Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. The Rice Chromosome 3 Sequencing Consortium

Genome Research

Volumn 15, Issue 9, 2005, Pages 1284-1291

  Buell, C Robin ^a   McCombie, W Richard ^d   Wing, Rod A ^b,c   Yuan, Qiaoping ^a   Ouyang, Shu ^a   Liu, Jia ^a   Zhu, Wei ^a   Wang, Aihui ^a   Maiti, Rama ^a   Haas, Brian ^a   Wortman, Jennifer ^a   Pertea, Mihaela ^a   Jones, Kristine M ^a   Kim, Mary ^a   Overton, Larry ^a   Tsitrin, Tamara ^a   Fadrosh, Douglas ^a   Bera, Jayati ^a   Weaver, Jayati ^a   Jin, Shaohua ^a   Johri, Shivani ^a   Reardon, Matt ^a   Webb, Kristen ^a   Hill, Jessica ^a   Moffat, Kelly ^a   Tallon, Luke ^a   Van Aken, Susan ^a   Lewis, Matthew ^a   Utterback, Teresa ^a   Feldblyum, Tamara ^a   Zismann, Victoria ^a   Iobst, Stacey ^a   Hsiao, Joseph ^a   De Vazeille, Aymeric R ^a   Salzberg, Steven L ^a   White, Owen ^a   Fraser, Claire ^a   Yu, Yeisoo ^b,c   Kim, HeyRan ^b,c   Rambo, Teri ^b,c   Currie, Jennifer ^b,c   Collura, Kristi ^b,c   Kernodle Thompson, Shelly ^b,c   Wei, Fusheng ^b   Kudrna, David ^b   Ammiraju, Jetty Siva S ^b   Luo, Meizhong ^b,c   Goicoechea, Jos Luis ^b,c   Henry, David ^c   Oates, Ryan ^c   Palmer, Michael ^c   Pries, Gina ^c   Saski, Christopher ^c   Simmons, Jessica ^c   Soderlund, Carol ^b,c,c   Nelson, William ^b   De La Bastide, Melissa ^d   Spiegel, Lori ^d   Nascimento, Lidia ^d   Huang, Emily ^d   Preston, Raymond ^d   Zutavern, Theresa ^d   Palmer, Lance ^d   O'haughnessy, Andrew ^d   Dike, Sujit ^d   Minx, Pat ^e   Cordum, Holly ^e   Wilson, Richard ^e   Jin, Weiwei ^f   Lee, Hye Ran ^f   Jiang, Jiming ^f   Jackson, Scott ^g   more..

^a J CRAIG VENTER INSTITUTE   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c CLEMSON UNIVERSITY   (United States)

^d Simons Center for Quantitative Biology   (United States)

^e WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f UNIVERSITY OF WISCONSIN MADISON   (United States)

^g PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CEREAL; CHROMOSOME 3; CONTROLLED STUDY; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; GRASS; MEDICAL RESEARCH; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; RICE; SEQUENCE HOMOLOGY;

ARABIDOPSIS THALIANA; JAPONICA; ORYZA NIVARA; ORYZA SATIVA; TRITICUM AESTIVUM; ZEA MAYS;

EID: 24344490228     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.3869505     Document Type: Article

References (53)

1. Ahn, S., Anderson, J.A., Sorrells, M.E., and Tanksley, S.D. 1993. Homoeologous relationships of rice, wheat and maize chromosomes. Mol. Gen. Genet. 241: 483-490.
2. Altschul, S.F., Gish, W., Miller, W., Meyers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Baba, T., Katagiri, S., Tanoue, H., Tanaka, R., Chiden, Y., Saji, S., Hamada, M., Nakashima, M., Okamoto, M., Hayashi, M., et al. 2000. Construction and characterization of rice genomic libraries: PAC library of japonica variety, Nipponbare and BAC library of indica variety, Kasalath. Bull. NIAR 14: 41-49.
4. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
5. Chen, M., Presting, G., Barbazuk, W.B., Goicoechea, J.L., Blackmon, B., Fang, G., Kim, H., Frisch, D., Yu, Y., Sun, S., et al. 2002. An integrated physical and genetic map of the rice genome. Plant Cell 14: 537-545.
6. Cheng, Z., Buell, C.R., Wing, R.A., Gu, M., and Jiang, J. 2001. Toward a cytological characterization of the rice genome. Genome Res. 11: 2133-2141.
7. Cheng, Z., Dong, F., Langdon, T., Ouyang, S., Buell, C.R., Gu, M., Blattner, F.R., and Jiang, J. 2002. Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14: 1691-1704.
8. Coe, E., Cone, K., McMullen, M., Chen, S.S., Davis, G., Gardiner, J., Liscum, E., Polacco, M., Paterson, A., Sanchez-Villeda, H., et al. 2002. Access to the maize genome: An integrated physical and genetic map. Plant Physiol. 128: 9-12.
9. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium. 2000. The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100: 377-386.
10. Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., et al. 2002. Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
11. Feuillet, C. and Keller, B. 1999. High gene density is conserved at syntenic loci of small and large grass genomes. Proc. Natl. Acad. Sci. 96: 8265-8270.
12. Gale, M.D. and Devos, K.M. 1998. Comparative genetics in the grasses. Proc. Natl. Acad. Sci. 95: 1971-1974.
13. 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.
14. Greco, R., Ouwerkerk, P.B., Taal, A.J., Favalli, C., Beguiristain, T., Puigdomenech, P., Colombo, L., Hoge, J.H., and Pereira, A. 2001. Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis. Plant Mol. Biol. 46: 215-227.
15. 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.
16. Harushima, Y., Yano, M., Shomura, A., Sato, M., Shimano, T., Kuboki, Y., Yamamoto, T., Lin, S.Y., Antonio, B.A., Parco, A., et al. 1998. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479-494.
17. Kantety, R.V., La Rota, M., Matthews, D.E., and Sorrells, M.E. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510.
18. Kim, C.M., Piao, H.L., Park, S.J., Chon, N.S., Je, B.I., Sun, B., Park, S.H., Park, J.Y., Lee, E.J., Kim, M.J., et al. 2004. Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice. Plant J. 39: 252-263.
19. Lippman, Z., Gendrel, A.V., Black, M., Vaughn, M.W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D., et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
20. Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
21. Luo, M.C., Thomas, C., You, F.M., Hsiao, J., Ouyang, S., Buell, C.R., Malandro, M., McGuire, P.E., Anderson, O.D., and Dvorak, J. 2003. High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389.
22. Ma, J. and Bennetzen, J.L. 2004. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl. Acad. Sci. 101: 12404-12410.
23. Ma, J., Devos, K.M., and Bennetzen, J.L. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14: 860-869.
24. Miyao, A., Tanaka, K., Murata, K., Sawaki, H., Takeda, S., Abe, K., Shinozuka, Y., Onosato, K., and Hirochika, H. 2003. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15: 1771-1780.
25. Moore, G., Devos, K.M., Wang, Z., and Gale, M.D. 1995. Cereal genome evolution: Grasses, line up and form a circle. Curr. Biol. 5: 737-739.
26. Morgante, M., Hanafey, M., and Powell, W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194-200.
27. 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.
28. 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., et al. 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.
29. Quackenbush, J., Cho, J., Lee, D., Liang, F., Holt, I., Karamycheva, S., Parvizi, B., Pertea, G., Sultana, R., and White, J. 2001. The TIGR Gene Indices: Analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29: 159-164.
30. The Rice Chromosome 10 Sequencing Consortium. 2003. In-depth view of structure, activity, and evolution of rice Chromosome 10. Science 300: 1566-1569.
31. Salamov, A.A. and Solovyev, V.V. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10: 516-522.
32. Sallaud, C., Gay, C., Larmande, P., Bes, M., Piffanelli, P., Piegu, B., Droc, G., Regad, F., Bourgeois, E., Meynard, D., et al. 2004. High throughput T-DNA insertion mutagenesis in rice: A first step towards in silico reverse genetics. Plant J. 39: 450-464.
33. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., et al. 2002. The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.
34. Soderlund, C., Humphray, S., Dunham, A., and French, L. 2002 Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 10: 1772-1787.
35. Sorrells, M.E., La Rota, M., Bermudez-Kandianis, C.E., Greene, R.A., Kantety, R., Munkvold, J.D., Miftahudin, M.A., Ma, X., Gustafson, P.J., Qi, L.L., et al. 2003. Comparative DNA sequence analysis of wheat and rice genomes. Genome Res. 13: 1818-1827.
36. Werner, J.E., Endo, T.R., and Gill, B.S. 1992. Toward a cytogenetically based physical map of the wheat genome. Proc. Natl. Acad. Sci. 89: 11307-11311.
37. 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.
38. Wing, R.A., Ammiraju, J.S.S., Luo, M., Kim, H.R., Yu, Y., Kudrna, D., Goicoechea, J.L., Wang, W., Nelson, W., Rao, K., et al. 2005. The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species. Plant Mol. Biol. (in press).
39. Wortman, J.R., Haas, B.J., Hannick, L.I., Smith Jr., R.K., Maiti, R., Ronning, C.M., Chan, A.P., Yu, C., Ayele, M., Whitelaw, C.A., et al. 2003. Annotation of the Arabidopsis genome. Plant Physiol. 132: 461-468.
40. Wu, J., Maehara, T., Shimokawa, T., Yamamoto, S., Harada, C., Takazaki, Y., Ono, N., Mukai, Y., Koike, K., Yazaki, J., et al. 2002. A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525-535.
41. 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.
42. Yuan, Q., Hill, J., Hsiao, J., Moffat, K., Ouyang, S., Cheng, Z., Jiang, J., and Buell, C.R. 2002. Genome sequencing of a 239 kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast insertion. Mol. Genet. Genomics 267: 713-720.
43. ftp://ftp.tigr.org/pub/data/rice/rice.chr03.v2.1/; annotation data for chromosome 3.
44. http://www.agcol.arizona.edu; Arizona Computational Genomics Lab.
45. http://www.agcol.arizona.edu/symap; SyMAP.
46. http://www.cbs.dtu.dk/services/SignalP-2.0/; SignalP Server.
47. http://www.cbs.dtu.dk/services/TMHMM/; TMHMM Server v 2.0.
48. http://www.genome.arizona.edu; AGI/AGCoL.
49. http://www.omap.org; Oryza Map Alignment Project.
50. http://www.repeatmasker.org;: RepeatMasker.
51. http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp; Oryzabase Database.
52. http://www.tigr.org/tdb/e2k1/ath1; TIGR Arabidopsis.
53. http://www.tigr.org/tigr-scripts/tgi/T_index.cgi?species=rice; TIGR Rice Gene Index.