A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

BMC Biology

Volumn 9, Issue , 2011, Pages

  Griffin, Philippa C ^a   Robin, Charles ^a   Hoffmann, Ary A ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); EMBRYOPHYTA; POA; POACEAE;

PLANT DNA;

ARTICLE; AUSTRALIA; DNA SEQUENCE; EVALUATION; GENETICS; METHODOLOGY; POA; POLYPLOIDY; REPRODUCIBILITY;

AUSTRALIA; DNA, PLANT; POA; POLYPLOIDY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 79953122203     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-9-19     Document Type: Article

References (92)

1. Bennett M. Perspectives on polyploidy in plants - ancient and neo. Biol J Linn Soc Lond 2004, 82:411-423.
2. Soltis D, Soltis P, Tate J. Advances in the study of polyploidy since Plant speciation. New Phytol 2003, 161:173-191.
3. Mable B. Breaking down taxonomic barriers in polyploidy research. Trends Plant Sci 2003, 8:582-590. 10.1016/j.tplants.2003.10.006, 14659707.
4. Otto S. The evolutionary consequences of polyploidy. Cell 2007, 131:452-462. 10.1016/j.cell.2007.10.022, 17981114.
5. Adams K, Wendel J. Polyploidy and genome evolution in plants. Curr Opin Plant Biol 2005, 8:135-141. 10.1016/j.pbi.2005.01.001, 15752992.
6. Leitch A, Leitch I. Genomic plasticity and the diversity of polyploid plants. Science 2008, 320:481-483. 10.1126/science.1153585, 18436776.
7. Blanc G, Wolfe K. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 2004, 16:1667-1678. 10.1105/tpc.021345, 514152, 15208399.
8. Chen Z, Ha M, Soltis D. Polyploidy: genome obesity and its consequences. New Phytol 2007, 174:717-720. 10.1111/j.1469-8137.2007.02084.x, 1950720, 17504455.
9. Levy A, Feldman M. The impact of polyploidy on grass genome evolution. Plant Physiol 2002, 130:1587-1593. 10.1104/pp.015727, 1540263, 12481041.
10. Arnold M. Transfer and origin of adaptations through natural hybridization: were Anderson and Stebbins right?. Plant Cell 2004, 16:562-570. 10.1105/tpc.160370, 540259, 15004269.
11. Maddison W, Knowles L. Inferring phylogeny despite incomplete lineage sorting. Syst Biol 2006, 55:21-30. 10.1080/10635150500354928, 16507521.
12. Heled J, Drummond A. Bayesian inference of species trees from multilocus data. Mol Biol Evol 2010, 27:570-580. 10.1093/molbev/msp274, 2822290, 19906793.
13. Small R, Cronn R, Wendel J. Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany 2004, 17:145-170.
14. Degnan J, Rosenberg N. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 2009, 24:332-340. 10.1016/j.tree.2009.01.009, 19307040.
15. Jakob S, Blattner F. Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex. Mol Phylogenet Evol 2009, 55:650-659. 10.1016/j.ympev.2009.10.021, 19850141.
16. Lihová J, Shimizu K, Marhold K. Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene. Mol Phylogenet Evol 2006, 39:759-786.
17. Rousseau-Gueutin M, Gaston A, Aïnouche A, Aïnouche M, Olbricht K, Staudt G, Richard L, Denoyes-Rothan B. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Mol Phylogenet Evol 2009, 51:515-530. 10.1016/j.ympev.2008.12.024, 19166953.
18. Lundberg M, Töpel M, Eriksen B, Nylander J, Eriksson T. Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification. Mol Phylogenet Evol 2009, 51:269-280. 10.1016/j.ympev.2009.02.020, 19268709.
19. Fehrer J, Krak K, Chrtek J. Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise. BMC Evol Biol 2009, 9:239. 10.1186/1471-2148-9-239, 2759941, 19772642.
20. Fortune P, Pourtau N, Viron N, Ainouche M. Molecular phylogeny and reticulate origins of the polyploid Bromus species from section Genea (Poaceae). Am J Bot 2008, 95:454-464.
21. Patterson J, Larson S, Johnson P. Genome relationships in polyploid Poa pratensis and other Poa species inferred from phylogenetic analysis of nuclear and chloroplast DNA sequences. Genome 2005, 48:76-87. 10.1139/g04-102, 15729399.
22. Joly S, Heenan P, Lockhart P. A Pleistocene inter-tribal allopolyploidization event precedes the species radiation of Pachycladon (Brassicaceae) in New Zealand. Mol Phylogenet Evol 2009, 51:365-372. 10.1016/j.ympev.2009.02.015, 19254769.
23. Schmickl R, Jørgensen M, Brysting A, Koch M. The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier. BMC Evol Biol 2010, 10:98. 10.1186/1471-2148-10-98, 2858744, 20377907.
24. Jiang LY, Qian ZQ, Guo ZG, Wang C, Zhao GF. Polyploid origins in Gynostemma pentaphyllum (Cucurbitaceae) inferred from multiple gene sequences. Mol Phylogenet Evol 2009, 52:183-191. 10.1016/j.ympev.2009.03.004, 19292995.
25. Vickery J. A taxonomic study of the genus Poa L. in Australia. Contributions from the NSW National Herbarium 1970, 4:145-243.
26. Walsh N. Poaceae. Flora of Victoria: Volume 2 1994, 356-625. Melbourne: Inkata Press, Walsh N, Entwisle T.
27. Soreng R. Chloroplast-DNA phylogenetics and biogeography in a reticulating group: study in Poa (Poaceae). Am J Bot 1990, 77:1383-1400.
28. Bor N. The genus Poa L. in India. Part I. Journal of the Bombay Natural History Society 1952, 50:787-838.
29. Stebbins G. Variation and evolution in plants 1950, New York: Columbia University Press.
30. Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D. GenBank. Nucleic Acids Res 2005, 33:D34-D38. 10.1093/nar/gki063, 540017, 15608212.
31. Dawkins B. Siobhan's problem: the coupon collector revisited. The American Statistician 1991, 45:76-82.
32. Joly S, Starr J, Lewis W, Bruneau A. Polyploid and hybrid evolution in roses east of the Rocky Mountains. Am J Bot 2006, 93:412-425.
33. Martin D, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262. 10.1093/bioinformatics/bth490, 15377507.
34. Carver T, Rutherford K, Berriman M, Ranjandream M, Barrell B, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics 2005, 21:3422-3423. 10.1093/bioinformatics/bti553, 15976072.
35. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Ranjandream M, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:994-995.
36. Kelchner S, Wendel J. Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet 1996, 30:259-262. 10.1007/s002940050130, 8753656.
37. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
38. Jumpponen A, Jones K. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 2009, 184:438-448. 10.1111/j.1469-8137.2009.02990.x, 19674337.
39. Sønstebø J, Gielly L, Brysting A, Elven R, Edwards M, Haile J, Willerslev E, Coissac E, Rioux D, Sannier J, Taberlet P, Brochmann C. Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources 2010, 10:1009-1018.
40. Taudien S, Groth M, Huse K, Petzold A, Szafranski K, Hampe J, Rosenstiel P, Schreiber S, Platzer M. Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing. BMC Genomics 2010, 11:252. 10.1186/1471-2164-11-252, 2873476, 20403190.
41. Chenuil A, Hoareau T, Egea E, Penant G, Rocher C, Aurelle D, Mokhtar-Jamai K, Bishop J, Boisson E, Diaz A, Krakau M, Luttikhuizen PC, Patti FP, Blavet N, Mousset S. An efficient method to find potentially universal population genetic markers, applied to metazoans. BMC Evol Biol 2010, 10:276. 10.1186/1471-2148-10-276, 2949868, 20836842.
42. Roche. GS Junior System: Guidelines for Amplicon Experimental Design. 2010,
43. Roche. Amplicon fusion primer design guidelines for GS FLX Titanium series Lib-A chemistry. 2009,
44. Lennon N, Lintner R, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich R, Giannoukos G, Green L, Hollinger A, Hoover CA, Jaffe DB, Juhn F, McCarthy D, Perrin D, Ponchner K, Powers TL, Rizzolo K, Robbins D, Ryan E, Russ C, Sparrow T, Stalker J, Steelman S, Weiand M, Zimmer A, Henn MR, Nusbaum C, Nicol R. A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol 2010, 11:R15. 10.1186/gb-2010-11-2-r15, 2872875, 20137071.
45. Pirie M, Humphreys A, Galley C, Barker N, Verboom G, Orlovich D, Draffin S, Lloyd K, Baeza C, Negritto M, Ruiz E, Sanchez JH, Reimer E, Linder HP. A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses. Mol Phylogenet Evol 2008, 48:1106-1119. 10.1016/j.ympev.2008.05.030, 18599319.
46. Duan S, Lu B, Li Z, Tong J, Kong J, Yao W, Li S, Zhu Y. Phylogenetic analysis of AA-genome Oryza species (Poaceae) based on chloroplast, mitochondrial, and nuclear DNA sequences. Biochem Genet 2007, 45:113-129. 10.1007/s10528-006-9062-x, 17221300.
47. Ramsey J, Schemske D. Neopolyploidy in flowering plants. Annu Rev Ecol Syst 2002, 33:589-639.
48. Germplasm Resources Information Network (GRIN). , http://www.ars-grin.gov
49. Inda L, Segerra-Moragues J, Müller J, Peterson P, Catalán P. Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres. Mol Phylogenet Evol 2008, 46:932-957. 10.1016/j.ympev.2007.11.022, 18226932.
50. Blanc G, Wolfe K. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 2004, 16:1679-1691. 10.1105/tpc.021410, 514153, 15208398.
51. Whitlock B, Hale A, Groff P. Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PLoS One 2010, 5:e11533. 10.1371/journal.pone.0011533, 2903610, 20644717.
52. Sang T, Crawford D, Stuessy T. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am J Bot 1997, 84:1120-1136.
53. Bain J, Jansen R. A chloroplast DNA hairpin structure provides useful phylogenetic data within tribe Senecioneae (Asteraceae). Can J Bot 2006, 84:862-868.
54. Joly S, Pfeil B, Oxelman B, McLenachan P, Lockhart P. Correction. Am Naturalist 2010, 175:621-622.
55. Sha L, Fan X, Yang R, Kang H, Ding C, Zhang L, Zheng Y, Zhou Y. Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences. Mol Phylogenet Evol 2010, 54:327-335. 10.1016/j.ympev.2009.05.005, 19435606.
56. Liu Z, Chen Z, Pan J, Li X, Su M, Wang L, Li H, Liu G. Phylogenetic relationships in Leymus (Poaceae: Triticeae) revealed by the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences. Mol Phylogenet Evol 2008, 46:278-289. 10.1016/j.ympev.2007.10.009, 18024091.
57. Jakob S, Blattner F. A chloroplast genealogy of Hordeum (Poaceae): long-term persisting haplotypes, incomplete lineage sorting, regional extinction, and the consequences for phylogenetic inference. Mol Biol Evol 2006, 23:1602-1612. 10.1093/molbev/msl018, 16754643.
58. Triplett J, Clark L. Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis on Arundinaria and allies. Systematic Botany 2010, 35:102-120.
59. Souza-Chies T, Essi L, Rua G, Valls J, Miz R. A preliminary approach to the phylogeny of the genus Paspalum (Poaceae). Genetica 2006, 126:15-32. 10.1007/s10709-005-1428-1, 16502082.
60. Kress W, Erickson D. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS One 2007, 2:e508. 10.1371/journal.pone.0000508, 1876818, 17551588.
61. Doyle J, Doyle J, Rauscher J, Brown A. Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (Glycine subgenus Glycine). New Phytol 2003, 161:121-132.
62. Knowles L, Chan YH. Resolving species phylogenies of recent evolutionary radiations. Annals of the Missouri Botanical Garden 2008, 95:224-231.
63. Darmency H, Gasquez J. Spontaneous hybridization of the putative ancestors of the allotetraploid Poa annua. New Phytol 1997, 136:497-501.
64. Gillespie L, Soreng R. A phylogenetic analysis of the bluegrass genus Poa based on cpDNA restriction site data. Systematic Botany 2005, 30:84-105.
65. Grun P. Cytogenetic studies of Poa. I. Chromosome numbers and morphology of interspecific hybrids. Am J Bot 1954, 41:671-678.
66. Lambeck K, Chappell J. Sea level change through the last glacial cycle. Science 2001, 292:679-686. 10.1126/science.1059549, 11326090.
67. Furlan E, Umina P, Mitrovski P, Gust N, Griffiths J, Weeks A. High levels of genetic divergence between Tasmanian and Victorian platypuses, Ornithorhynchus anatinus, as revealed by microsatellite loci. Conserv Genet 2010, 11:319-323.
68. Nevill P, Bossinger G, Ades P. Phylogeography of the world's tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia. J Biogeogr 2010, 37:179-192.
69. Symula R, Keogh J, Cannatella D. Ancient phylogeographic divergence in southeastern Australia among populations of the widespread common froglet, Crinia signifera. Mol Phylogenet Evol 2008, 47:569-580. 10.1016/j.ympev.2008.01.011, 18348908.
70. Chapple D, Keogh J, Hutchinson M. Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species group. Mol Ecol 2005, 14:1279-1292. 10.1111/j.1365-294X.2005.02463.x, 15813770.
71. Schultz M, Smith S, Horwitz P, Richardson A, Crandall K, Austin C. Evolution underground: a molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Mol Phylogenet Evol 2009, 50:580-598. 10.1016/j.ympev.2008.11.025, 19118635.
72. Coleman R, Pettigrove V, Raadik T, Hoffmann A, Miller A, Carew M. Microsatellite markers and mtDNA indicate two distinct groups in dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae), a threatened freshwater fish from south-eastern Australia. Conserv Genet 2010, 11:1911-1928.
73. Dubey S, Shine R. Restricted dispersal and genetic diversity in populations of an endangered montane lizard (Eulamprus leuraensis, Scincidae). Mol Ecol 2010, 19:886-897. 10.1111/j.1365-294X.2010.04539.x, 20149087.
74. Koumoundouros T, Sumner J, Clemann N, Stuart-Fox D. Current genetic isolation and fragmentation contrasts with historical connectivity in an alpine lizard (Cyclodomorphus praealtus) threatened by climate change. Biol Conserv 2009, 142:992-1002.
75. Byars S, Parsons Y, Hoffmann A. Effect of altitude on the genetic structure of an Alpine grass, Poa hiemata. Ann Bot 2009, 103:885-899. 10.1093/aob/mcp018, 2707893, 19208670.
76. Rozen S, Skaletsky H. Primer3 on the www for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology 2000, 365-386. Totowa, NJ, USA: Humana Press, Krawetz S, Misener S.
77. Petersen G, Seberg O. Phylogenetic evidence for excision of Stowaway Miniature Inverted-Repeat Transposable Elements in Triticeae (Poaceae). Mol Biol Evol 2000, 17:1589-1596.
78. Shaw J, Lickey E, Beck J, Farmer S, Liu W, Miller J, Siripun K, Winder C, Schilling E, Small R. The tortoise and the hare II: relative utililty of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 2005, 92:142-166.
79. Shaw J, Lickey E, Schilling E, Small R. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 2007, 94:275-288.
80. Roche. GS FLX Titanium emPCR Method Manual. 2009,
81. Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Current Protocols in Bioinformatics 2007, Sep:Unit 10.15.
82. R Development Core Team R: A Language and Environment for Statistical Computing. 2009, R Foundation for Statistical Computing, Vienna, Austria, R Development Core Team.
83. Gene Codes Corporation Sequencher 4.7. 2006, Gene Codes Corporation.
84. Martin D, Posada D, Crandall K, Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 2005, 21:98-102. 10.1089/aid.2005.21.98, 15665649.
85. Posada D, Crandall K. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818. 10.1093/bioinformatics/14.9.817, 9918953.
86. Swofford D. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 2002, Sunderland, Massachusetts: Sinauer Associates, 4.
87. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
88. Huson D, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006, 23:254-267. 10.1093/molbev/msj030, 16221896.
89. Joly S, Bruneau A. Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: an example from Rosa in North America. Syst Biol 2006, 55:623-636. 10.1080/10635150600863109, 16969938.
90. Peakall R, Smouse P. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006, 6:288-295.
91. Drummond A, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007, 7:214. 10.1186/1471-2148-7-214, 2247476, 17996036.
92. Sikes D, Lewis P. PAUPRat: PAUP* implementation of the parsimony ratchet. 2001, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, USA.