Phylogenetics of Miscanthus, Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers

Journal of Plant Research

Volumn 115, Issue 5, 2002, Pages 381-392

  Hodkinson, Trevor R ^a,b   Chase, Mark W ^a   Lledó, M Dolores ^a   Salamin, Nicolas ^b   Renvoize, Stephen A ^a  

^a ROYAL BOTANIC GARDENS   (United Kingdom)

^b TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

Erianthus; Miscanthus; Molecular; Saccharum; Sugarcane; Systematics

Indexed keywords

ANDROPOGONEAE; ERIANTHUS; ERIANTHUS ROCKII; MISCANTHIDIUM; MISCANTHUS; MISCANTHUS FUSCUS; NARENGA; NARENGA PORPHYROCOMA; POACEAE; RIPIDIUM; SACCHARUM; SACCHARUM CONTORTUM; SACCHARUM HYBRID CULTIVAR; SACCHARUM OFFICINARUM; SACCHARUM SPONTANEUM;

EID: 23044533391     PISSN: 09189440     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10265-002-0049-3     Document Type: Article

References (64)

1. Adati S, Shiotani I (1962) The cytotaxonomy of the genus Miscanthus and its phylogenetic status. Bull Fac Agric Mie Univ 25:1-14
2. Al-Janabi SM, McClelland M, Petersen C, Sobral BWS (1994) Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae. Theor Appl Genet 88:933-944
3. Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Cambell CS, Donoghue MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Ann Mo Bot Gard 82:247-277
4. Besse P, McIntyre CL, Berding N (1996) Ribosomal DNA variations in Erianthus, a wild sugarcane relative (Andropogoneae - Saccharinae). Theor Appl Genet 92:733-743
5. Briggs BG, Johnson LAS (2000) Hopkinsiaceae and Lyginiaceae, two new families of Poales in Western Australia with revisions of Hopkinsia and Lyginia. Telopea 8:477-502
6. Briggs BG, Marchant AD, Gilmore S, Porter CL (2000) A molecular phylogeny of Restionaceae and allies. In: Wilson KL, Morrison DA (eds) Monocots - systematics and evolution. Proc 2nd Int Conf Comparative Biol Monocots, Sydney 1998. CSIRO, Melbourne, pp 661-667
7. Buckler ES 4th, Holtsford TP (1996) Zea systematics: ribosomal ITS evidence. Mol Biol Evol 13:612-622
8. Bullard MJ, Heath MC, Nixon PM (1995) Shoot growth, radiation interception and dry matter production and partitioning during the establishment phase of Miscanthus sinensis "Giganteus" grown at two densities in the UK. Ann Appl Biol 126:94-102
9. Burner DM (1991) Cytogenetic analyses of sugarcane relatives (Andropogoneae: Saccharinae). Euphytica 54:125-133
10. Carolan JC, Hook ILI, Walsh JJ, Hodkinson TR (2002) Using AFLP markers for species differentiation and assessment of genetic variability of in vitro-cultured Papaver bracteatum (Section Oxytona). In Vitro Cell Dev Biol Plant 38:300-307
11. Celarier RP (1956) Cytotaxonomy of the Andropogoneae I. Subtribes Dimeriinae and Saccharinae. Cytologia 21:272-291
12. Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duvall MR, Price RA, Hills HG, Qiu YL, Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim KJ, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang QY, Plunkett GM, Soltis PS, Swensen SM, Williams SE, Gadek PA, Quinn CJ, Eguiarte LE, Golenberg E, Learn GH, Graham SW, Barrett SCH, Dayanandan S, Albert VA (1993) Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann Missouri Bot Gard 80:528-580
13. Chase MW, de Bruijn AY, Reeves G, Cox AV, Rudall PJ, Johnson MAT, Eguiarte LE (2000) Phylogenetics of Asphodelaceae (Asparagales): an analysis of plastid rbcL and trnL-F DNA sequences. Ann Bot (Lond) 86:935-956
14. Clayton WD, Renvoize SA (1986) Genera Graminum, grasses of the world. Kew Bull Additional Series XIII
15. Clifton-Brown JC, Lewandowski I (2000) Over wintering problems of newly established Miscanthus plantations can be overcome by identifying genotypes with improved rhizome cold tolerance. New Phytol 148:287-294
16. Cronn RC, Zhao XP, Paterson AH, Wendel JF (1996) Polymorphism and concerted evolution in a tamdemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J Mol Evol 42:685-705
17. Daniels J, Roach BT (1987) Taxonomy and evolution. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, New York, pp 7-84
18. Daniels J, Smith P, Paton N, Williams CA (1975) The origin of the genus Saccharum. Sugarcane Breed Newsl 36:24-39
19. D'Hont A, Rao PS, Feldman P, Grivet L, Islam-Faridi N, Taylor P, Glaszmann JC (1995) Identification and characterization of sugarcane intergeneric hybrids, Saccharum officinarum x Erianthus arundinaceus, with molecular markers and DNA in situ hybridization. Theor Appl Genet 91:320-326
20. D'Hont A, Grivet L, Feldman P, Rao S, Berding N, Glaszmann JC (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum sp.) by molecular cytogenetics. Mol Gen Genet 250:405-413
21. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull Bot Soc Am 19:11-15
22. Dufour P, Deu M, Grivet L, D'Hont A, Paulet F, Bouet A, Lanaud C, Glaszmann JC, Hamon P (1997) Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid. Theor Appl Genet 94:409-418
23. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
24. Gielly L, Taberlet P (1994) The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol Biol Evol 11:769-777
25. 4 photosynthesis. Am J Bot 88:1993-2012
26. Grass Phylogeny Working Group (2001) Phylogeny and subfamilial classification of the grasses (Poaceae). Ann Mo Bot Gard 88:373-457
27. Grassl CO (1972) Taxonomy of Saccharum relatives: Sclerostachya, Narenga, and Erianthus. Proceedings of 14th Congress, ISSCT, pp 240-248
28. Guimaraes CT, Sills GR, Sobral BWS (1997) Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. Proc Natl Acad Sci USA 94:14261-14266
29. Hodkinson TR, Renvoize SA (2001) Nomenclature of Miscanthus x giganteus. Kew Bull 56:757-758
30. Hodkinson TR, Renvoize SA, Chase MW (1997) Systematics of Miscanthus. Aspects Appl Biol (Biomass Energy Crops) 49:189-198
31. Hodkinson TR, Renvoize SA, Ní Chonghaile G, Stapleton C, Chase MW (2000) A comparison of ITS Nuclear rDNA sequence data and AFLP markers for phylogenetic studies in Phyllostachys (Bambusoideae, Poaceae). J Plant Res 113:259-269
32. Hodkinson TR, Chase MW, Takahashi C, Leitch IJ, Bennett MD, Renvoize SA (2002a) The use of DNA sequencing (ITS and trnL-F), AFLP and fluorescent in-situ hybridisation to study allopolyploid Miscanthus (Poaceae). Am J Bot 89:279-286
33. Hodkinson TR, Chase MW, Renvoize SA (2002b) Characterisation of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR. Ann Bot (Lond) 89:627-636
34. Honda M (1930) Monographia Poacearum Japonicarum, Bambusoideis exclusis. J Fac Sci, Imperial Univ Tokyo Section 3 Bot 3:1-484
35. Hopper SD, Fay MF, Rossetto M, Chase MW (1999) A molecular phylogenetic analysis of the bloodroot and kangaroo paw family, Haemodoraceae: taxonomic, biogeographic and conservation implications. Bot J Linn Soc 131:285-299
36. Hsiao C, Chatterton NJ, Asay KH, Jensen KB (1994) Phylogenetic relationships of 10 grass species: an assessment of phylogenetic utility of the internal transcribed spacer region in nuclear ribosomal DNA in monocots. Genome 37:112-120
37. Hsiao C, Chatterton NJ, Asay KH, Jensen KB (1995a) Molecular phylogeny of the Pooideae (Poaceae) based on nuclear rDNA (ITS) sequences. Theor Appl Genet 90:389-398
38. Hsiao C, Chatterton NJ, Asay KH, Jensen KB (1995b) Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences. Genome 38:211-223
39. Hsiao C, Jacobs SWL, Chatterton NJ, Asay KH (1999) A molecular phylogeny of the grass family (Poaceae) based on the sequences of nuclear ribosomal DNA (ITS). Aust Syst Bot 11:667-668
40. Irvine JE (1999) Saccharum species as horticultural classes. Theor Appl Genet 98:186-194
41. Janoo N, Grivet L, Seguin M, Paulet F, Domaingue R, Rao PS, Dookun A, D'Hont A, Glaszmann JC (1999a) Molecular investigation of the genetic base of sugarcane cultivars. Theor Appl Genet 99:171-184
42. Janoo N, Grivet L, Dookun A, D'Hont A, Glaszmann JC (1999b) Linkage disequilibrium among modern sugarcane cultivars. Theor Appl Genet 99:1053-1060
43. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Missouri Bot Gard 87:182-198
44. Koyama T (1987) Grasses of Japan and its neighbouring regions: an identification manual. Kodansha Ltd, Tokyo
45. Lee YN (1964a) Taxonomic studies on the genus Miscanthus: anatomical patterns of leaves. Bot Mag (Tokyo) 77:122-130
46. Lee YN (1964b) Taxonomic studies on the genus Miscanthus: relationships among the section, subsection and species, part 1. J Jpn Bot 39:196-205
47. Lee YN (1964c) Taxonomic studies on the genus Miscanthus: relationships among the section, subsection and species, part 2, enumeration of species and varieties. J Jpn Bot 39:257-265
48. Lee YN (1964d) Taxonomic studies on the genus Miscanthus: relationships among the section, subsection and species, part 3, enumeration of species and varieties. J Jpn Bot 39:289-298
49. Lledó MD, Crespo MB, Cox AV, Fay MF, Chase MW (2000) Polyphyly of Limoniastrum (Plumbaginaceae): evidence from DNA sequences of plastid rbcL, trnL intron and trnL-F intergene spacer. Bot J Linn Soc 132:175-191
50. Mehra PN, Sharma ML (1975) Cytological studies in some central and eastern Himalayan grasses: 1 the Andropogoneae. Cytologia 40:61-74
51. Molvray M, Kores PJ, Chase MW (1999) Phylogenetic relationships within Korthalsella (Viscaceae) based on nuclear ITS and plastid trnL-F sequence data. Am J Bot 86:249-260
52. Price S (1963) Cytogenetics of modern sugarcanes. Econ Bot 17:97-106
53. Reeves G, Francis D, Davies MS, Rogers HJ, Hodkinson TR (1998) Genome size is negatively correlated with altitude in natural populations of Dactylis glomerata. Ann Bot (Lond) 82:99-105
54. Reeves G, Chase MW, Goldblatt P, Rudall P, Fay MF, Cox AV, Lejeune B, Sousa-Chies T (2001) Molecular systematics of Iridaceae. Evidence from four plastid DNA regions. Am J Bot 88:2074-2087
55. Salamin N, Hodkinson TR, Savolainen V (2002) Building supertrees: an empirical assessment using the grass family (Poaceae). Syst Biol 51:136-150
56. Sobral BWS, Braga DPV, LaHood ES, Keim P (1994) Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. subtribe of the Andropogoneae Dumort. tribe. Theor Appl Genet 87:843-853
57. Soltis PS, Soltis DE, Chase MW (1999) Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-404
58. Sun Y, Skinner DZ, Liang GH, Hulbert SH (1994) Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA. Theor Appl Genet 89:26-32
59. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony (* and other methods) version 4.0. Sinauer Associates, Sunderland, Mas
60. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105-1109
61. Thompson JD, Higgins DG, Gibson TJ (1995) CLUSTAL W: improving the sensitivity of progressive sequence alignment through sequence weighting, position, specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
62. Vos PR, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
63. White TJ, Bruns SL, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315-322
64. Yoder AD, Irwin JA, Payseur BA (2001) Failure of the ILD to determine data combinability for slow Loris phylogeny. Syst Biol 50:108-121