Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Mühlhausen, Stefanie ^a   Kollmar, Martin ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Myosin; Plant evolution; Whole genome duplication

Indexed keywords

AGE STRUCTURE; ANGIOSPERM; COTTON; EVOLUTIONARY BIOLOGY; GENOME; PHYLOGENETICS; PHYLOGENY; PROTEIN; TAXONOMY;

EMBRYOPHYTA; GOSSYPIUM; GOSSYPIUM RAIMONDII; LINUM USITATISSIMUM; MAGNOLIOPHYTA; MANIHOT ESCULENTA; NICOTIANA BENTHAMIANA; PHOENIX DACTYLIFERA;

MYOSIN; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; CLASSIFICATION; EVOLUTION; GENE DUPLICATION; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PLANT; PLANT GENOME;

AMINO ACID SEQUENCE; BIOLOGICAL EVOLUTION; GENE DUPLICATION; GENOME, PLANT; MOLECULAR SEQUENCE DATA; MYOSINS; PHYLOGENY; PLANT PROTEINS; PLANTS;

EID: 84884316711     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-202     Document Type: Article

References (72)

1. "Changing by doubling", the impact of whole genome duplications in the evolution of eukaryotes. Jaillon O, Aury J-M, Wincker P, C R Biol 2009 332 241 253 10.1016/j.crvi.2008.07.007 19281955
2. Consequences of genome duplication. Sémon M, Wolfe KH, Curr Opin Genet Dev 2007 17 505 512 10.1016/j.gde.2007.09.007 18006297 (Pubitemid 350186344)
3. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. D'Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Silva CD, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, et al. Nature 2012 488 213 217 10.1038/nature11241 22801500
4. The draft genome of a diploid cotton Gossypium raimondii. Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu Y-X, Wang J, Yu S, Nat Genet 2012 44 1098 1103 10.1038/ng.2371 22922876
5. The genome of the mesopolyploid crop species Brassica rapa. Wang X, Wang H, Wang J, et al. Nat Genet 2011 43 1035 1039 10.1038/ng.919 21873998
6. Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Fawcett JA, Maere S, Van de Peer Y, Proc Natl Acad Sci U S A 2009 106 5737 5742 10.1073/pnas.0900906106 19325131
7. A mystery unveiled. Van de Peer Y, Genome Biol 2011 12 113 10.1186/gb-2011-12-5-113 21635712
8. The genome of the domesticated apple (Malus × domestica Borkh.). Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Ri AD, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, et al. Nat Genet 2010 42 833 839 10.1038/ng.654 20802477
9. Genome sequence of the palaeopolyploid soybean. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, et al. Nature 2010 463 178 183 10.1038/nature08670 20075913
10. Polyploidy and genome restructuring: a variety of outcomes. Hufton AL, Panopoulou G, Curr Opin Genet Dev 2009 19 600 606 10.1016/j.gde.2009.10.005 19900800
11. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, et al. Nature 2007 449 463 467 10.1038/nature06148 17721507 (Pubitemid 47509545)
12. A genome triplication associated with early diversification of the core eudicots. Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GK-S, Soltis DE, Depamphilis CW, Genome Biol 2012 13 3 10.1186/gb-2012-13-1-r3 22280555
13. Unraveling Ancient Hexaploidy Through Multiply-Aligned Angiosperm Gene Maps. Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH, Genome Res 2008 18 1944 1954 10.1101/gr.080978.108 18832442
14. Ancestral polyploidy in seed plants and angiosperms. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, de Pamphilis CW, Nature 2011 473 97 100 10.1038/nature09916 21478875
15. The flowering world: a tale of duplications. Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K, Trends Plant Sci 2009 14 680 688 10.1016/j.tplants.2009.09.001 19818673
16. Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families. Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ, Syst Biol 2005 54 441 454 10.1080/10635150590945359 16012110 (Pubitemid 41040443)
17. Gene duplication within the Green Lineage: the case of TEL genes. Charon C, Bruggeman Q, Thareau V, Henry Y, J Exp Bot 2012 63 5061 5077 10.1093/jxb/ers181 22865910
18. A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method. Hatje K, Kollmar M, Front Plant Sci 2012 3 192 22952468
19. Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family. Sampedro J, Lee Y, Carey RE, de Pamphilis C, Cosgrove DJ, Plant J 2005 44 409 419 10.1111/j.1365-313X.2005.02540.x 16236151
20. Gene duplication and the evolution of plant MADS-box transcription factors. Airoldi CA, Davies B, J Genet Genomics 2012 39 157 165 10.1016/j.jgg.2012.02.008 22546537
21. Myosins: tails (and heads) of functional diversity. Krendel M, Mooseker MS, Physiology (Bethesda) 2005 20 239 251 10.1152/physiol.00014.2005 (Pubitemid 41215198)
22. Molecular motors. Schliwa M, Woehlke G, Nature 2003 422 759 765 10.1038/nature01601 12700770 (Pubitemid 36514119)
23. Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species. Odronitz F, Kollmar M, Genome Biol 2007 8 196 10.1186/gb-2007-8-9-r196 17877792 (Pubitemid 351895469)
24. CyMoBase-a database for cytoskeletal and motor proteins http://www.cymobase.org
25. Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase). Odronitz F, Kollmar M, BMC Genomics 2006 7 300 10.1186/1471-2164-7-300 17134497 (Pubitemid 44941453)
26. The greening of plant genomics. Pennisi E, Science 2007 317 317 317 10.1126/science.317.5836.317 17641179 (Pubitemid 47106346)
27. A myosin-like protein from a higher plant. Knight AE, Kendrick-Jones J, J Mol Biol 1993 231 148 154 10.1006/jmbi.1993.1266 7684453 (Pubitemid 23186607)
28. Molecular analysis of the myosin gene family in Arabidopsis thaliana. Kinkema M, Wang H, Schiefelbein J, Plant Mol Biol 1994 26 1139 1153 10.1007/BF00040695 7811972
29. A myosin from a higher plant has structural similarities to class V myosins. Kinkema M, Schiefelbein J, J Mol Biol 1994 239 591 597 10.1006/jmbi.1994.1400 8006972 (Pubitemid 24210430)
30. Expression, Splicing, and Evolution of the Myosin Gene Family in Plants. Peremyslov VV, Mockler TC, Filichkin SA, Fox SE, Jaiswal P, Makarova KS, Koonin EV, Dolja VV, Plant Physiol 2011 155 1191 1204 10.1104/pp.110.170720 21233331
31. Analysis of the myosins encoded in the recently completed Arabidopsis thaliana genome sequence. Reddy AS, Day IS, Genome Biol 2001 2 esearch0024.1 research0024.17 10.1186/gb-2001-2-7-research0024
32. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Stanke M, Morgenstern B, Nucleic Acids Res 2005 33 465 W467 10.1093/nar/gki458 15980513 (Pubitemid 44529963)
33. Prediction of complete gene structures in human genomic DNA. Burge C, Karlin S, J Mol Biol 1997 268 78 94 10.1006/jmbi.1997.0951 9149143 (Pubitemid 27192680)
34. Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio. Hatje K, Keller O, Hammesfahr B, Pillmann H, Waack S, Kollmar M, BMC Res Notes 2011 4 265 10.1186/1756-0500-4-265 21798037
35. Identification and molecular characterization of myosin gene family in Oryza sativa genome. Jiang S, Ramachandran S, Plant Cell Physiol 2004 45 590 599 10.1093/pcp/pch061 15169941 (Pubitemid 38791242)
36. A millennial myosin census. Berg JS, Powell BC, Cheney RE, Mol Biol Cell 2001 12 780 794 10.1091/mbc.12.4.780 11294886 (Pubitemid 33051978)
37. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Lagercrantz U, Genetics 1998 150 1217 1228 9799273 (Pubitemid 28510049)
38. SMART 7: recent updates to the protein domain annotation resource. Letunic I, Doerks T, Bork P, Nucleic Acids Res 2011 40 302 D305 22053084
39. The Pfam protein families database. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Nucleic Acids Res 2010 38 211 D222 10.1093/nar/gkp985 19920124
40. AF-6/cno: neither a kinesin nor a myosin, but a bit of both. Ponting CP, Trends Biochem Sci 1995 20 265 266 10.1016/S0968-0004(00)89040-4 7667878
41. Structural basis for myosin V discrimination between distinct cargoes. Pashkova N, Jin Y, Ramaswamy S, Weisman LS, EMBO J 2006 25 693 700 10.1038/sj.emboj.7600965 16437158 (Pubitemid 43292432)
42. The structure of the Myo4p globular tail and its function in ASH1 mRNA localization. Heuck A, Fetka I, Brewer DN, Hüls D, Munson M, Jansen R-P, Niessing D, J Cell Biol 2010 189 497 510 10.1083/jcb.201002076 20439999
43. WebLogo: a sequence logo generator. Crooks GE, Hon G, Chandonia JM, Brenner SE, Genome Res 2004 14 1188 1190 10.1101/gr.849004 15173120 (Pubitemid 38811555)
44. Rarely successful polyploids and their legacy in plant genomes. Arrigo N, Barker MS, Curr Opin Plant Biol 2012 15 140 146 10.1016/j.pbi.2012.03.010 22480430
45. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var "Ridge Pineapple": organization and phylogenetic relationships to other angiosperms. Bausher MG, Singh ND, Lee S-B, Jansen RK, Daniell H, BMC Plant Biol 2006 6 21 10.1186/1471-2229-6-21 17010212 (Pubitemid 44570355)
46. 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 P-F, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S-i, 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 64 69 10.1126/science.1150646 18079367
47. Widespread genome duplications throughout the history of flowering plants. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, de Pamphilis CW, Genome Res 2006 16 738 749 10.1101/gr.4825606 16702410 (Pubitemid 43830694)
48. DNA sequence evidence for the segmental allotetraploid origin of maize. Gaut BS, Doebley JF, PNAS 1997 94 6809 6814 10.1073/pnas.94.13.6809 11038553 (Pubitemid 27281946)
49. Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers. Missaoui AM, Paterson AH, Bouton JH, Theor Appl Genet 2005 110 1372 1383 10.1007/s00122-005-1935-6 15841364 (Pubitemid 40919999)
50. Patterns of evolution in western North American Mimulus (Phrymaceae). Beardsley PM, Schoenig SE, Whittall JB, Olmstead RG, Am J Bot 2004 91 474 489 10.3732/ajb.91.3.474 21653403 (Pubitemid 38370892)
51. The tomato genome sequence provides insights into fleshy fruit evolution. Consortium TTG, Nature 2012 485 635 641 10.1038/nature11119 22660326
52. Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana. Schlueter JA, Scheffler BE, Jackson S, Shoemaker RC, J Hered 2008 99 390 395 10.1093/jhered/esn010 18316321
53. Genome Duplication in Soybean (Glycine Subgenus Soja). Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR, Genetics 1996 144 329 338 8878696 (Pubitemid 26291940)
54. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Tuskan GA, DiFazio S, Jansson S, et al. Science 2006 313 1596 1604 10.1126/science.1128691 16973872 (Pubitemid 44414027)
55. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK-S, Wang J, Deyholos MK, Plant J 2012 72 461 473 10.1111/j.1365-313X.2012. 05093.x 22757964
56. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Bowers JE, Chapman BA, Rong J, Paterson AH, Nature 2003 422 433 438 10.1038/nature01521 12660784 (Pubitemid 36411396)
57. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Tang H, Bowers JE, Wang X, Paterson AH, PNAS 2010 107 472 477 10.1073/pnas.0908007107 19966307
58. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang M-L, Zhu YJ, et al. Nature 2008 452 991 996 10.1038/nature06856 18432245 (Pubitemid 351606145)
59. Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids. Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M, Plant Physiol 2008 148 1772 1781 10.1104/pp.108.124867 18952863 (Pubitemid 352847452)
60. The evolution of gene duplications: classifying and distinguishing between models. Innan H, Kondrashov F, Nat Rev Genet 2010 11 97 108 20051986
61. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo M, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee T, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, et al. Nature 2012 492 423 427 10.1038/nature11798 23257886
62. Insights into salt tolerance from the genome of Thellungiella salsuginea. Wu H-J, Zhang Z, Wang J-Y, Oh D-H, Dassanayake M, Liu B, Huang Q, Sun H-X, Xia R, Wu Y, Wang Y-N, Yang Z, Liu Y, Zhang W, Zhang H, Chu J, Yan C, Fang S, Zhang J, Wang Y, Zhang F, Wang G, Lee SY, Cheeseman JM, Yang B, Li B, Min J, Yang L, Wang J, Chu C, et al. Proc Natl Acad Sci U S A 2012 109 12219 12224 10.1073/pnas.1209954109 22778405
63. The Reference Genome of the Halophytic Plant Eutrema salsugineum. Yang R, Jarvis DE, Chen H, Beilstein MA, Grimwood J, Jenkins J, Shu S, Prochnik S, Xin M, Ma C, Schmutz J, Wing RA, Mitchell-Olds T, Schumaker KS, Wang X, Front Plant Sci 2013 4 46 23518688
64. WebScipio: an online tool for the determination of gene structures using protein sequences. Odronitz F, Pillmann H, Keller O, Waack S, Kollmar M, BMC Genomics 2008 9 422 10.1186/1471-2164-9-422 18801164
65. Multiple sequence alignment using ClustalW and ClustalX. Thompson JD, Gibson TJ, Higgins DG, Curr Protoc Bioinformatics 2002 Chapter 2 nit 2 3
66. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Li W, Godzik A, Bioinformatics 2006 22 1658 1659 10.1093/bioinformatics/btl158 16731699 (Pubitemid 43985301)
67. A rapid bootstrap algorithm for the RAxML Web servers. Stamatakis A, Hoover P, Rougemont J, Syst Biol 2008 57 758 771 10.1080/10635150802429642 18853362
68. ProtTest 3: fast selection of best-fit models of protein evolution. Darriba D, Taboada GL, Doallo R, Posada D, Bioinformatics 2011 27 1164 1165 10.1093/bioinformatics/btr088 21335321
69. MrBayes 3: Bayesian phylogenetic inference under mixed models. Ronquist F, Huelsenbeck JP, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/ btg180 12912839 (Pubitemid 37038874)
70. A new approach to protein fold recognition. Jones DT, Taylor WR, Thornton JM, Nature 1992 358 86 89 10.1038/358086a0 1614539
71. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Letunic I, Bork P, Bioinformatics 2007 23 127 128 10.1093/bioinformatics/btl529 17050570 (Pubitemid 46017867)
72. Hammesfahr B. Odronitz F.Mühlhausen S.Waack S.Kollmar M.