Viburnum phylogeny: Evidence from the duplicated nuclear gene GBSSI

Molecular Phylogenetics and Evolution

Volumn 33, Issue 1, 2004, Pages 109-126

  Winkworth, Richard C ^a   Donoghue, Michael J ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

GBSSI; Phylogeny; Polyploidy; Viburnum; waxy

Indexed keywords

GRANULE BOUND STARCH SYNTHASE I; GRANULE-BOUND STARCH SYNTHASE I; PRIMER DNA; STARCH SYNTHASE;

ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; DUPLICATE GENE; GENE STRUCTURE; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL; VIBURNUM;

BASE SEQUENCE; DNA PRIMERS; GENE COMPONENTS; GENES, DUPLICATE; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; STARCH SYNTHASE; VIBURNUM;

VIBURNUM; VIBURNUM CLEMENSIAE; VIBURNUM URCEOLATUM;

EID: 4344565193     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.05.006     Document Type: Article

References (71)

1. A. Backlund, and B. Bremer Phylogeny of the Asteridae s. str. based on rbcL sequences, with particular reference to the Dipsacales Plant Syst. Evol. 207 1997 225 254
2. Backlund, A., Donoghue, M.J., 1996. Morphology and phylogeny of the order Dipsacales. In: Backlund, A., (PhD dissertation) Phylogeny of the Dipsacales. Department of Systematic Botany, Uppsala University, Sweden, pp. 1-55
3. B.G. Baldwin, M.J. Sanderson, J.M. Porter, M.F. Wojciechowski, C.S. Campbell, and M.J. Donoghue The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny Ann. Missouri Bot. Gard. 82 1995 247 277
4. M. Barrier, B.G. Baldwin, R.H. Robichaux, and M.D. Purugganan Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian Silversword Alliance (Asteraceae) inferred from floral homeotic gene duplications Mol. Biol. Evol. 16 1999 1105 1113
5. Bell, C.D., 2001. PORN*: A hierarchical likelihood ratio calculator for LINUX. Yale University, New Haven, Connecticut. Published by the author http://www.phylodiversity.net/pornstar
6. C.D. Bell, E.J. Edwards, S.-T. Kim, and M.J. Donoghue Dipsacales phylogeny based on chloroplast DNA sequences Harvard Papers Bot. 6 2001 481 499
7. C.S. Campbell, M.F. Wojciechowski, B.G. Baldwin, L.A. Alice, and M.J. Donoghue Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae) Mol. Biol. Evol. 14 1997 81 90
8. M.W. Chase, D.E. Soltis, R.G. Olmstead, D. Morgan, D.H. Les, B.D. Mishler, M.R. Duvall, R.A. Price, H.G. Hills, Y.-L. Qiu, K.A. Kron, J.H. Rettig, E. Conti, J.D. Palmer, J.R. Manhart, K.J. Sytsma, H.J. Michaels, W.J. Kress, K.G. Karol, W.D. Clark, M. Hedrén, B.S. Gaut, R.K. Jansen, K.-L. Kim, C.F. Wimpee, J.F. Smith, G.R. Furnier, S.H. Strauss, Q.-Y. Xiang, G.M. Plunkett, P.S. Soltis, S.M. Swensen, S.E. Williams, P.A. Gadek, C.J. Quinn, L.E. Eguiarte, E. Golenberg, G.H. Learn, S.W. Graham, S.C.H. Barrett, S. Dayanandan, and V.A. Albert Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL Ann. Missouri Bot. Gard. 80 1993 528 580
9. J.R. Clark, M. Robertson, and C.C. Ainsworth Nucleotide sequence of a wheat (Triticum aestivum L.) cDNA clone encoding the waxy protein Plant Mol. Biol. 16 1991 1099 1101
10. R.C. Cronn, R.L. Small, and J.F. Wendel Duplicated genes evolve independently after polyploid formation in cotton Proc. Natl. Acad. Sci. USA 96 1999 14406 14411
11. Donoghue, M.J., 1982. Systematic studies in the genus Viburnum. Ph.D. Dissertation, Harvard University, Cambridge, MA
12. M.J. Donoghue A preliminary analysis of phylogenetic relationships in Viburnum (Caprifoliaceae s.l.) Syst. Bot. 8 1983 45 58
13. M.J. Donoghue The phylogenetic relationships of Viburnum N. Platnick V. Funk Advances in Cladistics vol. 2 1983 Columbia University Press New York 143 166
14. M.J. Donoghue, and B.G. Baldwin Phylogenetic analysis of Viburnum based on ribosomal DNA sequences from the internal transcribed spacer regions Am. J. Bot. 80 Suppl. 1993 146
15. M.J. Donoghue, and S. Mathews Duplicate genes and the root of angiosperms, with an example using phytochrome genes Mol. Phylogenet. Evol. 9 1998 489 500
16. M.J. Donoghue, and K. Sytsma Phylogenetic analysis of Viburnum based on chloroplast DNA restriction-site data Am. J. Bot. 80 Suppl. 1993 146
17. M.J. Donoghue, B.G. Baldwin, J. Li, and R.C. Winkworth Viburnum phylogeny based on chloroplast trnk intron and nuclear ribosomal ITS DNA sequences Syst. Bot. 29 2004 188 198
18. M.J. Donoghue, C.D. Bell, and R.C. Winkworth The evolution of reproductive characters in Dipsacales Int. J. Plant Sci. 164 Suppl. 5 2003 S453 S464
19. M.J. Donoghue, T. Eriksson, P.A. Reeves, and R.G. Olmstead Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae) Harvard Papers Bot. 6 2001 459 479
20. M.J. Donoghue, R.G. Olmstead, J.F. Smith, and J.D. Palmer Phylogenetic relationships of Dipsacales based on rbcL sequences Ann. Missouri Bot. Gard. 79 1992 333 345
21. J.J. Doyle, and J.L. Doyle Isolation of plant DNA from fresh tissue Focus 12 1990 13 15
22. J.J. Doyle, J.L. Doyle, and C. Harbison Chloroplast-expressed glutamine synthetase in Glycine and the related Leguminosae: phylogeny, gene duplication, and ancient polyploidy Syst. Bot. 28 2003 567 577
23. Egolf, D.R., 1956. Cytological and interspecific hybridization studies in the genus Viburnum. Ph.D. Dissertation. Cornell University, Ithaca, New York
24. E. Emshwiller, and J.J. Doyle Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae) Mol. Phylogenet. Evol. 12 1999 310 319
25. T. Eriksson, and M.J. Donoghue Phylogenetic analyses of Sambucus and Adoxa (Adoxoideae, Adoxaceae) based on nuclear ribosomal ITS sequences and preliminary morphological data Syst. Bot. 22 1997 555 573
26. R.C. Evans, L.A. Alice, C.S. Campbell, E.A. Kellogg, and T.A. Dickinson The granule-bound starch synthase (GBSSI) gene in the Rosaceae: multiple loci and phylogenetic utility Mol. Phylogenet. Evol. 17 2000 388 400
27. R.C. Evans, and C.S. Campbell The origin of the apple sub-family (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicate GBSSI genes Am. J. Bot. 89 2002 1478 1484
28. A. Force, M. Lynch, F.B. Pickett, A. Amores, Y. Yan, and J. Postlethwait Preservation of duplicated genes by complementary degenerative mutations Genetics 151 1999 1531 1545
29. J. Fuertes Aguilar, and G. Nieto Feliner Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae) Mol. Phylogenet. Evol. 28 2003 430 447
30. J. Fuertes Aguilar, J.A. Rossello, and G. Nieto Feliner Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of Armeria (Plumbaginaceae) Mol. Ecol. 8 1999 1341 1346
31. S. Ge, T. Sang, B.-R. Lu, and D.-Y. Hong Phylogeny of rice genomes with emphasis on the origins of allotetraploid species Proc. Natl. Acad. Sci. USA 96 1999 14400 14405
32. K.R. Gould, and M.J. Donoghue Phylogeny and biogeography of Triosteum (Caprifoliaceae) Harvard Papers Bot. 5 2000 157 166
33. H. Hara A Revision of the Caprifoliaceae of Japan with Reference to Allied Plants in other Districts and the Adoxaceae 1983 Academia Scientific Books Tokyo
34. D. Howarth, and D.A. Baum Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plants Mol. Phylogenet. Evol. 23 2002 525 528
35. Huson, D.H., 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14, 68-73 (SplitsTree 3.2: 〈http://www-ab.informatik. uni-tuebingen.de/software/splits/welcome_en.html〉)
36. A.L. Ingram, and J.J. Doyle The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps 16 Am. J. Bot. 90 2003 116 122
37. E.K. Janaki Ammal Chromosomes and the species problem in the genus Viburnum Curr. Sci. 22 1953 4 6
38. L.A. Johnson, and D.E. Soltis Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences Ann. Missouri Bot. Gard. 82 1995 149 175
39. W.S. Judd, R.W. Sanders, and M.J. Donoghue Angiosperm family pairs-preliminary phylogenetic analyses Harvard Papers Bot. 5 1994 1 51
40. J.H. Kern The genus Viburnum (Caprifoliaceae) in Malaysia Reinwardtia 1 1951 107 170
41. E.P. Killip, and A.C. Smith The South American species of Viburnum Bull. Torrey Bot. Club 57 1931 245 258
42. J. Li, and M.J. Donoghue More molecular evidence for interspecific relationships in Liquidambar (Hamamelidaceae) Rhodora 101 1999 87 91
43. R.J. Mason-Gamer Origin of the North American Elymus (Poaceae: Tritiaceae) allotetraploids based on granule-bound starch synthase gene sequences Syst. Bot. 26 2001 757 768
44. R.J. Mason-Gamer, C.F. Weil, and E.A. Kellog Granule-bound starch synthase: structure, function, and phylogenetic utility Mol. Biol. Evol. 15 1998 1658 1673
45. S. Mathews, J.G. Burleigh, and M.J. Donoghue Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms Mol. Biol. Evol. 20 2003 1087 1097
46. S. Mathews, and M.J. Donoghue The root of angiosperm phylogeny inferred from duplicate phytochrome genes Science 286 1999 947 950
47. S. Mathews, and M.J. Donoghue Basal angiosperm phylogeny inferred from duplicate phytochromes A and C Int. J. Plant Sci. 161 2000 S41 S55
48. A. Mérida, J.M. Rodríguez-Galán, C. Vincent, and J.M. Romero Expression of the granule bound starch synthase I (Waxy) gene from snapdragon is developmentally and circadian clock regulated Plant Physiol. 120 1990 401 409
49. R.E. Miller, M.D. Rausher, and P.S. Manos Phylogenetic systematic of Ipomoea (Convolvulaceae) based on ITS and Waxy sequences Syst. Bot. 24 1999 209 227
50. C.V. Morton The Mexican and Central American species of Viburnum Contrib. USA Natl. Herb. 26 1933 339 366
51. A.S. Oersted Til belysning af slaegten Viburnum Vid. Medd. Naturh. For. Kjobenhavn 13 1861 267 305
52. I. Peralta, and D.M. Spooner Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon) Am. J. Bot. 88 2001 1888 1902
53. N. Pyck, P. Roels, and E. Smets Tribal relationships in Caprifoliaceae: evidence from a cladistic analysis using ndhF sequences Syst. Geogr. Pl. 69 1999 145 159
54. J. Ramsey, and D.W. Schemske Neopolyploidy in flowering plants Ann. Rev. Ecol. Syst. 33 2002 589 639
55. A. Rehder The viburnums of eastern Asia C.S. Sargent Trees and Shrubs, vol. II, part II 1908 Houghton Mifflin Boston 105 116
56. T. Sang Utility of low copy nuclear gene sequences in plant phylogenetics Crit. Rev. Biochem. Mol. Biol. 37 2002 121 147
57. T. Sang, D.J. Crawford, and T.F. Stuessy Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae) Am. J. Bot. 84 1997 1120 1136
58. T. Sang, M.J. Donoghue, and D. Zhang Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative non-hybrid species Mol. Biol. Evol. 14 1997 994 1007
59. R.L. Small, J.A. Ryburn, R.C. Cronn, T. Seelanan, and J.F. Wendel The tortoise and the hare: choosing between noncoding plastome and nuclear adh sequences for phylogeny reconstruction in a recently diverged plant group Am. J. Bot. 85 1999 1301 1315
60. J.E.E. Smedmark, T. Eriksson, R.C. Evans, and C.S. Campbell Ancient allopolyploid speciation in Geinae (Rosaceae): evidence from nuclear granule-bound starch synthase (GBSSI) gene sequences Syst. Biol. 52 2003 374 385
61. D.E. Soltis, and R.K. Kuzoff Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae) Evolution 49 1995 727 742
62. G.L. Stebbins Polyploidy in plants: unsolved problems and prospects W.H. Lewis Polyploidy: Biological Relevance 1980 Plenum New York 495 520
63. D.L. Swofford PAUP*. Phylogenetic Analysis using Parsimony (* and Other Methods), Version 4 2002 Sinauer Associates Sunderland, MA
64. P. Taberlet, L. Gielly, G. Pautou, and J. Bouvet Universal primers for amplification of three non-coding regions of chloroplast DNA Plant Mol. Biol. 17 1991 1105 1109
65. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
66. F.R. van der Leij, R.G.F. Visser, A.S. Ponstein, E. Jacobsen, and W.J. Feenstra Sequence of the structural gene for granule-bound starch synthase of potato (Solanum tuberosum L.) and evidence for a single point deletion in the amf allele Mol. Gen. Genet. 228 1991 240 248
67. S.J. Wang, K.W. Yeh, and C.Y. Tsai Molecular characterization and expression of granule-bound starch synthase in the sink and source tissues of sweet potato Physiol. Plantarum 106 1999 253 261
68. Z. Wang, Z. Wu, Y. Xing, F. Zheng, X. Guo, W. Zang, and M. Hong Nucleotide sequence of the rice waxy gene Nucleic Acids Res. 18 1990 5898 5898
69. J.F. Wendel Genome evolution in polyploids Plant Mol. Biol. 42 2000 225 249
70. J.F. Wendel, A. Schnabel, and T. Seelanan Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium) Proc. Natl. Acad. Sci. USA 92 1995 280 284
71. A.M. Wilkinson Floral anatomy and morphology of some species of the genus Viburnum of the Caprifoliaceae Am. J. Bot. 35 1948 455 465