A Reference Rice Genome Sequence in the 10K Genome Era

  • Takeshi Itoh
  • Baltazar A. Antonio
  • Yoshihiro Kawahara
  • Tsuyoshi Tanaka
  • Hiroaki Sakai
  • Takashi Matsumoto
  • Takuji Sasaki
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 5)


The reference rice genome of japonica cultivar Nipponbare was determined by a map-based sequencing method. Currently, thousands of rice cultivars and several wild species are being sequenced to unravel the genetic variation among diverse cultivars, landraces, and related genomes in the genus Oryza. It is therefore an urgent issue to provide an ultrahigh quality reference genome sequence so that single nucleotide variations can be detected accurately between cultivars. With the aid of a large amount of next-generation sequencing data, we could thoroughly examine the rice reference genome and correct the sequencing errors that were previously overlooked. Our genome-wide annotation identified or predicted 37,872 loci, of which over 3,000 loci were newly found. This genome assembly will further enhance future breeding strategies in the era of large-scale genomics.


Bacterial Artificial Chromosome Genome Assembly Rice Genome International Rice Research Institute Rice Genome Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H et al (2009) Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 69:179–194PubMedCrossRefGoogle Scholar
  2. 2.
    Allen JE, Salzberg SL (2005) JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 15:3596–3603CrossRefGoogle Scholar
  3. 3.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402PubMedCrossRefGoogle Scholar
  4. 4.
    Amano N, Tanaka T, Numa H, Sakai H, Itoh T (2010) Efficient plant gene identification based on interspecies mapping of full-length cDNAs. DNA Res 17:271–279PubMedCrossRefGoogle Scholar
  5. 5.
    Barry GF (2001) The use of the Monsanto draft rice genome sequence in research. Plant Physiol 125:1164–1165PubMedCrossRefGoogle Scholar
  6. 6.
    Durbin RM, Altshuler DL, Durbin RM, Abecasis GAR, Bentley DR, Chakravarti A, Clark AG, Collins FS et al (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073PubMedCrossRefGoogle Scholar
  7. 7.
    Genome 10K Community of Scientists (2009) Genome 10K: a proposal to obtain whole-genome sequence for 10000 vertebrate species. J Hered 100:659–674CrossRefGoogle Scholar
  8. 8.
    Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100PubMedCrossRefGoogle Scholar
  9. 9.
    Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494PubMedGoogle Scholar
  10. 10.
    Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961–967PubMedCrossRefGoogle Scholar
  11. 11.
    Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q et al (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39CrossRefGoogle Scholar
  12. 12.
    International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800CrossRefGoogle Scholar
  13. 13.
    Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J et al (2006) Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J 48:710–727PubMedCrossRefGoogle Scholar
  14. 14.
    Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N et al (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301:376–379PubMedCrossRefGoogle Scholar
  15. 15.
    Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J et al (1994) A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet 8:365–372PubMedCrossRefGoogle Scholar
  16. 16.
    Kurata N, Umehara Y, Tanoue H, Sasaki T (1997) Physical mapping of the rice genome with YAC clones. Plant Mol Biol 35:101–113PubMedCrossRefGoogle Scholar
  17. 17.
    Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760PubMedCrossRefGoogle Scholar
  18. 18.
    Liu X, Lu T, Yu S, Li Y, Huang Y, Huang T et al (2007) A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Plant Mol Biol 65:403–415PubMedCrossRefGoogle Scholar
  19. 19.
    Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M (2005) Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Res 33:6494–6506PubMedCrossRefGoogle Scholar
  20. 20.
    Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20:2878–2879PubMedCrossRefGoogle Scholar
  21. 21.
    Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K et al (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol 156:20–28PubMedCrossRefGoogle Scholar
  22. 22.
    McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ et al (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106:12273–12278PubMedCrossRefGoogle Scholar
  23. 23.
    Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K (2009) TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol 150:1135–1146PubMedCrossRefGoogle Scholar
  24. 24.
    Ohyanagi H, Tanaka T, Sakai H, Shigemoto Y, Yamaguchi K, Habara T et al (2006) The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res 34:D741–D744PubMedCrossRefGoogle Scholar
  25. 25.
    Pruitt KD, Tatusova T, Brown GR, Maglott DR (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40:D130–D135PubMedCrossRefGoogle Scholar
  26. 26.
    Sasaki T, Burr B (2000) International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr Opin Plant Biol 3:138–141PubMedCrossRefGoogle Scholar
  27. 27.
    Sato K, Shin-I T, Seki M, Shinozaki K, Yoshida H, Takeda K et al (2009) Development of 5006 full-length CDNAs in barley: a tool for accessing cereal genomics resources. DNA Res 16:81–89PubMedCrossRefGoogle Scholar
  28. 28.
    Soderlund C, Descour A, Kudrna D, Bomhoff M, Boyd L, Currie J et al (2009) Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs. PLoS Genet 5:e1000740PubMedCrossRefGoogle Scholar
  29. 29.
    Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H et al (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 36:D1028–D1033PubMedGoogle Scholar
  30. 30.
    UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40:D71–D75CrossRefGoogle Scholar
  31. 31.
    Weigel D, Mott R (2009) The 1001 Genomes Project for Arabidopsis thaliana. Genome Biol 10:107PubMedCrossRefGoogle Scholar
  32. 32.
    Wing RA, Ammiraju J, Luo M, Kim H, Yu Y, Kudrna D et al (2005) The Oryza Map Alignment Project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59:53–62PubMedCrossRefGoogle Scholar
  33. 33.
    Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X et al (2011) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol 30:105–111PubMedCrossRefGoogle Scholar
  34. 34.
    Yamamoto K, Sasaki T (1997) Large-scale EST sequencing in rice. Plant Mol Biol 35:135–144PubMedCrossRefGoogle Scholar
  35. 35.
    Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214PubMedCrossRefGoogle Scholar
  36. 36.
    Zhao K, Tung CW, Eizenga G, Wright MH, Ali ML, Price AH et al (2011) Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:467PubMedCrossRefGoogle Scholar
  37. 37.
    Zhou S, Bechner MC, Place M, Churas P, Pape L, Leong S et al (2007) Validation of rice genome sequence by optimal mapping. BMC Genomics 8:278PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Takeshi Itoh
    • 1
  • Baltazar A. Antonio
    • 2
  • Yoshihiro Kawahara
    • 1
  • Tsuyoshi Tanaka
    • 1
  • Hiroaki Sakai
    • 1
  • Takashi Matsumoto
    • 3
  • Takuji Sasaki
    • 4
  1. 1.Bioinformatics Research UnitAgrogenomics Research Center, National Institute of Agrobiological SciencesTsukubaJapan
  2. 2.Genome Resource UnitAgrogenomics Research Center, National Institute of Agrobiological SciencesTsukubaJapan
  3. 3.Plant Genome Research UnitAgrogenomics Research Center, National Institute of Agrobiological SciencesTsukubaJapan
  4. 4.NODAI Research InstituteTokyo University of AgricultureTokyoJapan

Personalised recommendations