The PI/GLO-like locus in orchids: Duplication and purifying selection at synonymous sites within Orchidinae (Orchidaceae)

Gene

Volumn 481, Issue 1, 2011, Pages 48-55

  Cantone, Carmela ^a   Gaudio, Luciano ^a   Aceto, Serena ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

MADS box genes; Molecular evolution; PISTILLATA GLOBOSA

Indexed keywords

PROTEIN ORCPL2; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENE IDENTIFICATION; GENE ISOLATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORCHIDACEAE; ORCHIS ITALICA; PHYLOGENY; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; MADS DOMAIN PROTEINS; MOLECULAR SEQUENCE DATA; ORCHIDACEAE; PHYLOGENY; SELECTION, GENETIC; SEQUENCE ALIGNMENT;

HABENARIA; ORCHIDACEAE; ORCHIDINAE; ORCHIS ITALICA;

EID: 79957644169     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.04.004     Document Type: Article

References (47)

1. Aagaard J.E., Willis J.H., Phillips P.C. Relaxed selection among duplicate floral regulatory genes in Lamiales. J. Mol. Evol. 2006, 63:493-503.
2. Aceto S., Caputo P., Cozzolino S., Gaudio L., Moretti A. Phylogeny and evolution of Orchis and allied genera based on ITS DNA variation: morphological gaps and molecular continuity. Mol. Phylogenet. Evol. 1999, 13:67-76.
3. Aceto S., Montieri S., Sica M., Gaudio L. Molecular evolution of the OrcPI locus in natural populations of Mediterranean orchids. Gene 2007, 392:299-305.
4. Becker A., et al. A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes. Mol. Genet. Genomics 2002, 266:942-950.
5. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 1995, 57:289-300.
6. Bickel R.D., Schackwitz W.S., Pennacchio L.A., Nuzhdin S.V., Kopp A. Contrasting patterns of sequence evolution at the functionally redundant bric a brac paralogs in Drosophila melanogaster. J. Mol. Evol. 2009, 69:194-202.
7. Cantone C., Sica M., Gaudio L., Aceto S. The OrcPI locus: genomic organization, expression pattern, and noncoding regions variability in Orchis italica (Orchidaceae) and related species. Gene 2009, 434:9-15.
8. Chamary J.V., Hurst L.D. Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol. 2005, 6:R75.
9. Chamary J.V., Parmley J.L., Hurst L.D. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 2006, 7:98-108.
10. Conant G.C., Wagner A. Asymmetric sequence divergence of duplicate genes. Genome Res. 2003, 13:2052-2058.
11. Des Marais D.L., Rausher M.D. Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 2008, 454:762-765.
12. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small amounts of leaf tissue. Phytochem. Bull. 1987, 19:11-15.
13. Felix L.P., Guerra M. Basic chromosome numbers of terrestrial orchids. Plant Syst. Evol. 2005, 254:131-148.
14. Gorniak M., Paun O., Chase M.W. Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: congruence with organellar and nuclear ribosomal DNA results. Mol. Phylogenet. Evol. 2010, 56:784-795.
15. Gustafsson A.L., Verola C.F., Antonelli A. Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae). BMC Evol. Biol. 2010, 10:177.
16. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
17. Hernandez-Hernandez T., Martinez-Castilla L.P., Alvarez-Buylla E.R. Functional diversification of B MADS-box homeotic regulators of flower development: adaptive evolution in protein-protein interaction domains after major gene duplication events. Mol. Biol. Evol. 2007, 24:465-481.
18. Hurst L.D. Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. J. Mol. Evol. 2006, 63:174-182.
19. Jack T. Relearning our ABCs: new twists on an old model. Trends Plant Sci. 2001, 6:310-316.
20. Janssens S.B., Viaene T., Huysmans S., Smets E.F., Geuten K.P. Selection on length mutations after frameshift can explain the origin and retention of the AP3/DEF-like paralogues in Impatiens. J. Mol. Evol. 2008, 66:424-435.
21. Kass R.E., Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
22. Kaufmann K., Melzer R., Theissen G. MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants. Gene 2005, 347:183-198.
23. Kim S.-Y., et al. Expression of a DEFICIENS-like gene correlates with the differentiation between sepal and petal in the orchid, Habenaria radiata (Orchidaceae). Plant Sci. 2007, 172:319-326.
24. Kimchi-Sarfaty C., et al. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 2007, 315:525-528.
25. Kuraku S., Meyer A. The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. Int. J. Dev. Biol. 2009, 53:765-773.
26. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155.
27. Mondragon-Palomino M., Theissen G. MADS about the evolution of orchid flowers. Trends Plant Sci. 2008, 13:51-59.
28. Mondragon-Palomino M., Theissen G. Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes. Ann. Bot. - London 2009, 104:583-594.
29. Mondragon-Palomino M., Hiese L., Harter A., Koch M.A., Theissen G. Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses. BMC Evol. Biol. 2009, 9:81.
30. Montieri S., Gaudio L., Aceto S. Isolation of the LFY/FLO homologue in Orchis italica and evolutionary analysis in some European orchids. Gene 2004, 333:101-109.
31. Nylander J.A., Ronquist F., Huelsenbeck J.P., Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
32. Orban T.I., Olah E. Purifying selection on silent sites-a constraint from splicing regulation?. Trends Genet. 2001, 17:252-253.
33. Park J.H., Ishikawa Y., Ochiai T., Kanno A., Kameya T. Two GLOBOSA-like genes are expressed in second and third whorls of homochlamydeous flowers in Asparagus officinalis L. Plant Cell Physiol. 2004, 45:325-332.
34. Parmley J.L., Chamary J.V., Hurst L.D. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol. Biol. Evol. 2006, 23:301-309.
35. Pond S.L., Frost S.D., Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679.
36. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
37. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
38. Rudall P.J., Bateman R.M. Roles of synorganisation, zygomorphy and heterotopy in floral evolution: the gynostemium and labellum of orchids and other lilioid monocots. Biol. Rev. Camb. Philos. Soc. 2002, 77:403-441.
39. Shan H., et al. Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Mol. Biol. Evol. 2009, 26:2229-2244.
40. Tarraga J., et al. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res. 2007, 35:W38-W42.
41. Theissen G. Development of floral organ identity: stories from the MADS house. Curr. Opin. Plant Biol. 2001, 4:75-85.
42. Theissen G., Saedler H. Plant biology. Floral quartets. Nature 2001, 409:469-471.
43. Tsai W.C., et al. PeMADS6, a GLOBOSA/PISTILLATA-like gene in Phalaenopsis equestris involved in petaloid formation, and correlated with flower longevity and ovary development. Plant Cell Physiol. 2005, 46:1125-1139.
44. Van de Peer Y., Taylor J.S., Braasch I., Meyer A. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 2001, 53:436-446.
45. Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92:371-373.
46. Xu Y., Teo L.L., Zhou J., Kumar P.P., Yu H. Floral organ identity genes in the orchid Dendrobium crumenatum. Plant J. 2006, 46:54-68.
47. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.