Phylogenetic utility of the AP3/DEF K-domain and its molecular evolution in Impatiens (Balsaminaceae)

Molecular Phylogenetics and Evolution

Volumn 43, Issue 1, 2007, Pages 225-239

  Janssens, Steven ^a   Geuten, Koen ^a   Viaene, Tom ^a   Yuan, Yong Ming ^b   Song, Yi ^b   Smets, Erik ^a,c  

^a Institute of Botany and Microbiology   (Belgium)

^b UNIVERSITY OF NEUCHÂTEL   (Switzerland)

^c UNIVERSITEIT LEIDEN BRANCH   (Netherlands)

Author keywords

APETALA3 DEFICIENS; Gene duplication; Impatiens; ImpDEF1; ImpDEF2; K domain; Phylogenetic utility

Indexed keywords

CHLOROPLAST DNA; DEFICIENS PROTEIN; PRIMER DNA;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA SEQUENCE; GENE DOSAGE; GENETIC VARIABILITY; GENETICS; IMPATIENS; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; BASE SEQUENCE; BAYES THEOREM; DEFICIENS PROTEIN; DNA PRIMERS; DNA, CHLOROPLAST; EVOLUTION, MOLECULAR; GENE DOSAGE; IMPATIENS; INTRONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

BALSAMINACEAE; IMPATIENS; MAGNOLIOPHYTA;

EID: 33947604117     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.11.016     Document Type: Article

References (70)

1. Aagaard J.E., Olmstead R.G., Willis J.H., and Phillips P.C. Duplication of floral regulatory genes in the Lamiales. Am. J. Bot. 92 (2005) 1284-1293
2. Alvarez-Buylla E.R., Pelaz S., Liljegren S.J., Gold S.E., Burgeff C., Ditta G.S., Ribas de Pouplana L., Martinez-Castilla L., and Yanofsky M.F. An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc. Natl. Acad. Sci. USA 97 (2000) 5328-5333
3. Alvarez-Buylla E.R., Liljegren S.J., Pelaz S., Gold S.E., Burgeff C., Ditta G.S., Vergera-Silva F., and Yanofsky M.F. MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J. 24 (2000) 457-466
4. Anderberg A.A., Rydin C., and Källersjö M. Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes. Am. J. Bot. 89 (2002) 677-687
5. Bailey C.D., and Doyle J.J. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dictyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Mol. Phylogenet. Evol. 13 (1999) 20-30
6. Bailey C.D., Price R.A., and Doyle J.J. Systematics of the Halimolobine Brassicaceae: evidence from three loci and morphology. Syst. Bot. 27 (2002) 318-332
7. Bell M.V., Cowper A.E., Lefranc M.-P., Bell J.I., and Screaton G.R. Influence of intron length on alternative splicing of CD44. Mol. Cell Biol. 18 (1999) 5930-5941
8. Bremer B., Bremer K., Heidari N., Erixon P., Olmstead R.G., Anderberg A.A., Källersjö M., and Barkhordarian E. Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Mol. Phylogenet. Evol. 24 (2002) 274-301
9. Castillo-Davis C.I., Mekhedov S.L., Hartl D.L., Koonin E.V., and Kondrashov F.A. Selection for short introns in highly expressed genes. Nat. Genet. 31 (2002) 415-418
10. Comeron J.M., and Kreitmann M. The correlation between intron length and recombination in Drosophila: dynamic equilibrium between mutational and selective forces. Genetics 156 (2000) 1175-1190
11. Di Stilio V.S., Kramer E.M., and Baum D.A. Floral MADS box genes and homeotic gender dimorphism in Thalictrum dioicum (Ranunculaceae) - a new model for the study of dioecy. Plant J. 41 (2005) 755-766
12. Emschwiller E., and Doyle J.J. Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae). Mol. Phylogenet. Evol. 12 (1999) 310-319
13. Eperon L.P., Graham I.R., Griffiths A.D., and Eperon I.C. Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase?. Cell 54 (1988) 393-401
14. Fan C., Purugganan M.D., Thomas D.T., Wiegmann B.M., and Xiang Q.-Y. Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae). Mol. Phylogenet. Evol. 33 (2004) 580-594
15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
16. Filipowicz W., Gniadkowski M., Klahre U., and Liu H. Pre-mRNA splicing in plants. In: Lamond A.I. (Ed). Pre-mRNA Processing (1994), R.G. Landes Company, Austin 65-77
17. Gaut B.S. Molecular clocks and nucleotide substitution rates in higher plants. Evol. Biol. 30 (1998) 93-120
18. Geuten K., Becker A., Kaufmann K., Caris P., Janssens S., Viaene T., Theissen G., and Smets E. Petaloidy in the balsaminoid genera Impatiens and Marcgravia as interpreted by changes in B-class MADS-box gene expression. Plant J. 47 (2006) 501-518
19. Geuten K., Smets E., Schols P., Yuan Y.-M., Janssens S., Küpfer P., and Pyck N. Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: combing data in a Bayesian framework. Mol. Phylogenet. Evol. 31 (2004) 711-729
20. Goodall G.J., and Filipowicz W. The minimum functional length of pre-mRNA introns in monocots and dicots. Plant Mol. Biol. 14 (1990) 727-733
21. Goto K., and Meyerowitz E.M. Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev. 8 (1994) 1548-1560
22. Grob G.B.J., Gravendeel B., and Eurlings M.C.M. Phylogenetic utility of the nuclear FLORICAULA/LEAFY second intron: comparison with three chloroplast DNA regions in Amorphophallus (Araceae). Mol. Phylogenet. Evol. 30 (2004) 13-23
23. Hebsgaard S.M., Korning P.G., Tolstrup N., Engelbrecht J., Rouze P., and Brunak S. Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information. Nucl. Acids Res. 24 (1996) 3439-3452
24. Howarth D.G., and Baum D.A. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plant species. Mol. Phylogenet. Evol. 23 (2002) 525-528
25. Huelsenbeck J., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
26. Jack T., Brockman L., and Meyerowitz E. The homeotic gene APETALA3 of Arabidopsis thaliana encodes a MADS box and is expressed in petals and stamens. Cell 68 (1992) 683-697
27. Jack T., Fox G.L., and Meyerowitz E.M. Arabidopsis homeotic gene APETALA3 ectopic expression: transcriptional and posttranscriptional regulation determine floral organ identity. Cell 76 (1994) 703-716
28. Janssens S., Geuten K., Yuan Y.-M., Song Y., Küpfer P., and Smets E. Phylogenetics of Impatiens and Hydrocera using chloroplast atpB-rbcL spacer sequences. Syst. Bot. 31 (2006) 171-180
29. Kaufmann K., Melzer R., and Theissen G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene 347 (2005) 183-198
30. Kim S., Yoo M.-J., Albert V.A., Farris J.S., Soltis P.S., and Soltis D.E. Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am. J. Bot. 91 (2004) 2102-2118
31. Kosakovsky Pond S.L., Frost S.D.W., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676-679
32. Kramer E.M., Di Stilio V.S., and Schlüter P.M. Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae. Int. J. Plant Sci. 164 (2003) 1-11
33. Kramer E.M., and Irish V.F. Evolution of the petal and stamen developmental programs: Evidence from comparative studies of the lower eudicots and basal angiosperms. Int. J. Plant Sci. 161 (2000) 29-40
34. Kramer E.M., Dorit R.L., and Irish V.F. Molecular evolution of genes controlling petal and stamen development: duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages. Genetics 149 (1998) 765-783
35. Kramer E.M., Su H.-J., Wu C.-C., and Hu J.-H. A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage. BMC Evol. Biol. 6 (2006) 30-47
36. Kolaczkowski B., and Thornton J.W. Is there a star tree paradox?. Mol. Biol. Evol. 23 (2006) 1819-1823
37. Kupfermann H., Satta Y., Takahata N., Tichy H., and Klein J. Evolution of Mhc-DRB introns: implications for the origin of primates. J. Mol. Evol. 48 (1999) 663-674
38. Lecharny A., Boudet N., Gy I., Aubourg S., and Kreis M. Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure. J. Struct. Funct. Genomics 3 (2003) 111-116
39. Lewis C.E., and Doyle J.J. Phylogenetic utility of the nuclear gene malate synthase in the palm family (Arecaceae). Mol. Phylogenet. Evol. 19 (2001) 409-420
40. Li W.-H. Molecular Evolution (1998), Sinauer Associates, Sunderland
41. Litt A., and Irish V.F. Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics 165 (2003) 821-833
42. Mason-Gamer R.J., Weill C.F., and Kellogg E.A. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 15 (1998) 1658-1673
43. Maddison D., and Maddison W. MacClade (2002), Sinauer Associates, Sunderland
44. Möller M., Clokie M., Cubas P., and Cronk Q.C.B. Integrating molecular phylogenies and developmental genetics: a Gesneriaceae case study. In: Hollingsworth P.M., Bateman R.M., and Gornall R.J. (Eds). Molecular Systematics and Plant Evolution (1999), Taylor & Francis, London 375-402
45. Moriyama E.N., Petrov D.A., and Hartl D.L. Genome size and intron size in Drosophila. Mol. Biol. Evol. 15 (1998) 770-773
46. Mount S.M., Burks C., Hertz G., Storme G.D., White O., and Fields C. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucl. Acids Res. 20 (1992) 4255-4262
47. Munster T., Pahnke J., Di Rosa A., Kim J.T., Martin W., Saedler H., and Theisssen G. Floral homeotic genes were recruited from homologous MADS-box genes preexisting in the common ancestor of ferns and seed plants. Proc. Natl. Acad. Sci. USA 94 (1997) 2415-2420
48. Muse S.V., and Gaut B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol. Biol. Evol. 11 (1994) 715-724
49. Nielsen R., and Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
50. Parsch J. Selective constraints on intron evolution in Drosophila. Gen. Soc. Am. 165 (2003) 1843-1851
51. Popp M., and Oxelman B. Evolution of a RNA Polymerase Gene Family in Silene (Caryophyllaceae)-Incomplete Concerted Evolution and Topological Congruence Among Paralogues. Syst. Biol. 53 (2004) 914-932
52. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
53. Phillipe H., Sorhannus U., Baroin A., Perasso R., Gasse F., and Adouette A. Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record. J. Evol. Biol. 7 (1994) 247-265
54. Oh S.-H., and Potter D. Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Mol. Phylogenet. Evol. 29 (2003) 203-215
55. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
56. Riechmann J.L., Wang M., and Meyerowitz E.M. DNA-binding properties of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA and AGAMOUS. Nucl. Acids Res. 24 (1996) 3134-3141
57. Rijpkema A.S., Royaert S., Zethof J., vander Weerden G., Gerats T., and Vandenbussche M. Analysis of the Petunia TM6 MADS box gene reveals functional divergence within the DEF/AP3 lineage. Plant Cell 18 (2006) 1819-1832
58. Sang T. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Mol. Biol. 27 (2002) 121-147
59. Sang T., Donoghue M.J., and Zhang D. Evolution of alcohol dehydrogenase genes in Peonies (Paeonia): phylogenetic relationships of putative nonhybrid species. Mol. Biol. Evol. 14 (1997) 994-1007
60. Schönenberger J., Anderberg A.A., and Sytsma K.J. Molecular phylogenetics and patterns of floral evolution in the Ericales. Int. J. Plant Sci. 166 (2005) 265-288
61. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
62. Stellari G.M., Jaramillo M.A., and Kramer E.M. Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Mol. Biol. Evol. 21 (2004) 506-519
63. Suzuki Y., Glazko G.V., and Nei M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99 (2002) 16138-16143
64. Swofford, D.L., 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland.
65. Theissen G., Kim J., and Saedler H. Classifiacation and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes. Gene 156 (1996) 155-166
66. Theissen G., Becker A., Di Rosa A., Kanno A., Kim J.T., Munster T., Winter K.U., and Saedler H. A short history of MADS-box genes in plants. Plant Mol. Biol. 42 (2000) 115-149
67. Vandenbussche M., Zethof J., Royaert S., Weterings K., and Gerats T. The duplicated B-class heterodimer model: whorl-specific effects and complex genetic interactions in Petunia hybrida flower development. Plant Cell 16 (2004) 741-754
68. Yang Y., Fanning L., and Jack T. The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA. Plant J. 33 (2003) 47-60
69. Yuan Y.-M., Song Y., Geuten K., Rahelivololona E., Wohlhauser S., Fischer E., Smets E., and Küpfer P. Phylogeny and biogeography of Balsaminaceae inferred from ITS sequence data. Taxon 53 (2004) 391-403
70. Zahn L.M., Leebens-Mack J., DePamphilis C.W., Ma H., and Theissen G. To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms. J. Hered. 96 (2005) 225-240