Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

  1. Takeshi Itoh1,2,
  2. Tsuyoshi Tanaka1,3,
  3. Roberto A. Barrero3,
  4. Chisato Yamasaki2,4,
  5. Yasuyuki Fujii2,4,
  6. Phillip B. Hilton2,4,
  7. Baltazar A. Antonio1,
  8. Hideo Aono3,
  9. Rolf Apweiler5,
  10. Richard Bruskiewich6,
  11. Thomas Bureau7,
  12. Frances Burr8,
  13. Antonio Costa de Oliveira9,
  14. Galina Fuks10,
  15. Takuya Habara2,4,
  16. Georg Haberer11,
  17. Bin Han12,
  18. Erimi Harada2,4,
  19. Aiko T. Hiraki2,4,
  20. Hirohiko Hirochika1,
  21. Douglas Hoen7,
  22. Hiroki Hokari4,
  23. Satomi Hosokawa13,
  24. Yue Hsing14,
  25. Hiroshi Ikawa15,
  26. Kazuho Ikeo3,
  27. Tadashi Imanishi2,16,
  28. Yukiyo Ito13,
  29. Pankaj Jaiswal17,
  30. Masako Kanno2,4,
  31. Yoshihiro Kawahara2,18,
  32. Toshiyuki Kawamura4,
  33. Hiroaki Kawashima4,
  34. Jitendra P. Khurana19,
  35. Shoshi Kikuchi1,
  36. Setsuko Komatsu1,20,
  37. Kanako O. Koyanagi16,
  38. Hiromi Kubooka4,
  39. Damien Lieberherr21,
  40. Yao-Cheng Lin14,
  41. David Lonsdale5,
  42. Takashi Matsumoto1,
  43. Akihiro Matsuya4,
  44. W. Richard McCombie22,
  45. Joachim Messing10,
  46. Akio Miyao1,
  47. Nicola Mulder5,
  48. Yoshiaki Nagamura1,
  49. Jongmin Nam23,24,
  50. Nobukazu Namiki13,
  51. Hisataka Numa1,
  52. Shin Nurimoto4,
  53. Claire O’Donovan5,
  54. Hajime Ohyanagi3,15,
  55. Toshihisa Okido3,
  56. Satoshi OOta25,
  57. Naoki Osato3,
  58. Lance E. Palmer22,26,
  59. Francis Quetier27,
  60. Saurabh Raghuvanshi19,
  61. Naomi Saichi2,4,
  62. Hiroaki Sakai1,4,
  63. Yasumichi Sakai15,
  64. Katsumi Sakata15,
  65. Tetsuya Sakurai28,
  66. Fumihiko Sato4,
  67. Yoshiharu Sato2,4,
  68. Heiko Schoof11,29,30,
  69. Motoaki Seki31,
  70. Michie Shibata13,
  71. Yuji Shimizu15,
  72. Kazuo Shinozaki32,
  73. Yuji Shinso4,
  74. Nagendra K. Singh33,
  75. Brian Smith-White34,
  76. Jun-ichi Takeda2,4,
  77. Motohiko Tanino2,4,
  78. Tatiana Tatusova34,
  79. Supat Thongjuea35,
  80. Fusano Todokoro4,
  81. Mika Tsugane13,
  82. Akhilesh K. Tyagi19,
  83. Apichart Vanavichit35,
  84. Aihui Wang36,
  85. Rod A. Wing37,
  86. Kaori Yamaguchi4,
  87. Mayu Yamamoto13,
  88. Naoyuki Yamamoto4,
  89. Yeisoo Yu37,
  90. Hao Zhang4,
  91. Qiang Zhao12,
  92. Kenichi Higo38,39,
  93. Benjamin Burr8,
  94. Takashi Gojobori1,2,3,
  95. Takuji Sasaki38, and
  96. for the Rice Annotation Project
  1. 1 Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
  2. 2 Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan;
  3. 3 Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan;
  4. 4 Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan;
  5. 5 EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom;
  6. 6 Biometrics and Bioinformatics Unit, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines;
  7. 7 Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada;
  8. 8 Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA;
  9. 9 Department of Genetics, The University of Georgia, Athens, Georgia, 30602-7223, USA;
  10. 10 Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA;
  11. 11 Institute for Bioinformatics, GSF National Research Center for Environment and Health, D-85764 Neuherberg, Germany;
  12. 12 Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China;
  13. 13 Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan;
  14. 14 Institute of Botany, Academia Sinica, Nankang, Taipei 11529, Taiwan;
  15. 15 Tsukuba Division, Mitsubishi Space Software Co., Ltd., Tsukuba, Ibaraki 305-0032, Japan;
  16. 16 Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan;
  17. 17 Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA;
  18. 18 Department of Biological Sciences, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan;
  19. 19 Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India;
  20. 20 National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan;
  21. 21 SWISS-PROT Group, Swiss Institute of Bioinformatics, CH-1211 Geneva 4, Switzerland;
  22. 22 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11723, USA;
  23. 23 Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;
  24. 24 Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
  25. 25 RIKEN BioResource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305-0074, Japan;
  26. 26 Department of Molecular Genetics and Microbiology, and Center for Infectious Diseases, The State University of New York at Stony Brook, Stony Brook, New York 11794, USA;
  27. 27 Genoscope, 91057 Evry Cedex, France;
  28. 28 Metabolomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan;
  29. 29 Technische Universität München, Genome Oriented Bioinformatics, D-85354 Freising-Weihenstephan, Germany;
  30. 30 Plant Computational Biology, Max-Planck-Institute for Plant Breeding Research, D 50829 Cologne, Germany;
  31. 31 Plant Functional Genomics Research Group, RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan;
  32. 32 RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan;
  33. 33 National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India;
  34. 34 National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA;
  35. 35 Rice Gene Discovery Unit, Kasetsart University, Nakorn Pathom 73140, Thailand;
  36. 36 The Institute for Genomic Research, Rockville, Maryland 20850, USA;
  37. 37 Arizona Genomics Institute, The University of Arizona, Tucson, Arizona 85721, USA;
  38. 38 National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;
  39. 39 Bio-Oriented Technology Research Advancement Institution, Minato-ku, Tokyo 105-0001, Japan.

Abstract

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Footnotes

  • ↵2 Corresponding author: Takashi Gojobori.

    ↵2 E-mail tgojobor{at}genes.nig.ac.jp; fax 81-55-981-6848.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.5509507

    • Received May 17, 2006.
    • Accepted October 31, 2006.

  • Freely available online through the Genome Research Open Access option.

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  1. Published in Advance January 8, 2007, doi: 10.1101/gr.5509507 Genome Res. 17: 175-183 Copyright © 2007, Cold Spring Harbor Laboratory Press

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