The genomes of Oryza sativa: A history of duplications

PLoS Biology

Volumn 3, Issue 2, 2005, Pages 0266-0281

  Yu, Jun ^a,b   Wang, Jun ^a,b   Lin, Wei ^a   Li, Songgang ^a,c   Li, Heng ^a,b,d   Zhou, Jun ^a   Ni, Peixiang ^a   Dong, Wei ^a   Hu, Songnian ^b   Zeng, Changqing ^a   Zhang, Jianguo ^a   Zhang, Yong ^a,c   Li, Ruiqiang ^a   Xu, Zuyuan ^a   Li, Shengting ^a   Li, Xianran ^a   Zheng, Hongkun ^a   Cong, Lijuan ^a   Lin, Liang ^a   Yin, Jianning ^a   Geng, Jianing ^a   Li, Guangyuan ^a   Shi, Jianping ^a   Liu, Juan ^a   Lv, Hong ^a   Li, Jun ^a   Wang, Jing ^a,c   Deng, Yajun ^a   Ran, Longhua ^e   Shi, Xiaoli ^a,c   Wang, Xiyin ^a,c   Wu, Qingfa ^a   Li, Changfeng ^a   Ren, Xiaoyu ^a   Wang, Jingqiang ^a   Wang, Xiaoling ^a   Li, Dawei ^a   Liu, Dongyuan ^a   Zhang, Xiaowei ^a   Ji, Zhendong ^a   Zhao, Wenming ^a   Sun, Yongqiao ^a   Zhang, Zhenpeng ^a   Bao, Jingyue ^a   Han, Yujun ^a   Dong, Lingli ^a   Ji, Jia ^a   Chen, Peng ^a   Wu, Shuming ^a   Liu, Jinsong ^a   Xiao, Ying ^a   Bu, Dongbo ^f   Tan, Jianlong ^f   Yang, Li ^a   Ye, Chen ^a   Zhang, Jingfen ^f   Xu, Jingyi ^f   Zhou, Yan ^b   Yu, Yingpu ^b   Zhang, Bing ^b   Zhuang, Shulin ^b   Wei, Haibin ^b   Liu, Bin ^a   Lei, Meng ^a   Yu, Hong ^b   Li, Yuanzhe ^a   Xu, Hao ^b   Wei, Shulin ^a   He, Ximiao ^a   Fang, Lijun ^b   Zhang, Zengjin ^a   Zhang, Yunze ^a   Huang, Xiangang ^a   Su, Zhixi ^b   Tong, Wei ^a   Li, Jinhong ^b   Tong, Zongzhong ^a   Li, Shuangli ^a   Ye, Jia ^b   Wang, Lishun ^a   Fang, Lin ^a   Lei, Tingting ^a   Chen, Chen ^a   Chen, Huan ^b   Xu, Zhao ^a   Li, Haihong ^a   Huang, Haiyan ^a   Zhang, Feng ^a   Xu, Huayong ^b   Li, Na ^a   Zhao, Caifeng ^a   Li, Shuting ^a   Dong, Lijun ^a   Huang, Yanqing ^a   Li, Long ^a   Xi, Yan ^a   Qi, Qiuhui ^a   Li, Wenjie ^a   Zhang, Bo ^a   Hu, Wei ^a   Zhang, Yanling ^a   Tian, Xiangjun ^b   Jiao, Yongzhi ^a   Liang, Xiaohu ^a   Jin, Jiao ^a,g   Gao, Lei ^a,d   Zheng, Weimou ^a,d   Hao, Bailin ^a,d   Liu, Siqi ^a,b   Wang, Wen ^b,h   Yuan, Longping ⁱ   Cao, Mengliang ⁱ   McDermott, Jason ^j   Samudrala, Ram ^j   Wang, Jian ^a,b   Wong, Gane Ka Shu ^a,b,j   Yang, Huanming ^a,b   more..

^a BGI SHENZHEN   (China)

^b Hangzhou Genomics Institute   (China)

^c PEKING UNIVERSITY   (China)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^e Beijing North Computation Center   (China)

^f INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^g BEIJING NORMAL UNIVERSITY   (China)

^h KUNMING INSTITUTE OF ZOOLOGY   (China)

ⁱ China National Hybrid R and D Center   (China)

^j UNIVERSITY OF WASHINGTON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; SCAFFOLD PROTEIN;

ARTICLE; CHROMOSOME 11; CHROMOSOME 12; CHROMOSOME ANALYSIS; CHROMOSOME DUPLICATION; CHROMOSOME IDENTIFICATION; DNA SEQUENCE; ERROR; FRAGMENTATION REACTION; GENE MAPPING; GENETIC VARIABILITY; GENOME; GRASS; MATERIALS; PREDICTION; REDUNDANCY ANALYSIS; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; TIME; CHINA; CHROMOSOME MAP; GENE; GENE DUPLICATION; GENETICS; NUCLEOTIDE SEQUENCE;

JAPONICA; ORYZA SATIVA; POACEAE;

BASE SEQUENCE; CHINA; CHROMOSOME MAPPING; GENE DUPLICATION; GENES, PLANT; GENOME, PLANT; ORYZA SATIVA;

EID: 20144366003     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030038     Document Type: Article

References (90)

1. Yu J, Hu S, Wang J, Wong GK, Li S, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
2. Goff SA, Ricke D, Lan TH, Presting G, Wang R, et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
3. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, et al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.
4. Feng Q, Zhang Y, Hao P, Wang S, Fu G, et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
5. The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolutionof rice chromosome 10. Science 300: 1566-1569.
6. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
7. Olson MV (2001) The maps. Clone by clone by clone. Nature 409: 816-818.
8. Bennetzen J (2002) The rice genome. Opening the door to comparative plant biology. Science 296: 60-63.
9. Feuillet C, Keller B (2002) Comparative genomics in the grass family: Molecular characterization of grass genome structure and evolution. Ann Bot (Lond) 89: 3-10.
10. Livingstone K, Rieseberg LH (2002) Rice genomes: A grainy view of future evolutionary research. Curr Biol 12: R470-R471.
11. Shimamoto K, Kyozuka J (2002) Rice as a model for comparative genomics of plants. Annu Rev Plant Biol 53: 399-419.
12. Delseny M (2003) Towards an accurate sequence of the rice genome. Curr Opin Plant Biol 6: 101-105.
13. Sasaki T, Sederoff RR (2003) Genome studies and molecular genetics. The rice genome and comparative genomics of higher plants. Curr Opin Plant Biol 6: 97-100.
14. Vandepoele K, Simillion C, Van de Peer Y (2003) Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15: 2192-2202.
15. Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101: 9903-9908.
16. Zhao W, Wang J, He X, Huang X, Jiao Y, et al. (2004) BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res 32: D377-D382.
17. Buell CR (2002) Current status of the sequence of the rice genome and prospects for finishing the first monocot genome. Plant Physiol 130: 1585-1586.
18. Buell CR (2002) Obtaining the sequence of the rice genome and lessons learned along the way. Trends Plant Sci 7: 538-542.
19. Leach J, McCouch S, Slezak T, Sasaki T, Wessler S (2002) Why finishing the rice genome matters. Science 296: 45-45.
20. Palmer LE, McCombie WR (2002) On the importance of being finished. Genome Biol 3: comment2010.1-2010.4.
21. Reugels AM, Kurek R, Lammermann U, Bunemann H (2000) Mega-introns in the dynein gene DhDhc7(Y) on the heterochromatic Y chromosome give rise to the giant threads loops in primary spermatocytes of Drosophila hydei. Genetics 154: 759-769.
22. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021-1029.
23. Mayer K, Mewes HW (2002) How can we deliver the large plant genomes? Strategies and perspectives. Curr Opin Plant Biol 5: 173-177.
24. Rabinowicz PD, McCombie WR, Martienssen RA (2003) Gene enrichment in plant genomic shotgun libraries. Curr Opin Plant Biol 6: 150-156.
25. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
26. Wang J, Wong GK, Ni P, Han Y, Huang X, et al. (2002) RePS: A sequence assembler that masks exact repeats identi.ed from the shotgun data. Genome Res 12: 824-831.
27. Zhong L, Zhang K, Huang X, Ni P, Han Y, et al. (2003) A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the lengthdistribution of clone-inserts.GenoProt Bioinfo 1: 43-51.
28. Mullikin JC, Ning Z (2003) The phusion assembler. Genome Res 13: 81-90.
29. Lander ES, Waterman MS (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2: 231-239.
30. Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, et al. (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14: 537-545.
31. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, et al. (1998) A highdensity rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479-494.
32. Kent WJ (2002) BLAT - The BLAST-like alignment tool. Genome Res 12: 656-664.
33. Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14: 988-995.
34. Brenner SE, Chothia C, Hubbard TJ (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci U S A 95: 6073-6078.
35. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10: 516-522.
36. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860-869.
37. McDermott J, Samudrala R (2003) Bioverse: Functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res 31: 3736-3737.
38. McDermott J, Samudrala R (2004) Enhanced functional information from predicted protein networks. Trends Biotechnol 22: 60-62.
39. Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, et al. (2003) The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 13: 662-672.
40. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31: 315-318.
41. Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, et al. (2002) Gramene, a tool for grass genomics. Plant Physiol 130: 1606-1613.
42. Westbrook J, Feng Z, Chen L, Yang H, Berman HM (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res 31: 489-491.
43. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, et al. (2002) DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
44. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
45. Ohno S (1970) Evolution by gene duplication. Berlin: Springer-Verlag. 160 p.
46. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
47. Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
48. Soltis PS, Soltis DE (2000) The role of genetic and genomic attributes in the success of polyploids. Proc Natl Acad Sci U S A 97: 7051-7057.
49. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42: 225-249.
50. Levy AA, Feldman M (2002) The impact of polyploidy on grass genome evolution. Plant Physiol 130: 1587-1593.
51. Osborn TC, Pires JC, Birchler JA, Auger DL, Chen ZJ, et al. (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19: 141-147.
52. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
53. Blanc G, Wolfe KH (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
54. Blanc G, BarakatA, Guyot R, Cooke R, DelsenyM(2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101.
55. The Arabidopsis Genome Initiative(2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
56. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
57. Simillion C, Vandepoele K, Van Montagu MC, Zabeau M, Van de Peer Y (2002) The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A 99: 13627-13632.
58. Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
59. Dominguez I, Graziano E, Gebhardt C, Barakat A, Berry S, et al. (2003) Plant genome archaeology: Evidence for conserved ancestral chromosome segments in dicotyledonous plant species. Plant Biotechnol J 1: 91-99.
60. Kishimoto N, Higo H, Abe K, Arai S, Saito A, et al. (1994) Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions. Theor Appl Genet 88: 722-726.
61. Nagamura Y, Inoue T, Antonio B, Shimano T, Kajiya H, et al. (1995) Conservation of duplicated segments between rice chromosomes 11 and 12. Breeding Sci 45: 373-376.
62. Wang P, Liu KD, Zhang QF (2000) Segmental duplications are common in rice genome. Acta Bot Sin 42: 1150-1155.
63. Comeron JM (1999) K-Estimator: Calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15: 763-764.
64. Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci U S A 93: 10274-10279.
65. ang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
66. Doyle JJ, Gaut BS (2000) Evolution of genes and taxa: A primer. Plant Mol Biol 42: 1-23.
67. Wolfe KH (2001) Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2: 333-341.
68. Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125: 1198-1205.
69. Yang YW, Lai KN, Tai PY, Li WH (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol 48: 597-604.
70. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci U S A 95: 1971-1974.
71. Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, et al. (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48: 463-481.
72. Salse J, Piegu B, Cooke R, Delseny M (2004) New in silico insight into the synteny between rice (Oryza sativa L.) and maize (Zea mays L.) highlights reshuffling and identifies new duplications in the rice genome. Plant J 38: 396-409.
73. Graur D, Li WH (2000) Fundamentals of molecular evolution, 2nd edition. Sunderland: Sinauer. 481 p.
74. Nembaware V, Crum K, Kelso J, Seoighe C (2002) Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res 12: 1370-1376.
75. Domazet-Loso T, Tautz D (2003) An evolutionary analysis of orphan genes in Drosophila. Genome Res 13: 2213-2219.
76. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154: 15-28.
77. Bennetzen JL, Ma J (2003) The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol 6: 128-133.
78. Delseny M (2004) Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr Opin Plant Biol 7: 126-131.
79. Prince VE, Pickett FB (2002) Splitting pairs: The diverging fates of duplicated genes. Nat Rev Genet 3: 827-837.
80. Kellogg EA (2003) What happens to genes in duplicated genomes. Proc Natl Acad Sci U S A 100: 4369-4371.
81. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
82. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
83. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, et al. (2000) Rice transposable elements: A survey of 73,000 sequence-tagged-connectors. Genome Res 10: 982-990.
84. Wang J, Li S, Zhang Y, Zheng H, Xu Z, et al. (2003) Vertebrate gene predictions and the problem of large genes. Nat Rev Genet 4: 741-749.
85. Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, et al. (2000) A SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.
86. Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, et al. (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135: 1198-1205.
87. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, et al. (2004) Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs. Genome Res 14: 1107-1118.
88. Yamaguchi M, Fabian T, Sauter M, Bhalerao RP, Schrader J, et al. (2000) Activation of CDK-activating kinase is dependent on interaction with H-type cyclins in plants. Plant J 24: 11-20.
89. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci U S A 94: 6809-6814.
90. Bennetzen JL, Coleman C, Liu R, Ma J, Ramakrishna W (2004) Consistent over-estimation of gene number in complex plant genomes. Curr Opin Plant Biol 7: 732-736.