Evolutionary importance of generative polyploidy for genome evolution of haploid-dominant land plants

Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes

Volumn , Issue , 2013, Pages 295-305

  Rensing, Stefan A ^a   Beike, Anna K ^a   Lang, Daniel ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84901019833     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-7091-1160-4_18     Document Type: Chapter

References (89)

1. Alboresi A, Gerotto C, Giacometti GM, Bassi R, Morosinotto T (2010) Physcomitrella patens mutants affected on heat dissipation clarify the evolution of photoprotection mechanisms upon land colonization. Proc Natl Acad Sci USA 107:11128-11133
2. Ando H (1980) Evolution of bryophytes in relation to their sexuality. Proc Bryol Soc Jpn 2:129-130
3. Andrews AL (1918) A new hybrid in Physcomitrium. Torreya 18:52-54
4. Andrews AL (1942) Taxonomic notes II. Another natural hybrid in the Funariaceae. Bryologist 45:176-178
5. Beike AK, Rensing SA (2010) The Physcomitrella patens genome-a first stepping stone towards understanding bryophyte and land plant evolution. Trop Bryol 31:43-49
6. Blanc G, Wolfe KH (2004a) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678
7. Blanc G, Wolfe KH (2004b) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679-1691
8. Britton EG (1895) Contributions to American bryology IX. Bull Torrey Bot Club 22:62-68
9. Bryan VS (1957) Cytotaxonomic studies in the Ephemeraceae and Funariaceae. Bryologist 60:103-126
10. Cove DJ, Quatrano RS (2006) Agravitropic mutants of the moss Ceratodon purpureus do not complement mutants having a reversed gravitropic response. Plant Cell Environ 29:1379-1387
11. Cove D, Bezanilla M, Harries P, Quatrano R (2006) Mosses as model systems for the study of metabolism and development. Annu Rev Plant Biol 57:497-520
12. Cove DJ, Perroud P-F, Charron AJ, Mcdaniel SF, Khandelwal A, Quatrano RS (2009) The moss Physcomitrella patens: a novel model system for plant development and genomic studies. Cold Spring Harb Protoc 2009: pdb.emo115
13. Crawford M, Jesson LK, Garnock-Jones PJ (2009) Correlated evolution of sexual system and life-history traits in mosses. Evolution 63:1129-1142
14. Crow KD, Wagner GP (2006) What is the role of genome duplication in the evolution of complexity and diversity? Mol Biol Evol 23:887-892, In: Proceedings of the SMBE tri-national young investigators’ workshop 2005
15. Engel PP (1968) The induction of biochemical and morphological mutants in the moss Physcomitrella patens. Am J Bot 55:438-446
16. Fawcett JA, Maere S, Van de Peer Y (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci USA 106:5737-5742
17. Fawcett JA, Van de Peer Y, Maere S (2013) Significance and biological consequences of polyploidization in land plants. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 277-293
18. Frahm J-P (2001) Biologie der Moose. Spektrum Akademischer Verlag, Heidelberg/Berlin
19. Frahm J-P (2010) Die Laubmoosflora des Baltischen Bernsteinwaldes. Weißdorn-Verlag, Jena
20. Frank W, Decker EL, Reski R (2005) Molecular tools to study Physcomitrella patens. Plant Biol 7:220-227
21. Fritsch R (1991) Index to bryophyte chromosome counts. Bryophytorum Bibliotheka vol 40. J. Cramer/Gebrueder Borntraeger, Berlin/Stuttgart
22. Gout JF, Duret L, Kahn D (2009) Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol 26:1067-1072
23. Husband BC, Baldwin SJ, Suda J (2013) The incidence of polyploidy in natural plant populations: major patterns and evolutionary processes. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 255-276
24. Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11:97-108
25. Karlin EF, Boles SB, Ricca M, Temsch EM, Greilhuber J, Shaw AJ (2009) Three-genome mosses: complex double allopolyploid origins for triploid gametophytes in Sphagnum. Mol Ecol 18:1439-1454
26. Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature 389:33-39
27. Khandelwal A, Cho SH, Marella H, Sakata Y, Perroud PF, Pan A, Quatrano RS (2010) Role of ABA and ABI3 in desiccation tolerance. Science 327:546
28. Lang D (2008) Comparative genomic and phylogenomic analysis of the moss Physcomitrella patens (Hedw.) Bruch & Schimp. Albert-Ludwigs-Universität Freiburg, Freiburg
29. Lang D, Eisinger J, Reski R, Rensing SA (2005) Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism among mosses. Plant Biol 7:228-237
30. Lang D, Zimmer AD, Rensing SA, Reski R (2008) Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends Plant Sci 13:542-549
31. Lang D, Weiche B, Timmerhaus G, Richardt S, Riano-Pachon DM, Correa LG, Reski R, Mueller-Roeber B, Rensing SA (2010) Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol 2:488-503
32. Longton RE (1976) Reproductive biology and evolutionary potential in bryophytes. J Hattori Bot Lab 41:205-223
33. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155
34. Ma XF, Gustafson JP (2005) Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 109:236-249
35. Markmann-Mulisch U, Hadi MZ, Koepchen K, Alonso JC, Russo VE, Schell J, Reiss B (2002) The organization of Physcomitrella patens RAD51 genes is unique among eukaryotic organisms. Proc Natl Acad Sci USA 99:2959-2964
36. Markmann-Mulisch U, Wendeler E, Zobell O, Schween G, Steinbiss HH, Reiss B (2007) Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair. Plant Cell 19:3080-3089
37. Martin A, Lang D, Hanke ST, Mueller SJ, Sarnighausen E, Vervliet-Scheebaum M, Reski R (2009a) Targeted gene knockouts reveal overlapping functions of the five Physcomitrella patens FtsZ isoforms in chloroplast division, chloroplast shaping, cell patterning, plant development, and gravity sensing. Mol Plant 2:1359-1372
38. Martin A, Lang D, Heckmann J, Zimmer AD, Vervliet-Scheebaum M, Reski R (2009b) A uniquely high number of ftsZ genes in the moss Physcomitrella patens. Plant Biol 11:744-750
39. McDaniel SF (2005) Genetic correlations do not constrain the evolution of sexual dimorphism in the moss Ceratodon purpureus. Evolution 59:2353-2361
40. McDaniel SF, von Stackelberg M, Richardt S, Quatrano RS, Reski R, Rensing SA (2010) The speciation history of the Physcomitrium-Physcomitrella species complex. Evolution 64:217-231
41. Menand B, Yi K, Jouannic S, Hoffmann L, Ryan E, Linstead P, Schaefer DG, Dolan L (2007) An ancient mechanism controls the development of cells with a rooting function in land plants. Science 316:1477-1480
42. Mosquna A, Katz A, Decker EL, Rensing SA, Reski R, Ohad N (2009) Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution. Development 136:2433-2444
43. Mueller F (1995) Neue und bemerkenswerte Moosfunde aus Zaire. Trop Bryol 10:81-90
44. Müntzing A (1936) The evolutionary significance of autopolyploidy. Hereditas 21:363-378
45. Natcheva R, Cronberg N (2004) What do we know about hybridization among bryophytes in nature? Can J Bot 82:1687-1704
46. Newton AE, Wikström N, Bell N, Forrest LL, Ignatov MS (2007) Dating the diversification of the pleurocarpous mosses. In: Tangney N (ed) Pleurocarpous mosses: systematics and evolution. Systematics Association Special, vol 71. Systematics Association, CRC Press, Boca Raton
47. Ochi H (1968) A revision of the family Funariaceae (Musci) in Japan and the adjacent regions. Jpn J Bot 20:1-34
48. Odrzykoski IJ, Chudzinska E, Szweykowski J (1996) The hybrid origin of the polyploid liverwort Pellia borealis. Genetica 98:75-86
49. Ohno S (1970) Evolution by gene duplication. Springer, New York
50. Oliver MJ, Dowd SE, Zaragoza J, Mauget SA, Payton PR (2004) The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis. BMC Genomics 5:89
51. Orzechowska M, Siwinska D, Maluszynska J (2010) Molecular cytogenetic analyses of haploid and allopolyploid Pellia species. J Bryol 32:113-121
52. Parisod C, Holderegger R, Brochmann C (2010) Evolutionary consequences of autopolyploidy. New Phytol 186:5-17
53. Pettet A (1964) Hybrid sporophytes in Funariaceae. I. Hybrid sporophytes on Physcomitrella patens (Hedw.) B. & S., and Physcomitrium sphaericum (Schkuhr) Brid. in Britain. Trans Br Bryol Soc 4:642-648
54. Qiu YL, Li L, Wang B, Chen Z, Knoop V, Groth-Malonek M, Dombrovska O, Lee J, Kent L, Rest J, Estabrook GF, Hendry TA, Taylor DW, Testa CM, Ambros M, Crandall-Stotler B, Duff RJ, Stech M, Frey W, Quandt D, Davis CC (2006) The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA 103:15511-15516
55. Quatrano RS, McDaniel SF, Khandelwal A, Perroud PF, Cove DJ (2007) Physcomitrella patens: mosses enter the genomic age. Curr Opin Plant Biol 10:182-189
56. Rensing SA, Rombauts S, Van de Peer Y, Reski R (2002) Moss transcriptome and beyond. Trends Plant Sci 7:535-538
57. Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R (2007) An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol 7:130
58. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, SakakibaraK, Fujita T, OishiK, Shin IT, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, TuH, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319:64-69
59. Rensing SA, Lang D, Zimmer AD (2009) Comparative genomics. In: Knight C, Perroud P-F, Cove D (eds) The moss Physcomitrella patens, vol 36. Wiley-Blackwell, Oxford, pp 42-75
60. Reski R, Frank W (2005) Moss (Physcomitrella patens) functional genomics-gene discovery and tool development, with implications for crop plants and human health. Brief Funct Genomic Proteomic 4:48-57
61. Reski R, Faust M, Wang XH, Wehe M, Abel WO (1994) Genome analysis of the moss Physcomitrella patens (Hedw.) B.S.G. Mol Gen Genet 244:352-359
62. Ricca M, Shaw AJ (2010) Allopolyploidy and homoploid hybridization in the Sphagnum subsecundum complex (Sphagnaceae: Bryophyta). Biol J Linn Soc 99:135-151
63. Schween G, Egener T, Fritzkowsky D, Granado J, Guitton M-C, Hartmann N, Hohe A, Holtorf H, Lang D, Lucht JM, Reinhard C, Rensing SA, Schlink K, Schulte J, Reski R (2005a) Large-scale analysis of 73,329 gene-disrupted Physcomitrella mutants: production parameters and mutant phenotypes. Plant Biol 7:238-250
64. Schween G, Hohe A, Schulte J, Reski R (2005b) Effect of ploidy level on growth, differentiation and phenotype in Physcomitrella patens. Bryologist 108:27-35
65. Seoighe C, Gehring C (2004) Genome duplication led to highly selective expansion of the Arabidopsis thaliana genome. Trends Genet 20:461-464
66. Shaw AJ, Pokorny L, Shaw B, Ricca M, Boles S, Szovenyi P (2008) Genetic structure and genealogy in the Sphagnum subsecundum complex (Sphagnaceae: Bryophyta). Mol Phylogenet Evol 49:304-317
67. Sloover JL (1975) Note de bryologie africaine III. Physcomitrella magdalenae sp. nov. Bull Jard Bot Natl Belg/Bull Natl Plant Belg 45:131-135
68. Smith AJE (1979) Cytogenetics, biosystematics and evolution in the Bryophyta. Adv Bot Res 6:195-276
69. Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60:561-588
70. Soltis PS, Soltis DE (2013) Angiosperm phylogeny: A framework for studies of genome evolution. In: Leitch IJ, Greilhuber J, Doležel J, Wendel JF (eds) Plant genome diversity, vol 2, Physical structure, behaviour and evolution of plant genomes. Springer-Verlag, Wien, pp 1-11
71. Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M (2003) Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Nucleic Acids Res 31:5324-5331
72. Szovenyi P, Rensing SA, Lang D, Wray GA, Shaw AJ (2010) Generation-biased gene expression in a bryophyte model system. Mol Biol Evol 2010:20
73. Tan BC (1978) Physcomitrella patens (Musci: Funariaceae) in North America. Bryologist 81:561-567
74. Tan BC (1979) A new classification for the genus Physcomitrella B.S. G. J Hattori Bot Lab 46:327-336
75. Tanahashi T, Sumikawa N, Kato M, Hasebe M (2005) Diversification of gene function: homologs of the floral regulator FLO/LFY control the first zygotic cell division in the moss Physcomitrella patens. Development 132:1727-1736
76. Taylor PJ, Eppley SM, Jesson LK (2007) Sporophytic inbreeding depression in mosses occurs in a species with separate sexes but not in a species with combined sexes. Am J Bot 94:1853-1859
77. Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N (2007) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol 24:699-709
78. Van de Peer Y, Maere S, Meyer A (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10:725-732
79. van Hoek MJ, Hogeweg P (2009) Metabolic adaptation after whole genome duplication. Mol Biol Evol 26:2441-2453
80. Veron AS, Kaufmann K, Bornberg-Bauer E (2007) Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins. Mol Biol Evol 24:670-678
81. Wang X, Tang H, Bowers JE, Feltus FA, Paterson AH (2007) Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics 177:1753-1763
82. Wellman CH, Osterloff PL, Mohiuddin U (2003) Fragments of the earliest land plants. Nature 425:282-285
83. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225-249
84. Wettstein F (1924) Gattungskreuzungen bei Moosen. Z Indukt Abstammungs-Vererbungsl 33:253-257
85. Wettstein F (1932) Genetik. In: Verdoorn F (ed) Manual of bryology. Nijhoff, The Hague, pp 233-272
86. Wyatt R, Odrzykoski IJ, Stoneburner A, Bass HW, Galau GA (1988) Allopolyploidy in bryophytes: multiple origins of Plagiomnium medium. Proc Natl Acad Sci USA 85:5601-5604
87. Wyatt R, Odrzykoski IJ, Stoneburner A (1992) Isozyme evidence of reticulate evolution in mosses: Plagiomnium medium is an allopolyploid of P. ellipticum × P. insigne. Syst Bot 17:532-550
88. Zimmer A, Lang D, Richardt S, Frank W, Reski R, Rensing SA (2007) Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Mol Genet Genomics 278:393-402
89. Zobell O, Faigl W, Saedler H, Munster T (2010) MIKC* MADS-box proteins: conserved regulators of the gametophytic generation of land plants. Mol Biol Evol 27:1201-1211