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Gene and Repetitive Sequence Annotation in the Triticeae

  • Thomas Wicker
  • C. Robin Buell
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 7)

Abstract

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes.

Keywords

Bacterial Artificial Chromosome Genome Annotation Bacterial Artificial Chromosome Library Pfam Domain Target Site Duplication 
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.

Notes

Acknowledgments

Research in the Buell lab on wheat genomics is supported by the National Research Initiative (NRI) Plant Genome Program of the USDA Cooperative State Research, Education and Extension Service (CSREES).

References

  1. Arabidopsis Genome Initiative. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815.CrossRefGoogle Scholar
  2. Arumuganathan, K. and Earle, E. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208–218.CrossRefGoogle Scholar
  3. Bao, Z. and Eddy, S.R. (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269–1276.PubMedCrossRefGoogle Scholar
  4. Bennett, M.D. and Smith, J.B. (1976) Nuclear DNA amounts in angiosperms. Philos. Trans. R Soc. Lond. B Biol. Sci. 274, 227–274.PubMedCrossRefGoogle Scholar
  5. Bossolini, E., Wicker, T., Knobel, P.A. and Keller, B. (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J. 49, 704–717.PubMedCrossRefGoogle Scholar
  6. Castelli, V., Aury, J.M., Jaillon, O., Wincker, P., Clepet, C., Menard, M., Cruaud, C., Quetier, F., Scarpelli, C., Schachter, V., Temple, G., Caboche, M., Weissenbach, J. and Salanoubat, M. (2004) Whole genome sequence comparisons and “full-length” cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res. 14, 406–413.PubMedCrossRefGoogle Scholar
  7. Chao, S., Lazo, G.R., You, F., Crossman, C.C., Hummel, D.D., Lui, N., Laudencia-Chingcuanco, D., Anderson, J.A., Close, T.J., Dubcovsky, J., Gill, B.S., Gill, K.S., Gustafson, J.P., Kianian, S.F., Lapitan, N.L., Nguyen, H.T., Sorrells, M.E., McGuire, P.E., Qualset, C.O. and Anderson, O.D. (2006) Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.). Genome 49, 531–544.PubMedCrossRefGoogle Scholar
  8. Conley, E.J., Nduati, V., Gonzalez-Hernandez, J.L., Mesfin, A., Trudeau-Spanjers, M., Chao, S., Lazo, G.R., Hummel, D.D., Anderson, O.D., Qi, L.L., Gill, B.S., Echalier, B., Linkiewicz, A.M., Dubcovsky, J., Akhunov, E.D., Dvorak, J., Peng, J.H., Lapitan, N.L., Pathan, M.S., Nguyen, H.T., Ma, X.F., Miftahudin, Gustafson, J.P., Greene, R.A., Sorrells, M.E., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Sidhu, D., Dilbirligi, M., Gill, K.S., Choi, D.W., Fenton, R.D., Close, T.J., McGuire, P.E., Qualset, C.O. and Anderson, J.A. (2004) A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics 168, 625–637.PubMedCrossRefGoogle Scholar
  9. Devos, K.M., Ma, J., Pontaroli, A.C., Pratt, L.H. and Bennetzen, J.L. (2005) Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc. Natl. Acad. Sci. USA 102, 19243–19248.PubMedCrossRefGoogle Scholar
  10. Dubcovsky, J., Ramakrishna, W., SanMiguel, P.J., Busso, C.S., Yan, L., Shiloff, B.A. and Bennetzen, J.L. (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol. 125, 1342–1353.PubMedCrossRefGoogle Scholar
  11. Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, S.R., Sonnhammer, E.L. and Bateman, A. (2006) Pfam: clans, web tools and services. Nucl. Acids Res. 34, D247–D251.PubMedCrossRefGoogle Scholar
  12. Francki, M., Carter, M., Ryan, K., Hunter, A., Bellgard, M. and Appels, R. (2004) Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat. Funct. Integr. Genomics 4, 118–130.PubMedCrossRefGoogle Scholar
  13. Gill, B.S., Appels, R., Botha-Oberholster, A.M., Buell, C.R., Bennetzen, J.L., Chalhoub, B., Chumley, F., Dvorak, J., Iwanaga, M., Keller, B., Li, W., McCombie, W.R., Ogihara, Y., Quetier, F. and Sasaki, T. (2004) A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics 168, 1087–1096.Google Scholar
  14. Griffiths, S., Sharp, R., Foote, T.N., Bertin, I., Wanous, M., Reader, S., Colas, I. and Moore, G. (2006) Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439, 749–752.PubMedCrossRefGoogle Scholar
  15. 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., Salzberg, S.L. and White, O. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucl. Acids Res. 31, 5654–5666.PubMedCrossRefGoogle Scholar
  16. Haas, B.J., Wortman, J.R., Ronning, C.M., Hannick, L.I., Smith, R.K., Jr., Maiti, R., Chan, A.P., Yu, C., Farzad, M., Wu, D., White, O. and Town, C.D. (2005) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol. 3, 7.PubMedCrossRefGoogle Scholar
  17. Hossain, K.G., Kalavacharla, V., Lazo, G.R., Hegstad, J., Wentz, M.J., Kianian, P.M., Simons, K., Gehlhar, S., Rust, J.L., Syamala, R.R., Obeori, K., Bhamidimarri, S., Karunadharma, P., Chao, S., Anderson, O.D., Qi, L.L., Echalier, B., Gill, B.S., Linkiewicz, A.M., Ratnasiri, A., Dubcovsky, J., Akhunov, E.D., Dvorak, J., Miftahudin, Ross, K., Gustafson, J.P., Radhawa, H.S., Dilbirligi, M., Gill, K.S., Peng, J.H., Lapitan, N.L., Greene, R.A., Bermudez-Kandianis, C.E., Sorrells, M.E., Feril, O., Pathan, M.S., Nguyen, H.T., Gonzalez-Hernandez, J.L., Conley, E.J., Anderson, J.A., Choi, D.W., Fenton, D., Close, T.J., McGuire, P.E., Qualset, C.O. and Kianian, S.F. (2004) A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7. Genetics 168, 687–699.PubMedCrossRefGoogle Scholar
  18. Houde, M., Belcaid, M., Ouellet, F., Danyluk, J., Monroy, A.F., Dryanova, A., Gulick, P., Bergeron, A., Laroche, A., Links, M.G., MacCarthy, L., Crosby, W.L. and Sarhan, F. (2006) Wheat, E.S.T resources for functional genomics of abiotic stress. BMC Genomics 7, 149.PubMedCrossRefGoogle Scholar
  19. Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyere, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pe, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A.F., Weissenbach, J., Quetier, F. and Wincker, P. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467.PubMedCrossRefGoogle Scholar
  20. Jurka, J. (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418–420.PubMedCrossRefGoogle Scholar
  21. Kawaura, K., Mochida, K. and Ogihara, Y. (2005) Expression profile of two storage-protein gene families in hexaploid wheat revealed by large-scale analysis of expressed sequence tags. Plant Physiol. 139, 1870–1880.PubMedCrossRefGoogle Scholar
  22. Kronmiller, B.A. and Wise, R.P. (2008) TEnest: automated chronological annotation and visualization of nested plant transposable elements. Plant Physiol. 146, 45–59.PubMedCrossRefGoogle Scholar
  23. La Rota, M. and Sorrells, M.E. (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct. Integr. Genomics 4, 34–46.PubMedCrossRefGoogle Scholar
  24. Laudencia-Chingcuanco, D.L., Stamova, B.S., Lazo, G.R., Cui, X. and Anderson, O.D. (2006) Analysis of the wheat endosperm transcriptome. J. Appl. Genet. 47, 287–302.PubMedCrossRefGoogle Scholar
  25. Lazo, G.R., Chao, S., Hummel, D.D., Edwards, H., Crossman, C.C., Lui, N., Matthews, D.E., Carollo, V.L., Hane, D.L., You, F.M., Butler, G.E., Miller, R.E., Close, T.J., Peng, J.H., Lapitan, N.L., Gustafson, J.P., Qi, L.L., Echalier, B., Gill, B.S., Dilbirligi, M., Randhawa, H.S., Gill, K.S., Greene, R.A., Sorrells, M.E., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Dubcovsky, J., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Mahmoud, A.A., Miftahudin, Ma, X.F., Conley, E.J., Anderson, J.A., Pathan, M.S., Nguyen, H.T., McGuire, P.E., Qualset, C.O. and Anderson, O.D. (2004) Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map. Genetics 168, 585–593.PubMedCrossRefGoogle Scholar
  26. Li, W., Zhang, P., Fellers, J.P., Friebe, B. and Gill, B.S. (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J. 40, 500–511.PubMedCrossRefGoogle Scholar
  27. Linkiewicz, A.M., Qi, L.L., Gill, B.S., Ratnasiri, A., Echalier, B., Chao, S., Lazo, G.R., Hummel, D.D., Anderson, O.D., Akhunov, E.D., Dvorak, J., Pathan, M.S., Nguyen, H.T., Peng, J.H., Lapitan, N.L., Miftahudin, Gustafson, J.P., La Rota, C.M., Sorrells, M.E., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Sandhu, D., Bondareva, S.N., Gill, K.S., Conley, E.J., Anderson, J.A., Fenton, R.D., Close, T.J., McGuire, P.E., Qualset, C.O. and Dubcovsky, J. (2004) A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics 168, 665–676.PubMedCrossRefGoogle Scholar
  28. McCarthy, E.M. and McDonald, J.F. (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19, 362–367.PubMedCrossRefGoogle Scholar
  29. Miftahudin, Ross, K., Ma, X.F., Mahmoud, A.A., Layton, J., Milla, M.A., Chikmawati, T., Ramalingam, J., Feril, O., Pathan, M.S., Momirovic, G.S., Kim, S., Chema, K., Fang, P., Haule, L., Struxness, H., Birkes, J., Yaghoubian, C., Skinner, R., McAllister, J., Nguyen, V., Qi, L.L., Echalier, B., Gill, B.S., Linkiewicz, A.M., Dubcovsky, J., Akhunov, E.D., Dvorak, J., Dilbirligi, M., Gill, K.S., Peng, J.H., Lapitan, N.L., Bermudez-Kandianis, C.E., Sorrells, M.E., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Lazo, G.R., Chao, S., Anderson, O.D., Gonzalez-Hernandez, J., Conley, E.J., Anderson, J.A., Choi, D.W., Fenton, R.D., Close, T.J., McGuire, P.E., Qualset, C.O., Nguyen, H.T. and Gustafson, J.P. (2004) Analysis of expressed sequence tag loci on wheat chromosome group 4. Genetics 168, 651–663.CrossRefGoogle Scholar
  30. Mochida, K., Kawaura, K., Shimosaka, E., Kawakami, N., Shin, I.T., Kohara, Y., Yamazaki, Y. and Ogihara, Y. (2006) Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat. Mol. Genet. Genomics 276, 304–312.PubMedCrossRefGoogle Scholar
  31. Munkvold, J.D., Greene, R.A., Bermudez-Kandianis, C.E., La Rota, C.M., Edwards, H., Sorrells, S.F., Dake, T., Benscher, D., Kantety, R., Linkiewicz, A.M., Dubcovsky, J., Akhunov, E.D., Dvorak, J., Miftahudin, Gustafson, J.P., Pathan, M.S., Nguyen, H.T., Matthews, D.E., Chao, S., Lazo, G.R., Hummel, D.D., Anderson, O.D., Anderson, J.A., Gonzalez-Hernandez, J.L., Peng, J.H., Lapitan, N., Qi, L.L., Echalier, B., Gill, B.S., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Sandhu, D., Erayman, M., Gill, K.S., McGuire, P.E., Qualset, C.O. and Sorrells, M.E. (2004) Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics 168, 639–650.PubMedCrossRefGoogle Scholar
  32. Ogihara, Y., Mochida, K., Kawaura, K., Murai, K., Seki, M., Kamiya, A., Shinozaki, K., Carninci, P., Hayashizaki, Y., Shin, I.T., Kohara, Y. and Yamazaki, Y. (2004) Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet. Syst. 79, 227–232.PubMedCrossRefGoogle Scholar
  33. Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T., Fujii, Y., Antonio, B.A., Nagamura, Y., Imanishi, T., Ikeo, K., Itoh, T., Gojobori, T. and Sasaki, T. (2006) The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucl. Acids Res. 34, D741–D744.PubMedCrossRefGoogle Scholar
  34. Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L., Orvis, J., Haas, B., Wortman, J. and Buell, C.R. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucl. Acids Res. 35, D883–D887.PubMedCrossRefGoogle Scholar
  35. Paux, E., Roger, D., Badaeva, E., Gay, G., Bernard, M., Sourdille, P. and Feuillet, C. (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J. 48, 463–474.PubMedCrossRefGoogle Scholar
  36. Peng, J.H., Zadeh, H., Lazo, G.R., Gustafson, J.P., Chao, S., Anderson, O.D., Qi, L.L., Echalier, B., Gill, B.S., Dilbirligi, M., Sandhu, D., Gill, K.S., Greene, R.A., Sorrells, M.E., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Dubcovsky, J., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Mahmoud, A.A., Miftahudin, Conley, E.J., Anderson, J.A., Pathan, M.S., Nguyen, H.T., McGuire, P.E., Qualset, C.O., Lapitan, N.L. (2004) Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis. Genetics 168, 609–623.PubMedCrossRefGoogle Scholar
  37. Qi, L.L., Echalier, B., Chao, S., Lazo, G.R., Butler, G.E., Anderson, O.D., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Ratnasiri, A., Dubcovsky, J., Bermudez-Kandianis, C.E., Greene, R.A., Kantety, R., La Rota, C.M., Munkvold, J.D., Sorrells, S.F., Sorrells, M.E., Dilbirligi, M., Sidhu, D., Erayman, M., Randhawa, H.S., Sandhu, D., Bondareva, S.N., Gill, K.S., Mahmoud, A.A., Ma, X.F., Miftahudin, Gustafson, J.P., Conley, E.J., Nduati, V., Gonzalez-Hernandez, J.L., Anderson, J.A., Peng, J.H., Lapitan, N.L., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Pathan, M.S., Zhang, D.S., Nguyen, H.T., Choi, D.W., Fenton, R.D., Close, T.J., McGuire, P.E., Qualset, C.O. and Gill, B.S. (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168, 701–712.PubMedCrossRefGoogle Scholar
  38. Quesneville, H., Bergman, C.M., Andrieu, O., Autard, D., Nouaud, D., Ashburner, M. and Anxolabehere, D. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Comput. Biol. 1, 166–175.PubMedCrossRefGoogle Scholar
  39. Randhawa, H.S., Dilbirligi, M., Sidhu, D., Erayman, M., Sandhu, D., Bondareva, S., Chao, S., Lazo, G.R., Anderson, O.D., Miftahudin, Gustafson, J.P., Echalier, B., Qi, L.L., Gill, B.S., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Ratnasiri, A., Dubcovsky, J., Bermudez-Kandianis, C.E., Greene, R.A., Sorrells, M.E., Conley, E.J., Anderson, J.A., Peng, J.H., Lapitan, N.L., Hossain, K.G., Kalavacharla, V., Kianian, S.F., Pathan, M.S., Nguyen, H.T., Endo, T.R., Close, T.J., McGuire, P.E., Qualset, C.O. and Gill, K.S. (2004) Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags. Genetics 168, 677–686.PubMedCrossRefGoogle Scholar
  40. Salamov, A.A. and Solovyev, V.V. (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10, 516–522.PubMedCrossRefGoogle Scholar
  41. Salse, J., Bolot, S., Throude, M., Jouffe, V., Piegu, B., Quraishi, U.M., Calcagno, T., Cooke, R., Delseny, M. and Feuillet, C. (2008) Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. Plant Cell 20, 11–24.PubMedCrossRefGoogle Scholar
  42. See, D.R., Brooks, S., Nelson, J.C., Brown-Guedira, G., Friebe, B. and Gill, B.S. (2006) Gene evolution at the ends of wheat chromosomes. Proc. Natl. Acad. Sci. USA 103, 4162–4167.PubMedCrossRefGoogle Scholar
  43. Smith, D.B. and Flavell, R.B. (1975) Characterisation of the wheat genome by renaturation kinetics. Chromosoma 50, 223–242.CrossRefGoogle Scholar
  44. 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., Qi, L.L., Echalier, B., Gill, B.S., Matthews, D.E., Lazo, G.R., Chao, S., Anderson, O.D., Edwards, H., Linkiewicz, A.M., Dubcovsky, J., Akhunov, E.D., Dvorak, J., Zhang, D., Nguyen, H.T., Peng, J., Lapitan, N.L., Gonzalez-Hernandez, J.L., Anderson, J.A., Hossain, K., Kalavacharla, V., Kianian, S.F., Choi, D.W., Close, T.J., Dilbirligi, M., Gill, K.S., Steber, C., Walker-Simmons, M.K., McGuire, P.E. and Qualset, C.O. (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13, 1818–1827.PubMedGoogle Scholar
  45. Stein, N., Prasad, M., Scholz, U., Thiel, T., Zhang, H., Wolf, M., Kota, R., Varshney, R.K., Perovic, D., Grosse, I. and Graner, A. (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114, 823–839.PubMedCrossRefGoogle Scholar
  46. Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R. and Wu, C.H. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282–1288.PubMedCrossRefGoogle Scholar
  47. Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y.C., Wei, F.J., Hsing, Y.I., Zhao, Q., Han, B., Kramer, M.R., McCombie, R.W., Lonsdale, D., O’Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H., Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O. and Echeverria, M. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucl. Acids Res. 36, D1028–D1033.PubMedGoogle Scholar
  48. The International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature 436, 793–800.CrossRefGoogle Scholar
  49. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., Depamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C.J., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y. and Rokhsar, D. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604.PubMedCrossRefGoogle Scholar
  50. UniProt Consortium. (2007) The Universal Protein Resource (UniProt). Nucl. Acids Res. 35, D193–D197.CrossRefGoogle Scholar
  51. Wicker, T., Guyot, R., Yahiaoui, N. and Keller, B. (2003) CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol. 132, 52–63.PubMedCrossRefGoogle Scholar
  52. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P. and Schulman, A.H. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982.PubMedCrossRefGoogle Scholar
  53. Zhu, W. and Buell, C.R. (2007) Improvement of whole-genome annotation of cereals through comparative analyses. Genome Res. 17, 299–310.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Institute of Plant BiologyUniversity ZurichZurichSwitzerland
  2. 2.Department of Plant BiologyMichigan State UniversityEast LansingUSA

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