Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex

BMC Evolutionary Biology

Volumn 14, Issue 1, 2014, Pages

  Beike, Anna K ^a   Von Stackelberg, Mark ^a,b   Schallenberg Rüdinger, Mareike ^f   Hanke, Sebastian T ^a,f   Follo, Marie ^d   Quandt, Dietmar ^c   McDaniel, Stuart F ^e   Reski, Ralf ^a   Tan, Benito C ^g   Rensing, Stefan A ^a,f  

^a UNIVERSITY OF FREIBURG   (Germany)

^b Käthe Kollwitz Schule   (Germany)

^c UNIVERSITY OF BONN   (Germany)

^d UNIVERSITY OF FREIBURG   (Germany)

^e UNIVERSITY OF FLORIDA   (United States)

^f PHILIPPS UNIVERSITY MARBURG   (Germany)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Funariaceae; Hybridization; Physcomitrella patens; Polyploidization; Speciation

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; BRYOPSIDA; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETIC VARIABILITY; GENETICS; HYBRIDIZATION; MOLECULAR CLONING; MOLECULAR GENETICS; PHYLOGENY; POLYPLOIDY;

BIOLOGICAL EVOLUTION; BRYOPSIDA; CLONING, MOLECULAR; GENETIC VARIATION; HYBRIDIZATION, GENETIC; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYPLOIDY; SEQUENCE ANALYSIS, DNA;

CONVERGENT EVOLUTION; DISPERSAL; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; HYBRIDIZATION; MOLECULAR ANALYSIS; MOSS; POLYPLOIDY; SPECIATION (BIOLOGY);

AVES; BRYOPHYTA; FUNARIA HYGROMETRICA; FUNARIACEAE; PHYSCOMITRELLA; PHYSCOMITRELLA PATENS; PHYSCOMITRELLA READERI; PHYSCOMITRIUM;

EID: 84904083562     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-14-158     Document Type: Article

References (71)

1. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, 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, et al. Science 2008 319 5859 64 69 10.1126/science.1150646 18079367
2. Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R, BMC Genomics 2013 14 498 10.1186/1471-2164-14-498 23879659
3. Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M, Nucleic Acids Res 2003 31 18 5324 5331 10.1093/nar/gkg726 12954768 (Pubitemid 37441900)
4. The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N, Mol Biol Evol 2007 24 3 699 709 17175527 (Pubitemid 46355794)
5. A new classification for the genus Physcomitrella B.S.G. Tan BC, J Hattori Bot Lab 1979 46 327 336
6. Wijk R, Index Muscorum Utrecht, NL: Regnum Vegetabile 1959 1959 1969
7. Physcomitrella patens (Musci: Funariaceae) in North America. Tan BC, The Bryologist 1978 81 4 561 567 10.2307/3242342
8. A revision of the family Funariaceae (Musci) in Japan and the adjacent regions. Ochi H, Jap J Bot 1968 20 1 34
9. Neue und bemerkenswerte Moosfunde aus Zaire. Mueller F, Trop Bryology 1995 10 81 90
10. Note de bryologie africaine III.-Physcomitrella magdalenae sp. nov. Sloover JL, Bulletin du Jardin botanique national de Belgique/Bulletin van de National Plantentuin van België 1975 45 1/2 131 135 10.2307/3667591
11. Phylogenetic inference rejects sporophyte based classification of the Funariaceae (Bryophyta): rapid radiation suggests rampant homoplasy in sporophyte evolution. Liu Y, Budke JM, Goffinet B, Mol Phylogenet Evol 2012 62 1 130 145 10.1016/j.ympev.2011.09.010 21971055
12. The speciation history of the Physcomitrium-Physcomitrella species complex. McDaniel SF, von Stackelberg M, Richardt S, Quatrano RS, Reski R, Rensing SA, Evolution 2010 64 1 217 231 10.1111/j.1558-5646.2009.00797.x 19659592
13. BRICK1 is required for apical cell growth in filaments of the moss Physcomitrella patens but not for gametophore morphology. Perroud PF, Quatrano RS, Plant Cell 2008 20 2 411 422 10.1105/tpc.107.053256 18263777 (Pubitemid 352844021)
14. The induction of biochemical and morphological mutants in the moss Physcomitrella patens. Engel PP, Am J Bot 1968 55 4 438 446 10.2307/2440573
15. Genome analysis of the moss Physcomitrella patens (Hedw.) B.S.G. Reski R, Faust M, Wang XH, Wehe M, Abel WO, Mol Gen Genet 1994 244 4 352 359 8078460 (Pubitemid 24266093)
16. The Physcomitrella patens genome-a first stepping stone towards understanding bryophyte and land plant evolution. Beike AK, Rensing SA, Trop Bryology 2010 31 43 49
17. Frahm J-P, Biologie der Moose Heidelberg, Berlin: Spektrum Akademischer Verlag 2001
18. Fritsch R, Index To Bryophyte Chromosome Counts, vol. 40 Berlin, Stuttgart: J. Cramer/Gebrueder Borntraeger 1991
19. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. What is the role of genome duplication in the evolution of complexity and diversity? Crow KD, Wagner GP, Mol Biol Evol 2006 23 5 887 892 10.1093/molbev/msj083 16368775 (Pubitemid 43726052)
20. Ohno S, Evolution by gene duplication New York: Springer 1970
21. The role of hybridization in plant speciation. Soltis PS, Soltis DE, Annu Rev Plant Biol 2009 60 561 588 10.1146/annurev.arplant.043008.092039 19575590
22. The evolutionary significance of ancient genome duplications. Van de Peer Y, Maere S, Meyer A, Nat Rev Genet 2009 10 10 725 732 10.1038/nrg2600 19652647
23. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R, BMC Evol Biol 2007 7 1 130 10.1186/1471-2148-7-130 17683536 (Pubitemid 47329460)
24. Gattungskreuzungen bei Moosen. Wettstein F, Z Indukt Abstammungs- Vererbungsl 1924 33 253 257
25. Genetik. Wettstein F, Manual of Bryology Hague: The Netherlands: (ed. F. Verdoorn). Martinus Niehoff, Verdoorn F, 1932 233 272
26. What do we know about hybridization among bryophytes in nature? Natcheva R, Cronberg N, Can J Bot 2004 82 1687 1704 10.1139/b04-139 (Pubitemid 40335750)
27. Evolutionary importance of generative polyploidy for genome evolution of haploid-dominant land plants. Rensing SA, Beike AK, Lang D, Greilhuber J, Wendel JF, Leitch IJ, Doležel J, Plant Genome Diversity vol. in press. Vienna, New York: Springer; 2012
28. A new hybrid in Physcomitrium. Andrews AL, Torreya 1918 18 52 54
29. Taxonomic notes. II. Another natural hybrid in the Funariaceae. Andrews AL, The Bryologist 1942 45 6 176 178 10.1639/0007-2745(1942)45[176:TNIANH]2.0. CO;2
30. Contributions to American Bryology IX. Britton EG, Bulletin of the Torrey Botanical Club 1895 22 2 62 68 10.2307/2478381
31. Hybrid sporophytes in Funariaceae. I. Hybrid sporophytes on Physcomitrella patens (Hedw.) B. & S., and Physcomitrium sphaericum (Schkuhr) Brid. in Britain. Pettet A, Trans Br Bryol Soc 1964 4 642 648 10.1179/006813864804812164
32. RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V, Mol Genet Genomics 2009 24 24
33. Chloroplast ribosomal S14 protein transcript is edited to create a translation initiation codon in the moss Physcomitrella patens. Miyata Y, Sugiura C, Kobayashi Y, Hagiwara M, Sugita M, Biochim Biophys Acta 2002 1576 3 346 349 10.1016/S0167-4781(02)00346-9 12084583 (Pubitemid 34655779)
34. Assigning DYW-type PPR proteins to RNA editing sites in the funariid mosses Physcomitrella patens and Funaria hygrometrica. Rüdinger M, Szovenyi P, Rensing SA, Knoop V, Plant J 2011 67 2 370 380 10.1111/j.1365-313X.2011. 04600.x 21466601
35. Axenic bryophyte in vitro cultivation. Beike AK, Horst NA, Rensing SA, Endocyt Cell Res 2010 20 102 108
36. In vitro studies in abnormal growth of prothalli of the brachen fern. Steeves TA, Sussex IM CRP, Am J Bot 1955 42 232 245 10.2307/2438559
37. Induction of budding on chloronemata and caulonemata of the moss, Physcomitrella patens, using isopentenyladenine. Reski R, Abel WO, Planta 1985 165 3 354 358 10.1007/BF00392232 24241140
38. Isolation of plant DNA from fresh tissue. Doyle JJ, Doyle JL, Focus 1990 12 13 15
39. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. Edgar RC, BMC Bioinformatics 2004 5 113 10.1186/1471-2105-5-113 15318951 (Pubitemid 40195393)
40. The Jalview Java alignment editor. Clamp M, Cuff J, Searle SM, Barton GJ, Bioinformatics 2004 20 3 426 427 10.1093/bioinformatics/btg430 14960472 (Pubitemid 38262778)
41. Frickenhaus S, Beszteri B, Quicktree-SD 2008
42. QuickTree: building huge Neighbour-Joining trees of protein sequences. Howe K, Bateman A, Durbin R, Bioinformatics 2002 18 11 1546 1547 10.1093/bioinformatics/18.11.1546 12424131 (Pubitemid 35422615)
43. MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839 (Pubitemid 37038874)
44. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Schmidt HA, Strimmer K, Vingron M, von Haeseler A, Bioinformatics 2002 18 3 502 504 10.1093/bioinformatics/18.3.502 11934758 (Pubitemid 34284960)
45. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Edwards K, Johnstone C, Thompson C, Nucleic Acids Res 1991 19 6 1349 10.1093/nar/19.6.1349 2030957
46. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 10 2731 2739 10.1093/molbev/msr121 21546353
47. PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation. Lenz H, Knoop V, Bioinform Biol Insights 2013 7 1 19 23362369
48. Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. von Stackelberg M, Rensing SA, Reski R, BMC Plant Biol 2006 6 9 10.1186/1471-2229-6-9 16734891 (Pubitemid 44166638)
49. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. Nei M, Tajima F, Tateno Y, J Mol Evol 1983 19 2 153 170 10.1007/BF02300753 6571220 (Pubitemid 13042712)
50. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 4 406 425 3447015
51. Langella O, Populations 1.2.28. Population Genetic Software (Individuals or Populations Distances, Phylogenetic Trees) available at http://www. bioinformatics.org/downloads/index.php?file-id=538. 2002
52. Application of phylogenetic networks in evolutionary studies. Huson DH, Bryant D, Mol Biol Evol 2006 23 2 254 267 16221896 (Pubitemid 43100040)
53. Unique tissue-specific cell cycle in Physcomitrella. Schween G, Gorr G, Hohe A, Reski R, Plant Biol 2003 5 1 50 58 10.1055/s-2003-37984 (Pubitemid 36435019)
54. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines. Perroud PF, Cove DJ, Quatrano RS, McDaniel SF, New Phytol 2011 2 10 1469 8137
55. Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Ungerer MC, Strakosh SC, Zhen Y, Curr Biol 2006 16 20 872 R873 10.1016/j.cub.2006.09.020 17055967 (Pubitemid 44573827)
56. The evolutionary fate and consequences of duplicate genes. Lynch M, Conery JS, Science 2000 290 1151 1155 10.1126/science.290.5494.1151 11073452
57. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. Flagel L, Udall J, Nettleton D, Wendel J, BMC Biol 2008 6 16 10.1186/1741-7007-6-16 18416842 (Pubitemid 351594157)
58. Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium). Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF, Genetics 2009 182 2 503 517 10.1534/genetics.109.102608 19363125
59. Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. Flagel LE, Wendel JF, New Phytol 2010 186 1 184 193 10.1111/j.1469-8137.2009.03107.x 20002320
60. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF, Mol Biol Evol 2003 20 4 633 643 10.1093/molbev/msg065 12679546 (Pubitemid 36437913)
61. Targeted gene disruption identifies three PPR-DYW proteins involved in RNA editing for five editing sites of the moss mitochondrial transcripts. Ohtani S, Ichinose M, Tasaki E, Aoki Y, Komura Y, Sugita M, Plant Cell Physiol 2010 51 11 1942 1949 10.1093/pcp/pcq142 20837503
62. Dating The Diversification Of The Pleurocarpous Mosses. Newton AE, Wikström N, Bell N, Forrest LL, Ignatov MS, Pleurocarpous mosses: Systematics and Evolution Boca Raton: Systematics Association: CRC Press, Tangney N, vol. Special Volume 71. 2006
63. MIKC* MADS-box proteins: conserved regulators of the gametophytic generation of land plants. Zobell O, Faigl W, Saedler H, Munster T, Mol Biol Evol 2010 27 5 1201 1211 10.1093/molbev/msq005 20080864
64. Bryophyte Ecology. Glime JM, Volume 1 Physiological Ecology, Glime JM, 2007 vol. 1: Ebook sponsored by Michigan Technological University and the International Association of Bryologists
65. Sexual life cycle of three species of Funariaceae in culture. Nakosteen PC, Hughes KW, Bryologist 1978 81 307 314 10.2307/3242191
66. Selective sweeps and intercontinental migration in the cosmopolitan moss Ceratodon purpureus (Hedw.) Brid. McDaniel SF, Shaw AJ, Mol Ecol 2005 14 1121 1132 10.1111/j.1365-294X.2005.02484.x 15773940 (Pubitemid 40466239)
67. First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds. Lewis LR, Behling E, Gousse H, Qian E, Elphick CS, Lamarre JF, Bety J, Liebezeit J, Rozzi R, Goffinet B, PeerJ 2014 2 424 24949241
68. Boere GC, Stroud DA, The Flyway Concept: What It Is And What It Isn't Edinburgh, UK: The Stationery Office 2006
69. Ephemerella readeri Müll. Hal. (Physcomitrella readeri (Müll. Hal.) I.G. Stone & G.A.M. Scott, Funariidae, Bryophyta): a genus and species new to Europe. Hooper EJ, Duckett JG, Cuming AC, Kunin WE, Pressel S, J Bryol 2010 32 256 264 10.1179/037366810X12814321877589
70. Adaptive Modes of the Moss Sporophyte. Vitt DH, The Bryologist 1981 84 2 166 186 10.2307/3242820
71. A sequence-anchored genetic linkage map for the moss, Physcomitrella patens. Kamisugi Y, von Stackelberg M, Lang D, Care M, Reski R, Rensing SA, Cuming AC, Plant J 2008 56 5 855 866 10.1111/j.1365-313X.2008.03637.x 18657236