The evolutionary history of Ehrhartoideae, Oryzeae, and Oryza

Rice

Volumn 2, Issue 1, 2009, Pages 1-14

  Kellogg, Elizabeth A ^a  

^a UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

Ehrharta; Evolution; Genome; Grasses; Oryza; Phylogeny; Rice

Indexed keywords

EHRHARTA; EHRHARTEAE; EHRHARTOIDEAE; ORYZA; ORYZEAE; POACEAE;

EID: 70649107255     PISSN: 19398425     EISSN: 19398433     Source Type: Journal    
DOI: 10.1007/s12284-009-9022-2     Document Type: Review

References (86)

1. Ambrose BA, Lerner DR, Ciceri P, Padilla CM, Yanofsky MF, Schmidt RJ. Molecular and genetic analyses of the Silky1 gene reveal conservation in floral organ specification between eudicots and monocots. Mol Cell 2000;5:569-79.
2. Ammiraju JSS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, et al. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 2007;52:342-51.
3. Arber A. The Gramineae: A study of cereal, bamboo, and grass. Cambridge: The University Press; 1934.
4. Bao Y, Ge S. Origin and phylogeny of Oryza species with the CD genome based on multiple-gene sequence data. Plant Syst Evol 2004;249:55-66.
5. Bommert P, Satoh-Nagasawa N, Jackson D, Hirano HY. Genetics and evolution of inflorescence and flower development in grasses. Plant Cell Physiol 2005;46:69-78.
6. Bouchenak-Khelladi Y, Salamin N, Savolainen V, Forest F, van der Bank M, Chase MW, et al. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic taxon sampling. Mol Phylog Evol 2008;47:488-505.
7. Brown R. Prodromus Flora Novae Hollandiae et insulae van Diemen. London: Richard Taylor; 1810.
8. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fiedel-Alon A, York TL, et al. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet 2007;3:1745-56.
9. Campbell CS, Kellogg EA. Sister group relationships of the Poaceae. In: Soderstrom TR, Hilu KW, Campbell CS, Barkworth ME, editors. Grass systematics and evolution. Washington, DC: Smithsonian Institution; 1987. p. 217-24.
10. Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, et al. Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major compnent in rice fragrance. Plant Cell 2008;20:1850-61.
11. Chung M-C, Lee Y-I, Cheng Y-Y, Chou Y-J, Lu C-F. Chromosomal polymorphism of ribosomal genes in the genus Oryza. Theor Appl Genet 2008;116:745-53.
12. Clark LG, Zhang W, Wendel JF. A phylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst Bot 1995;20:436-60.
13. Clayton WD, Renvoize SA. Genera graminum. London: Her Majesty's Stationery Office; 1986.
14. Duistermaat H. A revision of Oryza (Gramineae) in Malesia and Australia. Blumea 1987;32:157-93.
15. Gao L, Innan H. Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. Genetics 2008;179:965-76.
16. Gaut BS. Evolutionary dynamics of grass genomes. New Phytol 2002;154:15-28.
17. Ge S, Sang T, Lu B-R, Hong D-Y. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci U S A 1999;96:14400-5.
18. Ge S, Li A, Lu B-R, Zhang S-Z, Hong D-Y. A phylogeny of the rice tribe Oryzeae (Poaceae) based on matK sequence data. Amer J Bot 2002;89:1967-72.
19. Grass Phylogeny Working Group. Phylogeny and subfamlial classification of the Poaceae. Ann Missouri Bot Gard 2001;88:373-457.
20. Guo Y-L, Ge S. Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genome. Amer J Bot 2005;92:1548-58.
21. Hegarty MJ, Hiscock SJ. Genomic clues to the evolutionary success of polyploid plants. Curr Biol 2008;18:R435-44.
22. Hu FY, Tao DY, Sacks E, Fu BY, Xu P, Li J, et al. Convergent evolution of perenniality in rice and sorghum. Proc Natl Acad Sci U S A 2003;100:4050-4.
23. International Code of Botanical Nomenclature (Vienna Code). 2006;146:A. R. G. Gantner KG.
24. Janssen T, Bremer K. The age of major monocot groups inferred from 800+ rbcL sequences. Bot J Linn Soc 2004;146:385-98.
25. Jiang H, Liu D, Gu Z, Wang W. Rapid evolution in a pair of recent duplicate segments of rice. J Exp Zool (Mol Dev Evol) 2007;308B:50-7.
26. Kellogg EA. The grasses: a case study in macroevolution. Ann Rev Ecol Syst 2000;31:217-38.
27. Kellogg EA, Linder HP. Phylogeny of Poales. In: Rudall PJ, Cribb PJ, Cutler DF, Humphries CJ, editors. Monocotyledons: systematics and evolution. Kew: Royal Botanic Gardens; 1995. p. 511-42.
28. Kellogg EA, Watson L. Phylogenetic studies of a large data set. I. Bambusoideae, Andropogonodae, and Pooideae. Bot Rev 1993;59:273-343.
29. Kennard WC, Phillips RL, Porter RA, Grombacher AW. A comparative map of wild rice (Zizania palustris L. 2n=2x=30). Theor Appl Genet 2000;101:677-84.
30. Kim H, Hurwitz B, Yu Y, Collura K, Gill N, SanMiguel P, et al. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol 2008;9:R45.
31. Komatsu M, Chujo A, Nagato Y, Shimamoto K, Kyozuka J. FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. Development 2003;130:3841-50.
32. Kunth KS. Révision des Graminées 1:6. Paris: Librairie-Gide; 1829.
33. Lee H-R, Zhang W, Langdon T, Jin W, Yan H, Cheng Z, et al. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A 2005;102:11793-8.
34. LeRoux LG, Kellogg EA. Floral development and the formation of unisexual spikelets in the Andropogoneae (Poaceae). Amer J Bot 1999;86:354-66.
35. Les DH, Crawford DJ, Kimball RT, Moody ML, Landolt E. Biogeography of discontinuously distributed hydrophytes: a molecular appraisal of intercontinental disjunctions. Int J Plant Sci 2003;164:917-32.
36. Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, et al. Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 2008;9:58.
37. Li C-B, Zhang D-M, Ge S, Lu B-R, Hong D-Y. Differentiation and intergenomic relationships among C, E, and D genomes in the Oryza officinalis complex (Poaceae) as revealed by multicolor genomic in situ hybridization. Theor Appl Genet 2001;103:197-203.
38. Lin H, Ouyang S, Egan A, Nobuta K, Haas B, Zhu W, Gu X, Silva JC, Meyers BC, Buell CR. Characterization of paralogous protein families in rice. BMC Plant Biol 2008;8:18.
39. Litke R. Uber den Nachweis tertiarer Gramineen. Monats Deutschen Akad Wissenschaft Berlin 1968;10:462-71.
40. Lu B-R, Ge S. Oryza coarctata: the name that best reflects the relationships of Porteresia coarctata (Poaceae: Oryzeae). Nordic J Bot 2004;23:555-8.
41. Ma J, Wing RA, Bennetzen JL, Jackson SA. Evolutionary history and positional shift of a rice centromere. Genetics 2007;177:1217-20.
42. Maddison DR, Maddison WP. MacClade 4: Analysis of phylogeny and character evolution. Release version 4.08. Massachusetts: Sinauer Associates, Sunderland; 2005.
43. Maddison W, Maddison D (1997-2008)Mesquite version 2.5 (build 77). http://mesquiteproject.org
44. Malcomber ST, Kellogg EA. Evolution of unisexual flowers in grasses (Poaceae) and the putative sex-determination gene, TASSELSEED2 (TS2). New Phytol 2006;170:885-99.
45. Malcomber ST, Preston JC, Reinheimer R, Kossuth J, Kellogg EA. Developmental gene evolution and the origin of grass inflorescence diversity. Adv Bot Res 2006;44:425-81.
46. Marchant AD, Briggs BG. Ecdeiocoleaceae and Joinvilleaceae, sisters of Poaceae (Poales): evidence from rbcL and matK data. Telopea 2007;11:437-50.
47. Martínez-y-Pérez JL, Mejía-Saulés T, Sosa V. Phylogenetic relationships of Luziola (Poaceae: Oryzeae) and related genera from aquatic habitats. Can J Bot 2005;84:1753-70.
48. Martínez-y-Pérez JL, Mejía-Saulés T, Sosa V. A taxonomic revision of Luziola (Poaceae: Oryzeae). Syst Bot 2008;33:702-18.
49. Mason-Gamer RJ. Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Syst Biol 2004;53:25-37.
50. Murray BG, DeLange PJ, Ferguson AR. Nuclear DNA variation, chromosome numbers and polyploidy in the endemic and indigenous grass flora of New Zealand. Ann Bot 2005;96:1293-305.
51. Nagaki K, Cheng ZK, Ouyang S, Talbert PB, Kim M, Jones KM, et al. Sequencing of a rice centromere uncovers active genes. Nature Genet 2004;36:138-45.
52. Ohtsubo H, Kumekawa N, Ohtsubo E. RIRE2, a novel gypsy-type retrotransposon form rice. Genes Genet Syst 1999;74:83-91.
53. Paterson AH, Bowers JE, Chapman BA. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 2004;101: 9903-8.
54. Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, et al. Doubling genome size without polyploidization: Dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 2006;16: 1262-9.
55. Prasad K, Sriram P, Kumar CS, Kushalappa K, Vijayraghavan U. Ectopic expression of rice OsMADS1 reveals a role in specifying the lemma and palea, grass floral organs analogous to sepals. Devel Genet Evol 2001;211:281-90.
56. Preston JC, Kellogg EA. Conservation and divergence of APETALA1/ FRUITFULL-like gene function in grasses: evidence from gene expression analyses. Plant J 2007;52:69-81.
57. Reeder JR. The embryo in grass systematics. Amer J Bot 1957;44:756-68.
58. Rice Chromosomes 11 and 12 Sequencing Consortia. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol 2005;3:20.
59. Roxburgh W. Flora indica; or, descriptions of Indian Plants. London: Serampore, Calcutta; 1832.
60. Rudall PJ, Stuppy W, Cunniff J, Kellogg EA, Briggs BG. Evolution of reproductive structures in grasses inferred by sister-group comparisons with their putative closest living relatives. Amer J Bot 2005;92:1432-43.
61. Sánchez-Ken JG, Clark LG, Kellogg EA, Kay EE. Reinstatement and emendation of subfamily Micrairoideae. Syst Bot 2007;32:71-80.
62. Schweickerdt HG. Graminearum species nova et genus novum. Zur Kenntnis einiger südafrikanischer gramineen. Züchter 1961;31: 193-5.
63. Stapf O, (ed). Gramineae. Flora of tropical Africa. London: Lowell Reeve & Co.; 1917.
64. Stebbins GL. Coevolution of grasses and herbivores. Ann Missouri Bot Gard 1981;68:75-86.
65. Stevens PF. Angiosperm phylogeny website. Version 9, June 2008 [and more or less continuously updated since]. 2001 onwards. http://www.mobot.org/MOBOT/research/APweb/.
66. Tateoka T. Notes on some grasses. XIII. Relationship between Oryzeae and Ehrharteae, with special reference to leaf anatomy and histology. Bot Gaz 1963;124:264-70.
67. Tateoka T. Notes on some grasses. XVI. Embryo structure of the genus Oryza in relation to the systematics. Amer J Bot 1964;51:539-43.
68. Tateoka T. Porteresia, a new genus of Graminae. Bull Nat Sci Mus, Tokyo 1965;8:405-6.
69. Terrell EE, Robinson H. Luziolinae, a new subtribe of oryzoid grasses. Bull Torr Bot Club 1974;101:235-45.
70. Terrell EE, Peterson PM, Wergin WP. Epidermal features and spikelet micromorphology in Oryza and related genera (Poaceae: Oryzeae). Smithsonian Contr Bot 2001;91:1-50.
71. Thomas G, Sreejayan, Joseph L, Kuriachan P. Genetic variation and population structure in Oryza malampuzhaensis Krish. et Chand. endemic to Weatern Ghats, South India. J Genet 2001;80:141-8.
72. Thomasson JR. Fossil grasses: 1820-1986 and beyond. In: Soderstrom TR, Hilu KW, Campbell CS, Barkworth ME, editors. Grass systematics and evolution. Washington: Smithsonian Institution; 1987.
73. Vaughan DA, Lu B-R, Tomooka N. The evolving story of rice evolution. Plant Sci 2008a;174:394-408.
74. Vaughan DA, Lu B-R, Tomooka N. Was Asian rice (Oryza sativa) domesticated more than once? Rice 2008b;1:16-24.
75. Verboom GA, Linder HP, Stock WD. Phylogenetics of the grass genus Ehrharta: evidence for radiation in the summer-arid zone of the South African Cape. Evolution 2003;57:1008-21.
76. 4 photosynthesis. Global Change Biol 2008;14:2963-77.
77. Wang X, Shi X, Hao B, Ge S, Luo J. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 2005;165:937-46.
78. Watson L, Dallwitz MJ. Grass genera of the world. Wallingford: CAB International; 1992.
79. Whipple CJ, Ciceri P, Padilla CM, Ambrose BA, Bandong SL, Schmidt RJ. Conservation of B-class floral homeotic gene function between maize and Arabidopsis. Development 2004;131:6083-91.
80. Whipple CJ, Zanis M, Kellogg EA, Schmidt RJ. Conservation of B class MADS-box gene expression in the second whorl of a basal grass and outgroups links the origin of lodicules and petals. Proc Natl Acad Sci U S A 2007;104:1081-6.
81. Willemse LPM. A discussion of the Ehrharteae (Gramineae) with special reference to the Malesian taxa formerly included in Microlaena. Blumea 1982;28:181-94.
82. Wu J, Kurata N, Tanoue H, Shimokawa T, Umehara Y, Yano M, et al. Physical mapping of duplicated genomic regions of two chromosome ends in rice. Genetics 1998;150:1595-603.
83. Zachos J, Pagani M, Sloan L, Thomas E, Billups K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 2001;292:686-93.
84. Zaitchik BF, leRoux LG, Kellogg EA. Development of male flowers in Zizania aquatica (North American wild-rice; Gramineae). Int J Plant Sci 2000;161:345-51.
85. Zou X-H, Zhang F-M, Zhang J-G, Zang L-L, Tang L, Wang J, et al. Analysis of 142 genes resolves the rapid diversification of the rice genus. Genome Biol 2008;9:R49.
86. Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, et al. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol 2007;7:152.