Improvement of whole-genome annotation of cereals through comparative analyses

Genome Research

Volumn 17, Issue 3, 2007, Pages 299-310

  Zhu, Wei ^a   Buell, C Robin ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ALGA; ANGIOSPERM; ARTICLE; CEREAL; COMPARATIVE STUDY; FERN; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GYMNOSPERM; MOSS; NONHUMAN; PLANT GENETICS; PRIORITY JOURNAL; RICE;

BASE SEQUENCE; CEREALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOMICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES SPECIFICITY;

ALGAE; BRYOPHYTA; FILICOPHYTA; GYMNOSPERMAE; MAGNOLIOPHYTA; POACEAE;

EID: 33847755100     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5881807     Document Type: Article

References (58)

1. Adai, A., Johnson, C., Mlotshwa, S., Archer-Evans, S., Manocha, V., Vance, V., and Sundaresan, V. 2005. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 15: 78-91.
2. Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
3. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Bedell, J.A., Budiman, M.A., Nunberg, A., Citek, R.W., Robbins, D., Jones, J., Flick, E., Rholfing, T., Fries, J., Bradford, K., et al. 2005. Sorghum genome sequencing by methylation filtration. PLoS Biol. 3: e13.
5. Bennetzen, J.L. 2000. Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions. Plant Cell 12: 1021-1029.
6. Berezikov, E., Cuppen, E., and Plasterk, R.H. 2006. Approaches to microRNA discovery. Nat. Genet. 38 (Suppl. 1): S2-S7.
7. Brendel, V., Xing, L., and Zhu, W. 2004. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20: 1157-1169.
8. Chan, A.P., Pertea, G., Cheung, F., Lee, D., Zheng, L., Whitelaw, C., Pontaroli, A.C., SanMiguel, P., Yuan, Y., Bennetzen, J., et al. 2006. The TIGR Maize Database. Nucleic Acids Res. 34: D771-D776.
9. Childs, K.L., Hamilton, J., Zhu, W., Ly, E., Cheung, F., Hank, W., Rabinowicz, P.D., Town, C.D., Buell, C.R., and Chan, A.P. 2007. The TIGR Plant Transcript Assemblies Database. Nucleic Acids Res. 35 (Database issue): D846-D851.
10. Dennis, P.P. and Omer, A. 2005. Small non-coding RNAs in Archaea. Curr. Opin. Microbiol. 8: 685-694.
11. Eddy, S.R. 2001. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2: 919-929.
12. Foissac, S., Bardou, P., Moisan, A., Cros, M.J., and Schiex, T. 2003. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res. 31: 3742-3745.
13. Gale, M.D. and Devos, K.M. 1998. Comparative genetics in the grasses. Proc. Natl. Acad. Sci. 95: 1971-1974.
14. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
15. Gross, S.S. and Brent, M.R. 2006. Using multiple alignments to improve gene prediction. J. Comput. Biol. 13: 379-393.
16. Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr., R.K., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., et al. 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31: 5654-5666.
17. International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature 436: 793-800.
18. Ito, Y., Arikawa, K., Antonio, B.A., Ohta, I., Naito, S., Mukai, Y., Shimano, A., Masukawa, M., Shibata, M., Yamamoto, M., et al. 2005. Rice Annotation Database (RAD): A contig-oriented database for map-based rice genomics. Nucleic Acids Res. 33: D651-D655.
19. Jiang, N., Bao, Z., Zhang, X., Eddy, S.R., and Wessler, S.R. 2004. Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.
20. Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. 2006. MicroRNAS and their regulatory roles in plants. Annu. Rev. Plant Biol. 57: 19-53.
21. Juretic, N., Hoen, D.R., Huynh, M.L., Harrison, P.M., and Bureau, T.E. 2005. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 15: 1292-1297.
22. Kikuchi, S., Satoh, K., Nagata, T., Kawagashira, N., Doi, K., Kishimoto, N., Yazaki, J., Ishikawa, M., Yamada, H., Ooka, H., et al. 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
23. Korf, I., Flicek, P., Duan, D., and Brent, M.R. 2001. Integrating genomic homology into gene structure prediction. Bioinformatics 17 (Suppl. 1): S140-S148.
24. Lin, H., Zhu, W., Silva, J.C., Gu, X., and Buell, C.R. 2006. Intron gain and loss in segmentally duplicated genes in rice. Genome Biol. 7: R41.
25. Liu, C., Bai, B., Skogerbo, G., Cai, L., Deng, W., Zhang, Y., Bu, D., Zhao, Y., and Chen, R. 2005. NONCODE: An integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 33: D112-D115.
26. Mathe, C., Sagot, M.F., Schiex, T., and Rouze, P. 2002. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30: 4103-4117.
27. Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T., Fujii, Y., Antonio, B.A., Nagamura, Y., Imanishi, T., et al. 2006. The Rice Annotation Project Database (RAP-DB): Hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res. 34: D741-D744.
28. Ouyang, S. and Buell, C.R. 2004. The TIGR Plant Repeat Databases: A collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 32: D360-D363.
29. Palmer, L.E., Rabinowicz, P.D., O'Shaughnessy, A.L., Balija, V.S., Nascimento, L.U., Dike, S., de la Bastide, M., Martienssen, R.A., and McCombie, W.R. 2003. Maize genome sequencing by methylation filtration. Science 302: 2115-2117.
30. Paterson, A.H., Bowers, J.E., and Chapman, B.A. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. 101: 9903-9908.
31. Peterson, D.G., Schulze, S.R., Sciara, E.B., Lee, S.A., Bowers, J.E., Nagel, A., Jiang, N., Tibbitts, D.C., Wessler, S.R., and Paterson, A.H. 2002. Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res. 12: 795-807.
32. Rabinowicz, P.D. and Bennetzen, J.L. 2006. The maize genome as a model for efficient sequence analysis of large plant genomes. Curr. Opin. Plant Biol. 9: 149-156.
33. Rabinowicz, P.D., Schutz, K., Dedhia, N., Yordan, C., Parnell, L.D., Stein, L., McCombie, W.R., and Martienssen, R.A. 1999. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat. Genet. 23: 305-308.
34. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. 2002. MicroRNAs in plants. Genes & Dev. 16: 1616-1626.
35. The Rice Chromosome 3 Sequencing Consortium. 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res. 15: 1284-1291.
36. Sakata, K., Nagamura, Y., Numa, H., Antonio, B.A., Nagasaki, H., Idonuma, A., Watanabe, W., Shimizu, Y., Horiuchi, I., Matsumoto, T., et al. 2002. RiceGAAS: An automated annotation system and database for rice genome sequence. Nucleic Acids Res. 30: 98-102.
37. Salamov, A.A. and Solovyev, V.V. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516-522.
38. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
39. Sorek, R., Shamir, R., and Ast, G. 2004. How prevalent is functional alternative splicing in the human genome? Trends Genet. 20: 68-71.
40. 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., et al. 2003. Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13: 1818-1827.
41. Stanke, M., Schoffmann, O., Morgenstern, B., and Waack, S. 2006. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7: 62.
42. Sunkar, R. and Zhu, J.K. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019.
43. Sunkar, R., Girke, T., Jain, P.K., and Zhu, J.K. 2005. Cloning and characterization of microRNAs from rice. Plant Cell 17: 1397-1411.
44. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
45. Ureta-Vidal, A., Ettwiller, L., and Birney, E. 2003. Comparative genomics: Genome-wide analysis in metazoan eukaryotes. Nat. Rev. Genet. 4: 251-262.
46. Usuka, J., Zhu, W., and Brendel, V. 2000. Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 16: 203-211.
47. Wang, B.B. and Brendel, V. 2006. Genomewide comparative analysis of alternative splicing in plants. Proc. Natl. Acad. Sci. 103: 7175-7180.
48. Wang, X., Shi, X., Hao, B., Ge, S., and Luo, J. 2005a. Duplication and DNA segmental loss in the rice genome: Implications for diploidization. New Phytol. 165: 937-946.
49. Wang, X., Zhang, J., Li, F., Gu, J., He, T., Zhang, X., and Li, Y. 2005b. MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610-3614.
50. Ware, D. and Stein, L. 2003. Comparison of genes among cereals. Curr. Opin. Plant Biol. 6: 121-127.
51. Whitelaw, C.A., Barbazuk, W.B., Pertea, G., Chan, A.P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J.L., et al. 2003. Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120.
52. Xie, K., Zhang, J., Xiang, Y., Feng, Q., Han, B., Chu, Z., Wang, S., Zhang, Q., and Xiong, L. 2005. Isolation and annotation of 10828 putative full length cDNAs from indica rice. Sci. China C Life Sci. 48: 445-451.
53. Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92.
54. Yu, J., Wang, J., Lin, W., Li, S., Li, H., Zhou, J., Ni, P., Dong, W., Hu, S., Zeng, C., et al. 2005. The Genomes of Oryza sativa: A history of duplications. PLoS Biol. 3: e38.
55. Yuan, Y., SanMiguel, P.J., and Bennetzen, J.L. 2003. High-Cot sequence analysis of the maize genome. Plant J. 34: 249-255.
56. Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., et al. 2005. The Institute for Genomic Research Osa1 rice genome annotation database. Plant Physiol. 138: 18-26.
57. Zhang, B., Pan, X., Cannon, C.H., Cobb, G.P., and Anderson, T.A. 2006. Conservation and divergence of plant microRNA genes. Plant J. 46: 243-259.
58. Zhao, W., Wang, J., He, X., Huang, X., Jiao, Y., Dai, M., Wei, S., Fu, J., Chen, Y., Ren, X., et al. 2004. BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res. 32: D377-D382.