Towards an accurate sequence of the rice genome

Current Opinion in Plant Biology

Volumn 6, Issue 2, 2003, Pages 101-105

  Delseny, Michel ^a  

^a UNIVERSITÉ DE PERPIGNAN   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0037393287     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5266(03)00010-4     Document Type: Review

References (30)

1. Moore G, Devos KM, Wang Z, Gale MD: Grasses, line up and form a circle. Curr Biol 1995, 5:737-739.
2. Bennetzen JL, SanMiguel P, Chen MS, Tikhonov A, Francki M, Avramova Z: Grass genomes. Proc Natl Acad Sci USA 1998, 95:1975-1978.
3. Sasaki T: The rice genome project in Japan. Proc Natl Acad Sci USA 1998, 95:2027-2028.
4. Sasaki T, Burr B: International rice genome sequencing project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 2000, 3:138-141.
5. Goff AS, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100. A complete analysis of the Nipponbare draft sequence, with many web supplements.
6. Yu J, Hu S, Wang J, Wong GKS, Li S, Lin B, Deng Y, Dai L, Zhou Y, Zhang X et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. Indica). Science 2002, 296:79-92. A complete analysis of the sequence of the rice subspecies indica.
7. Normile D, Pennisi E: Rice: boiled down to bare essentials. Science 2002, 296:32-36. A historical account of the sequencing of the rice genome. The authors comment this achievement and describe challenges that were overcome during the sequencing process. Several other papers in this Science issue comment on the achievements of both the Syngenta and the BGI groups.
8. Sasaki T, Matsumoto T, Yamamoto K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y: The genome sequence and structure of rice chromosome 1. Nature 2002, 402:312-316. A short report on the completely assembled rice chromosome 1 sequence. The authors include a critical comparison of the draft and the complete sequence.
9. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Liu Y, Hu X: Sequence and analysis of rice chromosome 4. Nature 2002, 420:316-320. A short report on the completely assembled sequence of rice chromosome 4. The authors also compare the indica and japonica sequences.
10. Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J et al.: A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 2002, 14:525-535. The authors describe a strategy for mapping ESTs on the physical map. They report the distribution of expressed genes from different abundance classes along the 12 rice chromosomes.
11. Cheng M, Presting G, Barbazuk WB, Goicoechea JL, Blackman B, Fang G, Kim H, Frisch D, Yu Y, Sun S et al.: An integrated physical and genetic map of the rice genome. Plant Cell 2002, 14:537-545. The authors present a comprehensive physical map of the rice genome.
12. Mao L, Wood TC, Yu YS, Budiman MA, Tomkins J, Woo SS, Sasinowski M, Presting G, Frisch D, Goff S et al.: Rice transposable elements: a survey of 73 000 sequence-tagged connectors. Genome Res 2000, 10:982-990.
13. Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J: High resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers revealed the centromere recombination along chromosome 10 of rice. Genetics 2001, 157:1749-1757.
14. Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B et al.: A fine physical map of the rice chromosome 4. Genome Res 2002, 12:817-823.
15. Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T et al.: Rice GAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Res 2002, 30:98-102.
16. Yu J, Hu S, Wang J, Li S, Wong KG, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al.: A draft sequence of the rice (Oryza sativa ssp. Indica) genome. Chinese Sci Bull 2001, 46:1937-1942.
17. Wang J, Wong GSK, Ni P, Han Y, Huang X, Zhang J, Ye C, Zhang Y, Hu J, Zhang K et al.: RePS: a sequence assembler that masks exact repeats identified from shotgun data. Genome Res 2002, 12:824-831.
18. Barry G: The use of the Monsanto draft rice genome sequence in research. Plant Physiol 2001, 125:1161-1165.
19. Barakat A, Carels N, Bernardi G: The distribution of genes in the genomes of graminae. Proc Natl Acad Sci USA 1997, 94:6857-6861.
20. Kumarc A, Bennetzen JL: Plant retrotransposons. Annu Rev Genet 1999, 33:479-532.
21. Turcotte KT, Srinivasan S, Bureau T: Survey of transposable elements of rice genomic sequences. Plant J 2001, 25:169-179.
22. Jiang N, Wessler SR: Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements. Plant Cell 2001, 13:2553-2564.
23. Cheng Z, Buell CR, Wing R, Gu M, Jiang J: Toward a cytological characterization of the rice genome. Genome Res 2002, 12:2133-2141.
24. Han B: Comparison of Oryza sativa subspecies japonica and indica. Curr Opin Plant Biol 2003, in press. An extensive analysis of the differences and similarities between the japonica and indica subspecies of rice.
25. Mayer K, Murphy G, Tarchini B, Wambutt R, Volckaert G, Pohl T, Dusterrhoft A, Stiekema W, Entian KD, Terryn N et al.: Conservation of microstructure between a sequence region of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Res 2001, 11:1167-1174.
26. Salse J, Piegu B, Cooke R, Delseny M: Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice sequencing project. Nucleic Acids Res 2002, 30:2316-2328. A detailed analysis of synteny between rice and Arabidopsis genome. The data discussed in the paper cover more than half of the rice genome, and there are updates on a website (http://Igdp.univ-perp.fr/~salse/nar_supplement)
27. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A: The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 2000, 12:381-391.
28. Song R, Llaca V, Messing J: Mosaic organizatien of orthologous sequences in grass genome. Genome Res 2002, 12:1549-1555.
29. Bennetzen J: Synteny between rice and other cereals based on genome sequence information. Curr Opin Plant Biol 2003, in press. The most update survey of synteny between cereal genomes, which benefits from the extensive sequencing.
30. Koller A, Washburn MP, Lange BM, Andon NL, Deciu C, Haynes PA, Hays L, Schieltz D, Ulaszek R, Wei J et al.: Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci USA 2002, 99:11969-11974.