Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Cai, Danying ^a,b   Rodríguez, Flor ^b,c   Teng, Yuanwen ^a   Ané, Cécile ^b   Bonierbale, Meredith ^d   Mueller, Lukas A ^e   Spooner, David M ^b  

^a State Agricultural Ministry   (China)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c INSTITUTO DE INVESTIGACIONES AGROPECUARIAS   (Chile)

^d INTERNATIONAL POTATO CENTER   (Peru)

^e United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; CLADISTICS; COHORT ANALYSIS; ENZYME ACTIVITY; EVOLUTIONARY BIOLOGY; GENE; GENETIC ANALYSIS; GENOMICS; POLYPLOIDY; POTATO; SPATIAL DISTRIBUTION; TAXONOMY; WILD POPULATION;

UNITED STATES;

SOLANUM; SOLANUM BERTHAULTII; SOLANUM DEMISSUM; SOLANUM HJERTINGII; SOLANUM HOUGASII; SOLANUM IOPETALUM; SOLANUM JAMESII; SOLANUM STOLONIFERUM; SOLANUM TUBEROSUM; SOLANUM VERRUCOSUM;

PLANT DNA;

ALLELE; ARTICLE; BIOLOGICAL MODEL; CENTRAL AMERICA; DNA SEQUENCE; EVOLUTION; GENETICS; PHYLOGENY; PLANT GENOME; POLYPLOIDY; POTATO; SEQUENCE ALIGNMENT; SOUTH AMERICA;

ALLELES; BIOLOGICAL EVOLUTION; CENTRAL AMERICA; DNA, PLANT; GENOME, PLANT; MODELS, GENETIC; PHYLOGENY; POLYPLOIDY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOLANUM TUBEROSUM; SOUTH AMERICA;

EID: 84861329445     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-70     Document Type: Article

References (78)

1. Polyploidy in angiosperms: monocotyledons. Goldblatt P, Polyploidy: biological relevance Plenum Press, New York, Lewis WH, 1980 219 239
2. Polyploidy in angiosperms: dicotyledons. Lewis WH, Polyploidy: biological relevance Plenum Press, New York, Lewis WH, 1980 241 268
3. Genome evolution in polyploids. Wendel JF, Plant Mol Biol 2000 42 225 249 10.1023/A:1006392424384 10688139
4. Polyploidy and angiosperm diversification. Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Patterson AH, Zheng C, Sankoff D, DePamphilis CW, Wall PK, Soltis PS, Amer J Bot 2009 96 336 348 10.3732/ajb.0800079
5. The role of genetic and genomic attributes in the success of polyploids. Soltis PS, Soltis DE, Proc Nat Acad Sci USA 2000 97 7051 7057 10.1073/pnas.97.13.7051 10860970
6. Yesterdays polyploidization and mystery of diploidization. Wolfe KH, Nat Rev Genet 2001 2 333 341 11331899
7. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Adams KL, Cronn R, Percifield R, Wendel JF, Proc Nat Acad Sci USA 2003 100 4649 4654 10.1073/pnas.0630618100 12665616
8. The advantages and disadvantages of being polyploid. Comai L, Nature Rev Genet 2005 6 836 846 16304599
9. The evolutionary consequences of polyploidy. Otto SP, Cell 2007 131 452 462 10.1016/j.cell.2007.10.022 17981114
10. Consequences of genome duplication. Sémon M, Wolfe KH, Curr Opin Genetics Dev 2007 17 505 512 10.1016/j.gde.2007.09.007
11. On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae). Tate JA, Joshi P, Soltis KA, Soltis PS, Soltis DE, BMC Plant Biol 2009 9 80 10.1186/1471-2229-9-80 19558696
12. Dating the origins of polyploidy events. Doyle JJ, Egan AN, New Phytol 2010 186 73 85 10.1111/j.1469-8137.2009.03118.x 20028472
13. Molecular mechanisms of polyploidy and hybrid vigor. Chen ZJ, Trends Plant Sci 2010 15 57 71 10.1016/j.tplants.2009.12.003 20080432
14. Terminology for polyploids based on their cytogenetic behavior: consequences in genetics and breeding. Carputo D, Camadro EL, Peloquin SJ, Plant Breed Rev 2006 26 105 124
15. Molecular data and the dynamic nature of polyploidy. Soltis DE, Soltis PS, Crit Rev Plant Sci 1993 12 243 273
16. Polyploidy: recurrent formation and genome evolution. Soltis DE, Soltis PS, Trends Ecol Evol 1999 14 348 352 10.1016/S0169-5347(99)01638-9 10441308
17. Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Segraves KA, Thompson JN, Soltis DE, Soltis PS, Mol Ecol 1999 8 253 262 10.1046/j.1365-294X.1999.00562.x
18. Multiple origins of allopolyploid Aegilops triuncialis. Vanichanon A, Blake NK, Sherman JD, Talbert LE, Theor Appl Genet 2003 106 804 810 12647053
19. Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Plantaginaceae). Albach DC, New Phytol 2007 176 481 498 10.1111/j.1469-8137. 2007.02172.x 17888125
20. Evidence for multiple, autoploid origins of agamospermous populations in Eupatorium sessilifolium (Asteraceae). Grubbs KC, Small RL, Schilling EE, Plant Syst Evol 2009 279 151 161 10.1007/s00606-009-0155-y
21. Multiple origins promote the ecological amplitude of allopolyploid Aegilops (Poaceae). Meimberg H, Njoku CC, McKay JK, Rice KJ, Milan NF, Amer J Bot 2009 96 1262 1273 10.3732/ajb.0800345
22. Recurring origins of allopolyploid species in Asplenium. Werth CR, Guttman SI, Eshbaugh WH, Science 1985 228 731 733 10.1126/science.228.4700.731 17841005
23. Genetic variation in Tragopogon species: additional origins of the allotetraploids T. mirus and T. miscellus (Compositae). Soltis PS, Plunkett GM, Novak SJ, Soltis DE, Amer J Bot 1995 82 1329 1341 10.2307/2446255
24. Recent and recurrent polyploidy in Tragopogon (Asteraceae): genetics, genomic, and cytogenetic comparisons. Soltis DE, Soltis PS, Pires JC, Kovarik A, Tate J, Mavrodiev E, Biol J Linn Soc 2004 82 485 501 10.1111/j.1095-8312.2004. 00335.x
25. Extensive simple sequence repeat genotyping of potato landraces supports a major reevaluation of their gene pool structure and classification. Spooner DM, Nú̃ez J, Trujillo G, del Rosario Herrera M, Guzmán F, Ghislain M, Proc Natl Acad Sci USA 2007 104 19398 19403 10.1073/pnas.0709796104 18042704
26. Taxonomy of cultivated potatoes (Solanum section Petota: Solanaceae). Ovchinnikova A, Krylova E, Gavrilenko T, Smekalova T, Zhuk M, Knapp S, Spooner DM, Bot J Linn Soc 2011 165 107 155 10.1111/j.1095-8339.2010.01107.x
27. DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Spooner DM, Amer J Bot 2009 96 1177 1189 10.3732/ajb.0800246
28. Geographic and environmental range expansion through polyploidy in wild potatoes (Solanum section Petota). Hijmans R, Gavrilenko T, Stephenson S, Bamberg J, Salas A, Spooner DM, Global Ecol Biogeogr 2007 16 485 495 10.1111/j.1466-8238.2007.00308.x
29. Hawkes JG, The potato: evolution, biodiversity, and genetic resources Belhaven Press, Washington, DC 1990
30. Assignment of endosperm balance numbers to the tuberbearing Solanums and their close non-tuber bearing relatives. Hanneman RE, Euphytica 1994 74 19 25 10.1007/BF00033762
31. Reexamination of series relationships of South American wild potatoes (Solanaceae: Solanum sect. Petota): evidence from chloroplast DNA restriction site variation. Spooner DM, Castillo R, Amer J Bot 1997 84 671 685 10.2307/2445904
32. Genomic origins of potato polyploids: GBSSI gene sequencing data. Spooner DM, Rodríguez F, Polgár Z, Ballard HE, Jansky SH, The Plant Genome, a Suppl to Crop Sci 2008 48 Suppl 1 27 S36
33. Nitrate reductase phylogeny of potato (Solanum sect. Petota) genomes with emphasis on the origins of the polyploid species. Rodríguez F, Spooner DM, Syst Bot 2009 34 207 219 10.1600/036364409787602195
34. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? Rodríguez F, Wu F, Ané C, Tanksley S, Spooner DM, BMC Evol Biol 2009 9 191 10.1186/1471-2148-9-191 19664206
35. Phylogeny of Solanum series Piurana and related species in Solanum section Petota based on five conserved ortholog sequences. Ames M, Spooner DM, Taxon 2010 59 1091 1104 + 4pg. foldout
36. Phylogenetic relationships of Solanum series Conicibaccata and related species in Solanum section Petota inferred from five conserved ortholog sequences. Fajardo D, Spooner DM, Syst Bot 2011 36 163 170 10.1600/ 036364411X553252
37. Hybrid origins of cultivated potatoes. Rodríguez F, Ghislain M, Clausen AM, Jansky SH, Spooner DM, Theor Appl Genet 2010 121 1187 1198 10.1007/s00122-010-1422-6 20734187
38. The taxonomy of tomatoes: a revision of wild tomatoes (Solanum section Lycopersicon) and their outgroup relatives in sections Juglandifolium and Lycopersicoides. Peralta IE, Spooner DM, Knapp S, Syst Bot Monogr 2008 84 1 186 + 3 plates
39. Examination of species boundaries of Solanum series Demissa and potentially related species in series Acaulia and series Tuberosa (sect. Petota). Spooner DM, Van den Berg RG, Bamberg JB, Syst Bot 1995 20 295 314 10.2307/2419497
40. Morphological variation within series Acaulia Juz. (Solanum sect. Petota). Kardolus JP, Solanaceae IV: advances in biology and utilization Royal Botanic Gardens, Kew, Nee M, Symon DE, Lester RN, Jessop JP, 1999 257 274
41. Species relationships between a wild tetraploid potato species, Solanum acaule Bitter, and its related species as revealed by RFLPs of chloroplast and nuclear DNA. Nakagawa K, Hosaka K, Amer J Potato Res 2002 79 85 98 10.1007/BF02881517
42. Wild potatoes (Solanum section Petota) of North and Central America. Spooner DM, Van den Berg RG, Rodríguez A, Bamberg J, Hijmans RJ, Lara-Cabrera SI, Syst Bot Monogr 2004 68 1 209
43. Phylogenetic relationships in the potato and its related species. Matsubayashi M, Chromosome engineering in plants: genetics, breeding, evolution, part B Elsevier Science BV, Amsterdam, Tsuchiya T, Gupta PK, 1991 93 118
44. Allopolyploid speciation of the tetraploid Mexican potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization. Pendinen G, Gavrilenko T, Jiang J, Spooner DM, Genome 2008 51 714 720 10.1139/G08-052 18772949
45. Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Wu FN, Mueller LA, Crouzillat D, Petiard V, Tanksley SD, Genetics 2006 174 1407 1420 10.1534/genetics.106.062455 16951058
46. The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae). Levin RA, Whelan A, Miller JS, Mol Phylogenet Evol 2009 53 881 890 10.1016/j.ympev.2009. 08.016 19698795
47. PCR-mediated recombination between Cryptosporidium spp. of lizards and snakes. Zhou L, Yang CF, Xiao LH, J Eukaryot Microbiol 2003 50 563 565 10.1111/j.1550-7408.2003.tb00630.x 14736163
48. Detection and isolation of nuclear haplotypes by SSCP. Ortí G, Hare MP, Avise JC, Mol Ecol 1997 6 575 580 10.1046/j.1365-294X.1997.00212.x 9200830
49. Asymmetric single-strand conformation polymorphism: an accurate and cost-effective method to amplify and sequence allelic variants. Rodríguez F, Cai D, Teng Y, Spooner DM, Amer J Bot 2011 98 1061 1067 10.3732/ajb.1000251
50. RFLP analysis of the wild potato species, Solanum acaule Bitter (Solanum sect. Petota). Hosaka K, Spooner DM, Theor Appl Genet 1992 84 851 858
51. A biosystematic analysis of Solanum acaule. Kardolus JP, Ph.D. Thesis Wageningen Agricultural University, Wageningen, The Netherlands 1998
52. Chloroplast and nuclear evidence for multiple origins of polyploids and diploids of Hedera (Araliaceae) in the Mediterranean basin. Valcárcel V, Fiz O, Vargas P, Molec Phylo Evol 2003 27 1 20 10.1016/S1055-7903(02)00364-0
53. Multiple origins and genetic diversity in the newly arisen allopolyploid species, Senecio cambrensis Rosser (Compositae). Ashton PA, Abbott RJ, Heredity 1992 68 25 32 10.1038/hdy.1992.3
54. Multiple origins of the octoploid Scandinavian endemic Draba cacuminum: electrophoretic and morphological evidence. Brochmann C, Soltis PS, Soltis DE, Nordic J Bot 1992 12 257 272 10.1111/j.1756-1051.1992.tb01303.x
55. Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3-D gene sequences. Doyle JJ, Doyle JL, Brown AHD, Palmer RG, Evolution 2002 56 1388 1402 12206240
56. Multiple origins and nrDNA internal transcribed spacer homeologue evolution in the Glycine tomentella (Leguminosae) allopolyploid complex. Rauscher JT, Doyle JJ, Brown AHD, Genetics 2004 166 987 998 10.1534/genetics. 166.2.987 15020482
57. Allopolyploidy in bryophytes: multiple origins of Plagiomnium medium. Wyatt R, Odrzykoski IJ, Stoneburner A, Bass HW, Galau GA, Proc Natl Acad Sci USA 1988 85 5601 5604 10.1073/pnas.85.15.5601 16593968
58. Genomic changes in resynthesized Brassica napus and their effects on gene expression and pheontype. Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC, Plant Cell 2007 19 3403 3417 10.1105/tpc.107.054346 18024568
59. Phenotypic and transcriptional changes associated with potato autopolyploidization. Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J, Genetics 2007 176 2055 2067 10.1534/genetics.107.074286 17565939
60. Evolutionary genetics of genome merger in plants. Doyle JJ, Flagel LE, Patterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF, Ann Rev Genet 2008 42 443 461 10.1146/annurev.genet.42.110807.091524 18983261
61. Plant speciation. Rieseberg L, Willis JH, Science 2007 317 910 914 10.1126/science.1137729 17702935
62. Have we grossly underestimated the number of species? Soltis DE, Soltis PS, Schemske DW, Hancock JF, Thompson JN, Husband BC, Judd WS, Taxon 2007 56 13 30
63. Estimating species trees: practical and theoretical aspects Wiley-Blackwell, Hoboken, New Jersey, Knowles LL, Kubatko LS S, 2010
64. Next-generation sequencing and genome evolution in allopolyploids. Buggs RJA, Renny-Byfield S, Chester M, Jordon-Thaden IE, Viccini LF, Chamala S, Leitch AR, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE, Amer J Bot 2012 99 372 382 10.3732/ajb.1100395
65. Genome sequence and analysis of the tuber crop potato. The Potato Sequencing Consortium, Nature 2011 475 189 197 10.1038/nature10158 21743474
66. DNA protocols for plants-CTAB total DNA isolation. Doyle J, Molecular techniques in taxonomy Springer, Berlin, Hewitt GM, Johnston A, 1991 283 293
67. Modeltest: testing the model of DNA substitution. Posada D, Crandall KA, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953
68. The Staden sequence analysis package. Staden R, Mol Biotechnol 1996 5 233 241 10.1007/BF02900361 8837029
69. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, Nucleic Acids Res 1997 24 4876 4882
70. Maddison DR, Maddison WP, MacClade 4.03: Analysis of phylogeny and character evolution Sinauer Associates, Suderland 2001
71. Bayesian inference of species trees from multilocus data. Heled J, Drummond AJ, Mol Biol Evol 2010 27 570 580 10.1093/molbev/msp274 19906793
72. APE: analyses of phylogenetics and evolution in R language. Paradis E, Claude J, Strimmer K, Bioinformatics 2004 20 289 290 10.1093/bioinformatics/ btg412 14734327
73. R Development Core Team, R: A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria 2011 ISBN 3-900051-07-0, URL http://www.R-project.org/.
74. Estimating species trees from unrooted gene trees. Liu L, Yu L, Syst Biol 2011 65 661 667
75. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
76. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. Desper R, Gascuel O, J Comput Biol 2002 9 687 705 software available: www.atgc-montpellier.fr/fastme/ 10.1089/106652702761034136 12487758
77. Neighbor-joining revealed. Gascuel O, Steel M, Mol Biol Evol 2006 23 1997 2000 10.1093/molbev/msl072 16877499
78. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Desper R, Gascuel O, Mol Biol Evol 2004 21 587 598 14694080