Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution

Genome Biology and Evolution

Volumn 2, Issue 1, 2010, Pages 225-239

  Cibrian Jaramillo, Angelica ^a,b   De La Torre Bárcenaf, Jose E ^c   Lee, Ernest K ^a   Katari, Manpreet S ^c   Little, Damon P ^b   Stevenson, Dennis W ^b   Martienssen, Rob ^d   Coruzzi, Gloria M ^c   Desalle, Rob ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b NEW YORK BOTANICAL GARDEN   (United States)

^c NEW YORK UNIVERSITY   (United States)

^d Cold Spring Harbor ^*  (United States)

Author keywords

Gene ontology; Micro RNAs; Orthologs; Partition metrics; Phylogenomics; Small interfering RNAs

Indexed keywords

PLANT RNA; RNA DIRECTED RNA POLYMERASE; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANGIOSPERM; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; DATA MINING; GENETIC EPIGENESIS; GENETIC SELECTION; GENETICS; GENOMICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTATION; PHYLOGENY; PLANT; PLANT GENE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANGIOSPERMS; DATA MINING; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENES, PLANT; GENOMICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PLANT PROTEINS; PLANTS; RNA REPLICASE; RNA, PLANT; SELECTION, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID;

MAGNOLIOPHYTA; SPERMATOPHYTA;

EID: 77958474295     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq012     Document Type: Article

References (103)

1. Adenot X, et al. 2006. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol. 16:927-932.
2. Albert VA, et al. 1994. Functional constraints and rbcL evidence for land plant phylogeny. Ann Mo Bot Gard. 81:534-567.
3. APGIII. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: aPG III.. Bot J Linn Soc. 161:105-121.
4. Bajguz A, Tretyn A. 2003. The chemical characteristic and distribution of brassinosteroids in plants. Phytochemistry. 62:1027-1046.
5. Baker RH, DeSalle R. 1997. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst Biol. 46:654-673.
6. Balasubramanian S, et al. 2006. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana.. Nat Genet. 38:711-715.
7. Barkman TJ, et al. 2007. Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants.. BMC Evol Biol. 7:248.
8. Becker A, Saedler H, Theissen G. 2003. Distinct MADS-box gene expression patterns in the reproductive cones of the gymnosperm Gnetum gnemon.. Dev Genes Evol. 213:567-572.
9. Biswas S, Akey JM. 2006. Genomic insights into positive selection. Trends Genet. 22:437-446.
10. Bohnert HJ, et al. 1988. Mesembryanthemum crystallinum, a higher plant model for the study of environmentally induced changes in gene expression.. Plant Mol Biol Rep. 6:10-28.
11. Bouchenak-Khelladi Y, et al. 2008. Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling.. Mol Phylogenet Evol. 47:488-505.
12. Bowe LM, Coat G, dePamphilis CW. 2000. Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.. Proc Natl Acad Sci U S A. 97:4092-4097.
13. Bremer K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 42:795-803.
14. Bremer K. 1994. Branch support and tree stability. Cladistics. 10:295-304.
15. Bridgham JB, Carroll SM, Thornton JW. 2007. Evolution of hormonereceptor complexity by molecular exploitation. Science. 312:87-101.
16. Brown D, Sjolander K. 2006. Functional classification using phylogenomic inference. PLoS Comput Biol. 2: e77.
17. Bull J, Huelsenbeck J, Cunningham C, Swofford D, Waddell P. 1993. Partitioning and combining data in phylogenetic analysis. Syst Biol. 42:384-397.
18. Burleigh JG, Hilu KW, Soltis DE. 2009. Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms. BMC Evol Biol. 9:61.
19. Burleigh JG, Mathews S. 2004. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life.. Am J Bot. 91:1599-1613.
20. Chase MW, et al. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann Mo Bot Gard. 80:528-580.
21. Chase MW, et al. 2006. Multigene analyses of monocot relationships: a summary. Aliso. 22:63-75.
22. Chiu JC, et al. 2006. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics. 22:699-707.
23. Creevey CJ, McInerney JO. 2002. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences.. Gene. 300:43-51.
24. Davis JI, et al. 2006. Are mitochondrial genes useful for the analysis of monocot relationships? Taxon. 55:857.
25. De la Torre-Bárcena JE, et al. 2009. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.. PLoS One. 4(6):e5764.
26. Dean AM, Thornton JW. 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet. 8:675-688.
27. DeSalle R, Branham MA, O'Grady P, Gatesy J. 2003. The evolution of HOM-C homeoboxes in the Dipteran family Drosophilidae. Insect Mol Biol. 12:345-351.
28. Doyle JA. 2006. Seed ferns and the origin of angiosperms. J Torrey Bot Soc. 133:169-209.
29. Dudoit S, van der Laan MJ, Pollard KS. 2004. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat App Genet Mol Biol. 3:1-69.
30. Duvall MR, et al. 1993. Phylogenetic hypotheses for the monocotyledons constructed from rbcL sequence data. Ann Mo Bot Gard. 80:607-619.
31. Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8:163-167.
32. Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science. 300:1706-1707.
33. Eisen JA, Wu M. 2002. Phylogenetic analysis and gene functional predictions: phylogenomics in action. Theor Popul Biol. 61:481-488.
34. Fahlgren N, et al. 2006. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis.. Curr Biol. 9:939-944.
35. Farris J, Albert V, KällersjöM, Lipscomb D, Kluge A. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics. 12:99-124.
36. Feild TS, Balun L. 2008. Xylem hydraulic and photosynthetic function of Gnetum (Gnetales) species from Papua New Guinea. New Phytol. 177:665-675.
37. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:783-791.
38. Franks SJ, Sim S, Weis AE. 2007. Rapid evolution of flowering time by an annual plant in response to a climate fluctuation. Proc Natl Acad Sci U S A. 104:1278.
39. Frohlich MW, Parker DS. 2000. The mostly male theory of flower evolutionary origins: from genes to fossils. Syst Bot. 25:155-170.
40. Garrigan D, Hedrick PW. 2003. Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution. 57:1707-1722.
41. Gatesy J, O'Grady P, Baker RH. 1999. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa.. Cladistics. 15:271-313.
42. Greguss P. 1955. Identification of living gymnosperms on the basis of xylotomy. Translated by L. Jocsik. Budapest (Hungary): Akademiai Kiado.
43. Gusmaroli G, Figueroa P, Serino G, Deng XW. 2007. Role of the MPN subunits in COP9 signalsome assembly and activity, and their regulatory interaction with Arabidopsis Cullin3-based E3 ligases.. Plant Cell. 19:564-581.
44. Gutiérrez R, Lejay L, Chiaromonte F, Shasha DE, Gm C. 2007. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive biomodules in Arabidopsis.. Genome Biol. 8: R7.
45. Harari-Steinberg O, Chamovitz DA. 2004. The COP9 signalosome: mediating between kinase signaling and protein degradation. Curr Protein Pept Sci. 5:185-189.
46. Hongyan S, et al. 2009. Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications.. Mol Biol Evol. 26:2229-2244.
47. Huelsenbeck JP, Dyer KA. 2004. Bayesian estimation of positively selected sites. J Mol Evol. 58:661-672.
48. Jansen RK, et al. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.. Proc Natl Acad Sci U S A. 104:19369-19374.
49. Jansen RK, et al. 2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.. BMC Evol Biol. 6:32.
50. Kidner CA, Martienssen RA. 2004. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature. 428:81-84.
51. Kidner CA, Martienssen RA. 2005. The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol. 280:504-517.
52. Kluge A. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes).. Syst Biol. 38:7-25.
53. Leister D. 2003. Chloroplast research in the genomic age. Trends Genet. 19:47-56.
54. Lockhart P, Penny D. 2005. The place of Amborella within the radiation of angiosperms. Trends Plant Sci. 10:201-202.
55. Loconte H, Stevenson DW. 1990. Cladistics of the Spermatophyta. Brittonia. 42:197-211.
56. Marchler-Bauer A, et al. 2007. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 5: D237-D240.
57. Mathews S. 2009. Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data.. Am J Bot. 96:228-236.
58. Mathews S, Donoghue MJ. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int J Plant Sci. 161:41-55.
59. Mitchell-Olds T, Clauss MJ. 2002. Plant evolutionary genomics. Curr Opin Plant Biol. 5:74-79.
60. Moore MJ, Bell CD, Soltis PS, Soltis DE. 2007. Using plastid genomescale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci U S A. 104:19363-19368.
61. Mouchel CF, Leyser O. 2007. Novel phytohormones involved in longrange signaling. Curr Opin Plant Biol. 10:473-476.
62. Nagasaki H, et al. 2007. The small interfering RNA production pathway is required for shoot meristem initiation in rice. Proc Natl Acad Sci U S A. 104:14867-14871.
63. Nelson G. 1979. Cladistic analysis and synthesis: principles and definitions, with a historical note on Adanson's Familles des Plantes (1763-1764).. Syst Biol. 28:1-21.
64. Nemhauser JL, Hong F, Chory J. 2006. Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses.. Cell. 126:467-475.
65. Nixon KC, Carpenter JM. 1996. On simultaneous analysis. Cladistics. 12:221-241.
66. Nixon KC, Crepet WL, Stevenson D, Friis EM. 1994. A reevaluation of seed plant phylogeny. Ann Mo Bot Gard. 81:484-533.
67. Ohashi M, Gyokusen K. 2007. Temporal change in spatial variability of soil respiration on a slope of Japanese cedar (Cryptomeria japonica D. Don) forest. Soil Biol Biochem. 39:1130-1138.
68. Palmé A, Pyhäjärvi T, Waxhiwiak W, Savolainen O. 2009. Selection on nuclear genes in a Pinus phylogeny. Mol Biol Evol. 26:893-905.
69. Paramvir D, Jeffrey B. 2006. A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics. 7:201.
70. Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. 2004. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis.. Genes Dev. 18:2368-2379.
71. Pickrell JK, et al. 2009. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19:826.
72. Poultney CS, et al. 2007. Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics. 23:259-261.
73. Purugganan M, Fuller D. 2009. The nature of selection during plant domestication. Nature. 457:843-848.
74. Qiu YL, et al. 2006. The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci U S A. 103:15511-15516.
75. Raubeson LA, et al. 2007. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus.. BMC Genomics. 8:174.
76. Rokas A, Williams BL, King N, Carroll SB. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 425:798-804.
77. Rothwell GW, Serbet R. 1994. Lignophyte phylogeny and the evolution of spermatophytes: a numerical cladistic analysis. Syst Bot. 19:443-482.
78. Sarkar IN, Egan MG, Coruzzi GM, Lee EK, DeSalle R. 2008. Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. BMC Bioinformatics. 9:103.
79. Sawata S, Kato H. 2007. Chemical properties of surface soil in relation to the quantity of stemflow, throughfall and litter in a mixed forest of Japanese cedar (Cryptomeria japonica) and beech (Fagus crenata) trees.. Jap J Forest Envir. 49:93-101.
80. Schmidt M, Schneider-Poetsch HA. 2002. The evolution of gymnosperms redrawn by phytochrome genes: the Gnetatae appear at the base of the gymnosperms.. J Mol Evol. 54:715-724.
81. Serino G, Deng XW. 2003. The COP9 signalosome: regulating plant development through the control of proteolysis. Annu Rev Plant Biol. 54:165-182.
82. Sjölander K. 2004. Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics. 20:170-179.
83. Smith SA, Donoghue MJ. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science. 322:86-89.
84. Soltis DE, Gitzendanner MA, Soltis PS. 2007. A 567-Taxon data set for angiosperms: the challenges posed by Bayesian analyses of large data sets. Int J Plant Sci. 168:137-157.
85. Soltis DE, Soltis PS, Endress PK, Chase MW. 2005. Phylogeny and evolution of Angiosperms. Sunderland (MA): Sinauer Associates Inc.
86. Staub JM, Wei N, Deng XW. 1996. Evidence for FUS6 as a component of the nuclear-localized COP9 complex in Arabidopsis. Plant Cell. 8:2047-2056.
87. Sunkar R, Zhu JK. 2007. Micro RNAs and short-interfering RNAs in plants. J Integr Plant Biol. 49:817-826.
88. *and other methods). Sunderland (MA): Sinauer Associates.
89. Thornton J, Need E, Crews D. 2003. Resurrecting the ancestral steroid receptor: ancient origin of estrogen signalling. Science. 301:1714-1717.
90. von Willert DJ, Armbruster N, Drees T, Zaborowski M. 2005. Welwitschia mirabilis: cAM or not CAM-what is the answer? Funct Plant Biol. 32:389-395.
91. Wang H, et al. 2009. Rosid radiation and the rapid rise of angiospermdominated forests. Proc Natl Acad Sci U S A. 106:3853.
92. Wang R, et al. 2004. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. 136:2512-2522.
93. Wang X, et al. 2003. The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development. Plant Cell. 15:1071-1082.
94. Wang Y, Stricker HM, Gou D, Liu L. 2007. MicroRNA: past and present. Front Biosci. 12:2316-2329.
95. Wei N, Deng XW. 1992. COP9: a new genetic locus involved in lightregulated development and gene expression in Arabidopsis.. Plant Cell. 4:1507-1518.
96. Willman MR, Poetig RS. 2005. Time to grow up: the temporal role of small RNAs in plants. Curr Opin Plant Biol. 8:548-552.
97. Windsor AJ, Mitchell-Olds T. 2006. Comparative genomics as a tool for gene discovery. Curr Opin Biotechnol. 17:161-167.
98. Winter KU, et al. 1999. MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants.. Proc Natl Acad Sci U S A. 96:7342-7347.
99. Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM. 2009. Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy.. Mol Phylogenet Evol. 52:115-124.
100. Yang Z, Bielawski JP. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 15(12):496-503.
101. Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46:409-481.
102. Zayed A, Whitfield C. 2008. A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera.. PNAS. 105:3421-3426.
103. Zhu XY, et al. 2007. Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids. BMC Evol Biol. 7:217.