Back to the sea twice: Identifying candidate plant genes for molecular evolution to marine life

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Wissler, Lothar ^a   Codõer, Francisco M ^b   Gu, Jenny ^a   Reusch, Thorsten Bh ^c   Olsen, Jeanine L ^d   Procaccini, Gabriele ^e   Bornberg Bauer, Erich ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b HOSPITAL UNIVERSITARI GERMANS TRIAS I PUJOL   (Spain)

^c GEOMAR HELMHOLTZ CENTRE FOR OCEAN RESEARCH KIEL   (Germany)

^d UNIVERSITY OF GRONINGEN   (Netherlands)

^e STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ANCESTRY; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; MARINE ECOSYSTEM; MOLECULAR ANALYSIS; PARALLEL EVOLUTION; PHYLOGENETICS; SEAGRASS;

MAGNOLIOPHYTA; POSIDONIA OCEANICA; ZOSTERA MARINA;

VEGETABLE PROTEIN;

ALISMATIDAE; AQUATIC SPECIES; ARTICLE; CLASSIFICATION; GENETICS; MARINE BIOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; SEA;

ALISMATIDAE; AQUATIC ORGANISMS; EVOLUTION, MOLECULAR; MARINE BIOLOGY; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; PLANT PROTEINS;

EID: 78651226508     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-8     Document Type: Article

References (81)

1. H Lambers FS Chapin TL Pons, Plant Physiological Ecology Berlin: Springer 1998
2. C den Hartog, The seagrasses of the world Amsterdam: North-Holland Publishing Company 1970
3. M Waycott G Procaccini DH Les TBH Reusch, Seagrasses: Biology, Ecology and Conservation. Seagrass Evolution, Ecology and Conservation: A Genetic Perspective Berlin: Springer 2006
4. Phylogenetic Studies in Alismatidae, II: Evolution of Marine Angiosperms (Seagrasses) and Hydroph (Pubitemid 28111173)
5. Light gradients and meadow structure in Posidonia oceanica: ecomorphological and functional correlates. J Dalla Via C Sturmbauer G Schönweger E Sötz S Mathekowitsch M Stifter R Rieger, Marine Ecology Progress Series 1998 163 267 278 10.3354/meps163267 (Pubitemid 28178585)
6. A Global Crisis for Seagrass Ecosystems. RJ Orth TJB Carruthers WC Dennison CM Duarte JW Fourqurean KLH Jr AR Hughes S Olyarnik SL Williams GA Kendrick WJ Kenworthy FT Short M Waycott, BioOne 2006 56 12 987 996 (Pubitemid 44927722)
7. Assessing water quality with submersed aquatic vegetation. WC Dennison RJ Orth KA Moore JC Stevenson V Carter S Kollar PW Bergstrom RA Batiuk, BioScience 1993 43 2 86 94 10.2307/1311969
8. Are seagrass growth and survival constrained by the reducing conditions of the sediment? J Terrados CM Duarte L Kamp-Nielsen NSR Agawin E Gacia D Lacap MD Fortes J Borum M Lubanski T Greve, Aquatic Botany 1999 65 1-4 175 197 10.1016/S0304-3770(99)00039-X
9. Overview of the physiological ecology of carbon metabolism in seagrasses. Touchette Burkholder, J Exp Mar Bio Ecol 2000 250 1-2 169 205 10.1016/S0022-0981(00)00196-9 10969168
10. Water-pollinated plants. PA Cox, Sci Am 1993 269 4 50 56 10.1038/scientificamerican1093-50 8235550
11. The acquisition of inorganic carbon by the seagrass Zostera marina. S Beer J Rehnberg, Aquatic Botany 1997 56 277 283 10.1016/S0304-3770(96)01109-6 (Pubitemid 27197772)
12. Bicarbonate utilization in seagrass photosynthesis: role of carbonic anhydrase in Posidonia oceanica (L.) Delile and Cymodocea nodosa (Ucria) Ascherson. O Invers M Pérez J Romero, J Exp Mar Bio Ecol 1999 235 125 133 10.1016/S0022-0981(98)00172-5 (Pubitemid 29125043)
13. Is any angiosperm an obligate halophyte? MG Barbour, Am Midl Nat 1970 84 105 120 10.2307/2423730
14. BH McConnaughey, Introduction to Marine Biology St. Louis, Missouri: Mosby Company 1978
15. Salinity response of the seagrass Amphibolis antarctica (Labill.) Sonder et Aschers: an experimental validation of field results. DI Walker AJ McComb, Aquatic Botany 1990 36 359 366 10.1016/0304-3770(90)90052-M
16. H Marschner, Mineral Nutrition of Higher Plants London: Academic Press 1995
17. Effects of salt stress on basic processes of photosynthesis. P Sudhir SDS Murthy, Photosynthetica 2004 42 481 486 10.1007/S11099-005-0001-6 (Pubitemid 40580347)
18. Evolution of aquatic angiosperm reproductive systems. CT Philbrick DH Les, BioScience 1996 46 813 826 10.2307/1312967
19. J Kuo C den Hartog, Seagrasses: Biology, Ecology and Conservation Seagrass Morphology, Anatomy, and Ultrastructure, Dordrecht Netherlands: Springer 2006
20. Convergent evolution: the need to be explicit. RF Doolittle, Trends Biochem Sci 1994 19 15 18 10.1016/0968-0004(94)90167-8 8140615 (Pubitemid 24028725)
21. Parallel genotypic adaptation: when evolution repeats itself. TE Wood JM Burke LH Rieseberg, Genetica 2005 123 1-2 157 170 10.1007/s10709-003-2738-9 15881688 (Pubitemid 40466126)
22. Adaptive gene expression divergence inferred from population genomics. AK Holloway MKN Lawniczak JG Mezey DJ Begun CD Jones, PLoS Genet 2007 3 10 2007 2013 10.1371/journal.pgen.0030187 17967066 (Pubitemid 350072063)
23. Evidence for widespread adaptive evolution of gene expression in budding yeast. HB Fraser AM Moses EE Schadt, Proc Natl Acad Sci USA 2010 107 7 2977 2982 10.1073/pnas.0912245107 20133628
24. C4 Photosynthesis evolved in grasses via parallel adaptive genetic changes. PA Christin N Salamin V Savolainen MR Duvall G Besnard, Curr Biol 2007 17 14 1241 1247 10.1016/j.cub.2007.06.036 17614282 (Pubitemid 47053908)
25. Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. PA Christin N Salamin AM Muasya EH Roalson F Russier G Besnard, Mol Biol Evol 2008 25 11 2361 2368 10.1093/molbev/msn178 18695049
26. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. J Zhang, Nat Genet 2006 38 7 819 823 10.1038/ng1812 16767103 (Pubitemid 43980604)
27. Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. ME Protas C Hersey D Kochanek Y Zhou H Wilkens WR Jeffey LI Zon R Borowsky CJ Tabin, Nat Genet 2006 38 107 111 10.1038/ng1700 16341223 (Pubitemid 43011890)
28. Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution. HH Zakon Y Lu DJ Zwickl DM Hillis, Proc Natl Acad Sci USA 2006 103 10 3675 3680 10.1073/pnas.0600160103 16505358 (Pubitemid 43376614)
29. Comparative analysis of Expressed Sequence Tag (EST) libraries in the seagrass Zostera marina subjected to temperature stress. TBH Reusch AS Veron C Preuss J Weiner L Wissler A Beck S Klages M Kube R Reinhardt E Bornberg-Bauer, Mar Biotechnol (NY) 2008 10 3 297 309 10.1007/s10126-007-9065-6 18239962
30. The Ka/Ks ratio: diagnosing the form of sequence evolution. LD Hurst, Trends Genet 2002 18 9 486 10.1016/S0168-9525(02)02722-1 12175810
31. Statistical methods for detecting molecular adaptation. Yang Bielawski, Trends Ecol Evol 2000 15 12 496 503 10.1016/S0169-5347(00)01994-7 11114436
32. TimeTree: a public knowledge-base of divergence times among organisms. SB Hedges J Dudley S Kumar, Bioinformatics 2006 22 23 2971 2972 10.1093/bioinformatics/btl505 17021158 (Pubitemid 44811578)
33. Early Cretaceous lineages of monocot flowering plants. K Bremer, Proc Natl Acad Sci USA 2000 97 9 4707 4711 10.1073/pnas.080421597 10759567 (Pubitemid 30238622)
34. The age of major monocot groups inferred from 800+ rbcL sequences. T Janssen K Bremer, Bot J Linn Soc 2004 146 385 398 10.1111/j.1095-8339.2004. 00345.x (Pubitemid 40033205)
35. C Anderson T Janssen, The Timetree of Life Monocots, Oxford University Press 2009
36. The B73 maize genome: complexity, diversity, and dynamics. PS Schnable D Ware RS Fulton JC Stein F Wei S Pasternak C Liang J Zhang L Fulton TA Graves P Minx AD Reily L Courtney SS Kruchowski C Tomlinson C Strong K Delehaunty C Fronick B Courtney SM Rock E Belter F Du K Kim RM Abbott M Cotton A Levy P Marchetto K Ochoa SM Jackson B Gillam W Chen L Yan J Higginbotham M Cardenas J Waligorski E Applebaum L Phelps J Falcone K Kanchi T Thane A Scimone N Thane J Henke T Wang J Ruppert N Shah K Rotter J Hodges E Ingenthron M Cordes S Kohlberg J Sgro B Delgado K Mead A Chinwalla S Leonard K Crouse K Collura D Kudrna J Currie R He A Angelova S Rajasekar T Mueller R Lomeli G Scara A Ko K Delaney M Wissotski G Lopez D Campos M Braidotti E Ashley W Golser H Kim S Lee J Lin Z Dujmic W Kim J Talag A Zuccolo C Fan A Sebastian M Kramer L Spiegel L Nascimento T Zutavern B Miller C Ambroise S Muller W Spooner A Narechania L Ren S Wei S Kumari B Faga MJ Levy L McMahan PV Buren MW Vaughn K Ying CT Yeh SJ Emrich Y Jia A Kalyanaraman AP Hsia WB Barbazuk RS Baucom TP Brutnell NC Carpita C Chaparro JM Chia JM Deragon JC Estill Y Fu JA Jeddeloh Y Han H Lee P Li DR Lisch S Liu Z Liu DH Nagel MC McCann P SanMiguel AM Myers D Nettleton J Nguyen BW Penning L Ponnala KL Schneider DC Schwartz A Sharma C Soderlund NM Springer Q Sun H Wang M Waterman R Westerman TK Wolfgruber L Yang Y Yu L Zhang S Zhou Q Zhu JL Bennetzen RK Dawe J Jiang N Jiang GG Presting SR Wessler S Aluru RA Martienssen SW Clifton WR McCombie RA Wing RK Wilson, Science 2009 326 5956 1112 1115 10.1126/science.1178534 19965430
37. The Sorghum bicolor genome and the diversification of grasses. AH Paterson JE Bowers R Bruggmann I Dubchak J Grimwood H Gundlach G Haberer U Hellsten T Mitros A Poliakov J Schmutz M Spannagl H Tang X Wang T Wicker AK Bharti J Chapman FA Feltus U Gowik IV Grigoriev E Lyons CA Maher M Martis A Narechania RP Otillar BW Penning AA Salamov Y Wang L Zhang NC Carpita M Freeling AR Gingle CT Hash B Keller P Klein S Kresovich MC McCann R Ming DG Peterson M ur Rahman D Ware P Westhoff KFX Mayer J Messing DS Rokhsar, Nature 2009 457 7229 551 556 10.1038/nature07723 19189423
38. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). J Yu S Hu J Wang GKS Wong S Li B Liu Y Deng L Dai Y Zhou X Zhang M Cao J Liu J Sun J Tang Y Chen X Huang W Lin C Ye W Tong L Cong J Geng Y Han L Li W Li G Hu X Huang W Li J Li Z Liu L Li J Liu Q Qi J Liu L Li T Li X Wang H Lu T Wu M Zhu P Ni H Han W Dong X Ren X Feng P Cui X Li H Wang X Xu W Zhai Z Xu J Zhang S He J Zhang J Xu K Zhang X Zheng J Dong W Zeng L Tao J Ye J Tan X Ren X Chen J He D Liu W Tian C Tian H Xia Q Bao G Li H Gao T Cao J Wang W Zhao P Li W Chen X Wang Y Zhang J Hu J Wang S Liu J Yang G Zhang Y Xiong Z Li L Mao C Zhou Z Zhu R Chen B Hao W Zheng S Chen W Guo G Li S Liu M Tao J Wang L Zhu L Yuan H Yang, Science 2002 296 5565 79 92 10.1126/science.1068037 11935017 (Pubitemid 34280064)
39. Genome sequencing and analysis of the model grass Brachypodium distachyon. International Brachypodium Initiative, Nature 2010 463 7282 763 768 10.1038/nature08747 20148030
40. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Arabidopsis Genome Initiative, Nature 2000 408 6814 796 815 10.1038/35048692 11130711
41. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). GA Tuskan S Difazio S Jansson J Bohlmann I Grigoriev U Hellsten N Putnam S Ralph S Rombauts A Salamov J Schein L Sterck A Aerts RR Bhalerao RP Bhalerao D Blaudez W Boerjan A Brun A Brunner V Busov M Campbell J Carlson M Chalot J Chapman GL Chen D Cooper PM Coutinho J Couturier S Covert Q Cronk R Cunningham J Davis S Degroeve A Dejardin C Depamphilis J Detter B Dirks I Dubchak S Duplessis J Ehlting B Ellis K Gendler D Goodstein M Gribskov J Grimwood A Groover L Gunter B Hamberger B Heinze Y Helariutta B Henrissat D Holligan R Holt W Huang N Islam-Faridi S Jones M Jones-Rhoades R Jorgensen C Joshi J Kangasjärvi J Karlsson C Kelleher R Kirkpatrick M Kirst A Kohler U Kalluri F Larimer J Leebens-Mack JC Leple P Locascio Y Lou S Lucas F Martin B Montanini C Napoli DR Nelson C Nelson K Nieminen O Nilsson V Pereda G Peter R Philippe G Pilate A Poliakov J Razumovskaya P Richardson C Rinaldi K Ritland P Rouzé D Ryaboy J Schmutz J Schrader B Segerman H Shin A Siddiqui F Sterky A Terry CJ Tsai E Uberbacher P Unneberg J Vahala K Wall S Wessler G Yang T Yin C Douglas M Marra G Sandberg YV de Peer D Rokhsar, Science 2006 313 5793 1596 1604 10.1126/science.1128691 16973872 (Pubitemid 44414027)
42. Sequencing the genespaces of Medicago truncatula and Lotus japonicus. ND Young SB Cannon S Sato D Kim DR Cook CD Town BA Roe S Tabata, Plant Physiol 2005 137 4 1174 1181 10.1104/pp.104.057034 15824279 (Pubitemid 43119318)
43. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. O'Jaillon JM Aury B Noel A Policriti C Clepet A Casagrande N Choisne S Aubourg N Vitulo C Jubin A Vezzi F Legeai P Hugueney C Dasilva D Horner E Mica D Jublot J Poulain C Bruyére A Billault B Segurens M Gouyvenoux E Ugarte F Cattonaro V Anthouard V Vico CD Fabbro M Alaux GD Gaspero V Dumas N Felice S Paillard I Juman M Moroldo S Scalabrin A Canaguier IL Clainche G Malacrida E Durand G Pesole V Laucou P Chatelet D Merdinoglu M Delledonne M Pezzotti A Lecharny C Scarpelli F Artiguenave ME Pé G Valle M Morgante M Caboche AF Adam-Blondon J Weissenbach F Quétier P Wincker for Grapevine Genome Characterization FIPC, Nature 2007 449 7161 463 467 10.1038/nature06148 17721507
44. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. SA Rensing D Lang AD Zimmer A Terry A Salamov H Shapiro T Nishiyama PF Perroud EA Lindquist Y Kamisugi T Tanahashi K Sakakibara T Fujita K Oishi T Shin-I Y Kuroki A Toyoda Y Suzuki SI Hashimoto K Yamaguchi S Sugano Y Kohara A Fujiyama A Anterola S Aoki N Ashton WB Barbazuk E Barker JL Bennetzen R Blankenship SH Cho SK Dutcher M Estelle JA Fawcett H Gundlach K Hanada A Heyl KA Hicks J Hughes M Lohr K Mayer A Melkozernov T Murata DR Nelson B Pils M Prigge B Reiss T Renner S Rombauts PJ Rushton A Sanderfoot G Schween SH Shiu K Stueber FL Theodoulou H Tu YV de Peer PJ Verrier E Waters A Wood L Yang D Cove AC Cuming M Hasebe S Lucas BD Mishler R Reski IV Grigoriev RS Quatrano JL Boore, Science 2008 319 5859 64 69 10.1126/science.1150646 18079367
45. The Chlamydomonas genome reveals the evolution of key animal and plant functions. SS Merchant SE Prochnik O Vallon EH Harris SJ Karpowicz GB Witman A Terry A Salamov LK Fritz-Laylin L Maréchal-Drouard WF Marshall LH Qu DR Nelson AA Sanderfoot MH Spalding VV Kapitonov Q Ren P Ferris E Lindquist H Shapiro SM Lucas J Grimwood J Schmutz P Cardol H Cerutti G Chanfreau CL Chen V Cognat MT Croft R Dent S Dutcher E Fernndez H Fukuzawa D Gonzlez-Ballester D Gonzlez-Halphen A Hallmann M Hanikenne M Hippler W Inwood K Jabbari M Kalanon R Kuras PA Lefebvre SD Lemaire AV Lobanov M Lohr A Manuell I Meier L Mets M Mittag T Mittelmeier JV Moroney J Moseley C Napoli AM Nedelcu K Niyogi SV Novoselov IT Paulsen G Pazour S Purton JP Ral DMR no Pachán W Riekhof L Rymarquis M Schroda D Stern J Umen R Willows N Wilson SL Zimmer J Allmer J Balk K Bisova CJ Chen M Elias K Gendler C Hauser MR Lamb H Ledford JC Long J Minagawa MD Page J Pan W Pootakham S Roje A Rose E Stahlberg AM Terauchi P Yang S Ball C Bowler CL Dieckmann VN Gladyshev P Green R Jorgensen S May eld B Mueller-Roeber S Rajamani RT Sayre P Brokstein I Dubchak D Goodstein L Hornick YW Huang J Jhaveri Y Luo D Mart nez WCA Ngau B Otillar A Poliakov A Porter L Szajkowski G Werner K Zhou IV Grigoriev DS Rokhsar AR Grossman, Science 2007 318 5848 245 250 10.1126/science.1143609 17932292
46. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. J Zhang R Nielsen Z Yang, Mol Biol Evol 2005 22 12 2472 2479 10.1093/molbev/msi237 16107592 (Pubitemid 41661383)
47. Sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome. J Gu VJ Hilser, Mol Biol Evol 2009 26 10 2217 2227 10.1093/molbev/msp140 19592668
48. AWD Larkum RJ Orth CM Duarte, Seagrasses: Biology, Ecology and Conservation Springer, Dordrecht, The Netherlands 2006
49. Seagrass-salinity interactions: physiological mechanisms used by submersed marine angiosperms for a life at sea. BW Touchette, J Exp Mar Bio Ecol 2007 350 194 215 10.1016/j.jembe.2007.05.037 (Pubitemid 47313464)
50. Potassium transport and plant salt tolerance. S Shabala TA Cuin, Physiol Plant 2007 133 651 669 10.1111/j.1399-3054.2007.01008.x
51. Plant metabolomics reveals conserved and divergent metabolic responses to salinity. DH Sanchez MR Siahpoosh U Roessner M Udvardi J Kopka, Physiol Plant 2008 132 2 209 219 18251862
52. Plant cellulcar and molecular responses to high salinity. PM Hasegawa RA Bressan JK Zhu HJ Bohnert, Annu Rev Plant Physiol Plant Mol Biol 2000 51 463 499 10.1146/annurev.arplant.51.1.463 15012199
53. The salty tale of Arabidopsis. D Sanders, Curr Biol 2000 10 13 486 R488 10.1016/S0960-9822(00)00554-6 10898972
54. Physiological responses of the seagrass Posidonia oceanica to elevated organic matter content in sediments: An experimental assessment. M Pérez O Invers JM Ruiz MS Frederiksen M Holmer, J Exp Mar Bio Ecol 2007 344 2 149 160 (Pubitemid 46464070)
55. The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. A Barakat K Szick-Miranda IF Chang R Guyot G Blanc R Cooke M Delseny J Bailey-Serres, Plant Physiol 2001 127 2 398 415 10.1104/pp.010265 11598216 (Pubitemid 32996745)
56. High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80 S ribosome. P Giavalisco D Wilson T Kreitler H Lehrach J Klose J Gobom P Fucini, Plant Mol Biol 2005 57 4 577 591 10.1007/s11103-005-0699-3 15821981 (Pubitemid 40580437)
57. Mutational alterations in 50 proteins of the Escherichia coli ribosome. ER Dabbs, Mol Gen Genet 1978 165 73 78 10.1007/BF00270378 362167 (Pubitemid 9021073)
58. RPS4Y gene family evolution in primates. O Andrés T Kellermann F Lápez-Girldez J Rozas X Domingo-Roura M Bosch, BMC Evol Biol 2008 8 142 18477388
59. Relative effects of grazers and nutrients on seagrasses: a meta-analysis approach. AR Hughes KJ Bando LF Rodriguez SL Williams, Marine Ecology Progress Series 2004 282 87 99 10.3354/meps282087 (Pubitemid 39661289)
60. Carbon metabolism in seagrasses: Patterns of photosynthetic CO2 incorporation. S Beer A Shomer-Ilan Y Waisel, J Exp Bot 1980 31 1019 1026 10.1093/jxb/31.4.1019
61. Significance of phosphoglycollate phosphatase and 3-phosphoglycerate phosphatase in photosynthetic carbon assimilation in some marine plants. A Waghmode G Joshi, Photosynthetica 1983 17 193 197
62. The quantum efficiency of photosynthesis in macroalgae and submerged angiosperms. H Frost-Christensen K Sand-Jensen, Oecologia 1992 91 377 384 10.1007/BF00317627
63. Evidence that inducible C4-type photosynthesis is a chloroplastic CO2-concentrating mechanism in Hydrilla, a submersed monocot. J Reiskind TV Ginkel G Browes, Plant Cell Environ 1997 20 211 220 10.1046/j.1365-3040.1997. d01-68.x (Pubitemid 27115059)
64. Seagrass light acclimation: 2-DE protein analysis in Posidonia leaves grown in chronic low light conditions. S Mazzuca A Spadafora D Filadoro C Vannini M Marsoni R Cozza M Bracale T Pangaro AM Innocenti, J Exp Mar Bio Ecol 2009 374 13 122 10.1016/j.jembe.2009.04.010
65. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
66. Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs. L Wissler E Dattolo AD Moore TBH Reusch JL Olsen M Migliaccio E Bornberg-Bauer G Procaccini, Database 2009 2009 ap009 10.1093/database/bap009 20157482
67. OrthoMCL: identification of ortholog groups for eukaryotic genomes. L Li CJ Stoeckert DS Roos, Genome Res 2003 13 9 2178 2189 10.1101/gr.1224503 12952885 (Pubitemid 37161775)
68. T-Coffee: A novel method for fast and accurate multiple sequence alignment. C Notredame DG Higgins J Heringa, J Mol Biol 2000 302 205 217 10.1006/jmbi.2000.4042 10964570
69. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucleic Acids Res 2004 32 5 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
70. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. M Suyama D Torrents P Bork, Nucleic Acids Res 2006 34 Web Server 609 W612 10.1093/nar/gkl315 16845082
71. PAML 4: phylogenetic analysis by maximum likelihood. Z Yang, Mol Biol Evol 2007 24 8 1586 1591 10.1093/molbev/msm088 17483113 (Pubitemid 47236688)
72. A codon-based model of nucleotide substitution for protein-coding DNA sequences. N Goldman Z Yang, Mol Biol Evol 1994 11 5 725 736 7968486
73. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. M Ashburner CA Ball JA Blake D Botstein H Butler JM Cherry AP Davis K Dolinski SS Dwight JT Eppig MA Harris DP Hill L Issel-Tarver A Kasarskis S Lewis JC Matese JE Richardson M Ringwald GM Rubin G Sherlock, Nat Genet 2000 25 25 29 10.1038/75556 10802651 (Pubitemid 30257031)
74. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. A Alexa J Rahnenführer T Lengauer, Bioinformatics 2006 22 13 1600 1607 10.1093/bioinformatics/btl140 16606683 (Pubitemid 43985293)
75. KEGG for linking genomes to life and the environment. M Kanehisa M Araki S Goto M Hattori M Hirakawa M Itoh T Katayama S Kawashima S Okuda T Tokimatsu Y Yamanishi, Nucleic Acids Res 2008 36 Database 480 D484 18077471
76. Early Cretaceous lineages of monocot flowering plants. K Bremer, Proc Natl Acad Sci USA 2000 97 9 4707 4711 10.1073/pnas.080421597 10759567 (Pubitemid 30238622)
77. Acc homoeoloci and the evolution of wheat genomes. D Chalupska HY Lee JD Faris A Evrard B Chalhoub R Haselkorn P Gornicki, Proc Natl Acad Sci USA 2008 105 28 9691 9696 10.1073/pnas.0803981105 18599450 (Pubitemid 352031362)
78. Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes. SM Chaw CC Chang HL Chen WH Li, J Mol Evol 2004 58 4 424 441 10.1007/s00239-003-2564-9 15114421
79. DNA sequence evidence for the segmental allotetraploid origin of maize. BS Gaut JF Doebley, Proc Natl Acad Sci USA 1997 94 13 6809 6814 10.1073/pnas.94.13.6809 11038553 (Pubitemid 27281946)
80. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. AH Paterson JE Bowers BA Chapman, Proc Natl Acad Sci USA 2004 101 26 9903 9908 10.1073/pnas.0307901101 15161969 (Pubitemid 38869334)
81. Sequence logos: a new way to display consensus sequences. TD Schneider RM Stephens, Nucleic Acids Res 1990 18 20 6097 6100 10.1093/nar/18.20.6097 2172928