Deciding among green plants for whole genome studies

Trends in Plant Science

Volumn 7, Issue 12, 2002, Pages 550-554

  Pryer, Kathleen M ^a   Schneider, Harald ^b   Zimmer, Elizabeth A ^c   Banks, Jo Ann ^d  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c DEPARTMENT OF PALEOBIOLOGY   (United States)

^d PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; BRYOPHYTA; BRYOPHYTES; CHLOROPHYTA; GYMNOSPERMAE; MAGNOLIOPHYTA; TRACHEOPHYTA; VIRIDIPLANTAE;

CHLOROPLAST DNA; MITOCHONDRIAL DNA; RIBOSOME DNA;

ANGIOSPERM; ARTICLE; BRYOPSIDA; FERN; GENETICS; GENOME; GENOMICS; GREEN ALGA; GYMNOSPERM; PHYLOGENY;

ALGAE, GREEN; ANGIOSPERMS; BRYOPSIDA; DNA, CHLOROPLAST; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; FERNS; GENOME, PLANT; GENOMICS; GYMNOSPERMS; PHYLOGENY;

EID: 0036885758     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1360-1385(02)02375-0     Document Type: Review

References (52)

1. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815
2. Yu, J. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79-92
3. Goff, S.A. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100
4. Karol, K.G. et al. (2001) The closest living relatives of land plants. Science 294, 2351-2353
5. Pryer, K.M. et al. (2001) Horsetails and ferns are a monophyletic group and the closest relatives to seed plants. Nature 409, 618-622
6. Nickrent, D.L. et al. (2000) Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol. Biol. Evol. 17, 1885-1895
7. Barkman, T.J. et al. (2000) Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny. Proc. Natl. Acad. Sci. U. S. A. 97, 13166-13171
8. Soltis, P.S. et al. (1999) Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402, 402-404
9. Mathews, S. and Donoghue, M.J. (1999) The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286, 947-950
10. Qiu, Y-L. et al. (1999) The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes. Nature 402, 404-407
11. Brown, K.S. (1999) Deep Green rewrites evolutionary history of plants. Science 285, 990-991
12. Walbot, V. (2000) A green chapter in the book of life. Nature 408, 794-795
13. Bevan, M. (2002) The first harvest of crop genes. Nature 416, 590-591
14. Mandoli, D.F. and Olmstead, R. (2000) The importance of emerging model systems in plant biology. J. Plant Growth Regul. 19, 249-252
15. Adam, D. (2000) Now for the hard ones. Nature 408, 792-793
16. Copeland, N.F. et al. (2002) Mmu 16-comparative genomic highlights. Science 296, 1617-1618
17. O'Brien, S.J. et al. (2001) On choosing mammalian genomes for sequencing. Science 292, 2264-2266
18. Pennisi, E. (2001) Insects rank low among genome priorities. Science 294, 1261-1262
19. Fishman, M.C. (2001) Zebrafish - the canonical vertebrate. Science 294, 1290-1291
20. Daly, D.C. et al. (2001) Plant systematics in the age of genomics. Plant Physiol. 127, 1328-1333
21. Rossberg, M. et al. (2001) Comparative sequence analysis reveals extensive microcolinearity in the Lateral Suppressor regions of the tomato, Arabidopsis, and Capsella genomes. Plant Cell 13, 979-988
22. Ku, H-M. et al. (2000) Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc. Natl. Acad. Sci. U. S. A. 97, 9121-9126
23. Grant, D. et al. (2000) Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 97, 4168-4173
24. Schmidt, R. (2002) Plant genome evolution: lessons from comparative genomics at the DNA level. Plant Mol. Biol. 48, 21-37
25. Bennett, M.D. and Smith, J.B. (1991) Nuclear DNA amounts in angiosperms. Philos. Trans. R. Soc. London Ser. B 334, 309-345
26. Bennett, M.D. and Leitch, I.J. (2001) Nuclear DNA amounts in pteridophytes. Ann. Bot. 87, 335-345
27. Obermayer, R. et al. (2002) Nuclear DNA C-values in 30 species double the familial representation in pteridophytes. Ann. Bot. 90, 209-217
28. Brenner, S. et al. (1993) Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366, 265-268
29. Aparacio, S. et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310
30. Hedges, S.B. and Kumar, S. (2002) Vertebrate genomes compared. Science 297, 1283-1285
31. Lewis, R. (2002) Pufferfish genomes probe human genes. The Scientist 16, 22-23
32. Deloukas, P. et al. (2001) The DNA sequence and comparative analysis of human chromosome 20. Nature 414, 865-871
33. Chatterjee, A. and Roux, S.J. (2000) Ceratopteris richardii: a productive model for revealing secrets of signaling and development. J. Plant Growth Regul. 19, 284-289
34. Schaefer, D.G. (2002) A new moss genetics: targeted mutagenesis in Physcomitrella patens. Annu. Rev. Plant Biol. 53, 477-501
35. Gray, M.W. et al. (1999) Mitochondrial evolution. Science 283, 1476-1481
36. Lang, B.F. et al. (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33, 351-397
37. Stewart, C-B. (1995) Active ancestral molecules. Nature 374, 12-13
38. Jermann, T.M. et al. (1995) Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57-59
39. Simpson, C.L. and Stern, D.B. (2002) The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications. Plant Physiol. 129, 957-966
40. Martin, W. et al. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. U. S. A. 99, 12246-12251
41. Palenik, B. (2002) The genomics of symbiosis: hosts keep the baby and the bath water. Proc. Natl. Acad. Sci. U. S. A. 99, 11996-11997
42. Petrov, D.A. (2001) Evolution of genome size: new approaches to an old problem. Trends Genet. 17, 23-28
43. Pennisi, E. (2001) Genome duplications: the stuff of evolution? Science 294, 2458-2460
44. Cronk, Q.C.B. (2001) Plant evolution and development in a post-genomic context. Nat. Rev. Genet. 2, 607-620
45. Vision, T.J. et al. (2000) The origins of genomic duplication in Arabidopsis. Science 290, 2114-2117
46. Doolittle, R.F. (2002) Microbial genomes multiply. Nature 416, 697-700
47. Bennetzen, J. (2002) Opening the door to comparative plant biology. Science 296, 60-63
48. Hall, A.E. et al. (2002) Beyond the Arabidopsis genome: opportunities for comparative genomics. Plant Physiol. 129, 1439-1447
49. Couzin, J. (2002) NSF's ark draws alligators, algae, and wasps. Science 297, 1638-1639
50. Pennisi, E. (2002) Comparative biology joins the molecular age. Science 296, 1792-1795
51. Macilwain, C. (2001) Fears for basic science as Bush backs use of investment criteria. Nature 413, 5
52. Turmel, M. et al. (2002) The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants. Mol. Biol. Evol. 19, 24-38