Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Nature

Volumn 402, Issue 6763, 1999, Pages 761-765

  Lin, Xiaoying ^a   Kaul, Samir ^a   Rounsley, Steve ^a,b   Shea, Terrance P ^a,b   Benito, Maria Ines ^a   Town, Christopher D ^a   Fujii, Claire Y ^a   Mason, Tanya ^a   Bowman, Cheryl L ^a   Barnstead, Mary ^a   Feldblyum, Tamara V ^a   Buell, C Robin ^a   Ketchum, Karen A ^a   Lee, John ^a   Ronning, Catherine M ^a   Koo, Hean L ^a   Moffat, Kelly S ^a   Cronin, Lisa A ^a   Shen, Mian ^a   Pal, Grace ^a   Van Aken, Susan ^a   Umayam, Lowell ^a   Tallon, Luke J ^a   Gill, John E ^a   Adams, Mark D ^a,c   Carrera, Ana J ^a   Creasy, Todd H ^a   Goodman, Howard M ^a,d   Somerville, Chris R ^a,e   Copenhaver, Greg P ^a,f   Preuss, Daphne ^a,f   Nierman, William C ^a   White, Owen ^a   Elsen, Jonathan A ^a   Salzberg, Steven L ^a   Fraser, Claire M ^a   Venter, J Craig ^a,c   more..

^a J CRAIG VENTER INSTITUTE   (United States)

^b Cereon Genomics   (United States)

^c CELERA GENOMICS   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e GEOPHYSICAL LABORATORY   (United States)

^f UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CHROMOSOME 2; CHROMOSOME 4; CHROMOSOME ANALYSIS; DNA SEQUENCE; GENE DUPLICATION; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ARABIDOPSIS; CELL NUCLEUS; CENTROMERE; CHROMOSOME MAPPING; DNA, PLANT; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EMBRYOPHYTA;

EID: 0033576611     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/45471     Document Type: Article

References (50)

1. Schmidt, R. & Dean, C. Towards construction of an overlapping YAC library of the Arabidopsis thaliana genome. Bioessays 15, 63-69 (1993).
2. Bevan, M. et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485-488 (1998).
3. Bevan, M. et al. Objective: the complete sequence of a plant genome. Plant Cell 9, 476-478 (1997).
4. Copenhaver, G. P. & Pikaard, C. S. Two-dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution. Plant J. 9, 273-282 (1996).
5. Copenhaver, G. P. & Picaard, C. S. RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. Plant J. 9, 259-272 (1996).
6. Schweizer, D., Loidl, J. & Hamilton, B. Heterochromatin and the phenomenon of chromosome banding. Results Probl. Cell Differ. 14, 235-254 (1987).
7. Martinez-Zapater, J. M., Estelle, M. A. & Somerville, C. R. A highly repeated DNA sequence in Arabidopsis thaliana. Mol. Gen. Genet. 204, 417-423 (1986).
8. Maluszynska, J. & Heslop-Harrison, J. S. Localization of tandemly repealed DNA sequences in Arabidopsis thaliana. Plant J. 1, 159-166 (1991).
9. Simoens, C. R., Gielen, J., Van Montagu, M. & Inze, D. Characterization of highly repetitive sequences of Arabidopsis thaliana. Nucleic Acids Res. 16, 6753-6766 (1988).
10. Pluta, A. F., Mackay, A. M., Ainsztein, A. M., Goldberg, I. G. & Earnshaw, W. C. The centromere: hub of chromosomal activities. Science 270, 1591-1594 (1995).
11. Round, E. K., Flowers, S. K. & Richards, E. J. Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res. 7, 1045-1053 (1997).
12. Zachgo, E. A. et al. A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res. 6, 19-25 (1996).
13. Marra, M. A. et al. High throughput fingerprint analysis of large-insert clones. Genome Res. 7, 1072-1084 (1997).
14. Copenhaver, G. P., Doelling, J. H., Gens, J. S. & Pikaard, C. S. Use of RFLPs larger than 100 kbp to map the position and internal organization of the nucleolus organizer region on chromosome 2 in Arabidopsis thaliana. Plant J. 7, 273-286 (1995).
15. Richards, E. J., Chao, S., Vongs, A. & Yang, J. Characterization of Arabidopsis thaliana telomeres isolated in yeast. Nucleic Acids Res. 20, 4039-4046 (1992).
16. Charrasse, S. et al. Characterization of the cDNA and pattern of expression of a new gene overexpressed in human hepatomas and colonic tumors. Eur. J. Biochem. 234, 406-413 (1995).
17. Sonnhammer, E. L., Eddy, S. R., Birney, E., Bateman, A. & Durbin, R. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 26, 320-322 (1998).
18. Leete, E. Recent developments in the biosynthesis of the tropane alkaloids. Planta Med. 56, 339-352 (1990).
19. Yamad, Y. et al. in Secondary Products from Plant Tissue Culture (eds Charlwood, B. V. & Rhodes, M. J. C.) 227-242 (Clarendon, Oxford, 1990).
20. Marrs, K. A. The functions and regulation of glutathione S-transferases in plants. Annu. Rev. Plant Physiol. 47, 127-158 (1996).
21. Terryn, N. et al. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. FEBS Lett. 445, 237-245 (1999).
22. Martin, W. & Hermann, R. G. Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol. 118, 9-17 (1998).
23. Blanchard, J. L. & Schmidt, G. W. Pervasive migration of organellar DNA to the nucleus in plants. J. Mol. Evol. 41, 397-406 (1995).
24. Unseld, M., Marienfeld, J. R., Brandt, P. & Brennicke, A. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet. 15, 57-61 (1997).
25. Klein, M. et al. Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones. Plant J. 6, 447-455 (1994).
26. Copenhaver, G. P. et al. Genetic definition and sequence analysis of Arabidopsis centromeres. Science (in the press).
27. Thompson, H. L., Schmidt, R. & Dean, C. Identification and distribution of seven classes of middle-repetitive DNA in the Arabidopsis thaliana genome. Nucleic Acids Res. 24, 3017-3022 (1996).
28. Thompson, H., Schmidt, R., Brandes, A., Heslop-Harrison, J. S. & Dean, C. A novel repetitive sequence associated with the centromeric regions of Arabidopsis thaliana chromosomes. Mol. Gen. Genet. 253, 247-252 (1996).
29. Thompson, H. L., Schmidt, R. & Dean, C. Analysis of the occurrence and nature of repeated DNA in an 850 kb region of Arabidopsis thaliana chromosome 4. Plant Mol. Biol. 32, 553-557 (1996).
30. Brandes, A., Thompson, H., Dean, C. & Heslop-Harrison, J. S. Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L. Chromosome Res. 5, 238-246 (1997).
31. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 (1998).
32. Gate, M. D. & Devos, K. M. Comparative genetics in the grasses. Proc. Natl Acad. Sci. USA 95, 1971-1974 (1997).
33. Wolfe, K. H. & Shields, D. C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713 (1997).
34. Hughes, A. L. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. B Biol. Sci. 256, 119-124 (1994).
35. The European Union Arabidopsis Genome Sequencing Consortium & The Cold Spring Harbor, Washington University in St Louis and PE Biosystems Arabidopsis Sequencing Consortium. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402, 769-777 (1999).
36. Choi, S., Creelman, R. A. Mullet, J. E. & Wing, R. A. Construction and characterization of bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol. Biol. Rep. 13, 124-128 (1995).
37. Mozo, T., Fischer, S., Meier-Ewert, S., Lehrach, H. & Altmann, T. Use of the IGF BAC library for physical mapping of the Arabidopsis thaliana genome. Plant J. 16, 377-384 (1998).
38. Liu, Y.-G., Mitsukawa, N., Vasquez-Tell, A. & Whittier, R. F. Generation of a high-quality P1 library of Arabidopsis suitable for chromosome walking. Plant J. 7, 351-358 (1995).
39. Sutton, G. G., White, O., Adams, M. D. & Kerlavage, A. R. TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome 1, 9-19 (1995).
40. Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94 (1997).
41. Uberbacher, E. C. & Mural, R. J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl Acad. Sci. USA 88, 11261-11265 (1991).
42. Hebsgaard, S. M. et al. Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information. Nucleic Acids Res. 24, 3439-3452 (1996).
43. Huang, X., Adams, M. D., Zhou, H. & Kerlavage, A. R. A tool for analyzing and annotating genomic sequences. Genomics 46, 37-45 (1997).
44. Lowe, T. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
45. Delcher, A. L. et al. Alignment of whole genomes. Nucleic Acids Res. 27, 2369-2376 (1999).
46. Claros, M. G. & von Heijne, G. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10, 685-686 (1994).
47. Nielsen, H., Brunak, S. & von Heijne, G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng. 12, 3-9 (1999).
48. Emanuelsson, O., Nielsen, H. & von Heijne, G. ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein. Sci. 8, 978-984 (1999).
49. Claros, M. G. & Vincens, P. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241, 779-786 (1996).
50. Nelson, K. E. et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329 (1999).