Town,C.D., Buell,C.R. and Chan,A.P. (2007) The TIGR Plant Transcript Assemblies Database. Nucleic Acids Res., in press.
26. Zhao,W., Wang,J., He,X., Huang,X., Jiao,Y., Dai,M., Wei,S., Fu,J., Chen,Y., Ren,X. et al. (2004) BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res., 32, D377-D382.
27. Vandepoele,K., Simillion,C. and Van de Peer,Y. (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell, 15, 2192-2202.
28. Guyot,R. and Keller,B. (2004) Ancestral genome duplication in rice. Genome, 47, 610-614.
29. Paterson,A.H., Bowers,J.E. and Chapman,B.A. (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl Acad. Sci. USA, 101, 9903-9908.
30. Lin,H., Zhu,W., Silva,J.C., Gu,X. and Buell,C.R. (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol., 7, R41.
31. Wang,X., Shi,X., Hao,B., Ge,S. and Luo,J. (2005) Duplication and DNA segmental loss in the rice genome: Implications for diploidization. New Phytol., 165, 937-946.
32. Haas,B.J., Delcher,A.L., Wortman,J.R. and Salzberg,S.L. (2004) DAGchainer: A tool for mining segmental genome duplications and synteny. Bioinformatics, 20, 3643-3646.