Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Qi, Xinshuai ^a,b,c   Chanderbali, André S ^c,d   Wong, Gane Ka Shu ^e,f   Soltis, Douglas E ^c   Soltis, Pamela S ^d  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c UNIVERSITY OF FLORIDA   (United States)

^d UNIVERSITY OF FLORIDA   (United States)

^e UNIVERSITY OF ALBERTA   (Canada)

^f BGI SHENZHEN   (China)

Author keywords

Gene duplication; Gene expression; GSK3; Land plant evolution

Indexed keywords

ANCESTRY; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; MORPHOLOGY; PHYLOGENETICS; PHYLOGENY; PLANT; PROTEIN; TAXONOMY;

AMBORELLA TRICHOPODA; ANIMALIA; ARABIDOPSIS; EMBRYOPHYTA; EUKARYOTA; EUPHYLLOPHYTA; FILICOPHYTA; GYMNOSPERMAE; MAGNOLIOPHYTA; SPERMATOPHYTA; TRACHEOPHYTA;

GLYCOGEN SYNTHASE KINASE 3; VEGETABLE PROTEIN;

ARTICLE; CLASSIFICATION; EMBRYOPHYTA; ENZYMOLOGY; GENE DUPLICATION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BASE SEQUENCE; EMBRYOPHYTA; EVOLUTION, MOLECULAR; GENE DUPLICATION; GLYCOGEN SYNTHASE KINASE 3; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS;

EID: 84879815608     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-143     Document Type: Article

References (33)

1. Function and evolution of "green" GSK3/Shaggy-like kinases. Saidi Y, Hearn TJ, Coates JC, Trends Plant Sci 2012 17 39 46 10.1016/j.tplants.2011.10.002 22051150
2. Wnt signaling and the polarity of the primary body axis. Petersen CP, Reddien PW, Cell 2009 139 1056 1068 10.1016/j.cell.2009.11.035 20005801
3. GSK3 is a multifunctional regulator of Dictyostelium development. Schilde C, Araki T, Williams H, Harwood A, Williams JG, Development 2004 131 4555 4565 10.1242/dev.01330 15342480 (Pubitemid 39409696)
4. GSK-3: tricks of the trade for a multi-tasking kinase. Doble BW, Woodgett JR, J Cell Sci 2003 116 Pt 7 1175 1186 12615961 (Pubitemid 36410657)
5. The Arabidopsis SHAGGY-related protein kinase (ASK) gene family: structure, organization and evolution. Dornelas MC, Lejeune B, Dron M, Kreis M, Gene 1998 212 249 257 10.1016/S0378-1119(98)00147-4 9611268 (Pubitemid 28274470)
6. Arabidopsis thaliana SHAGGY-related protein kinases (AtSK11 and 12) function in perianth and gynoecium development. Dornelas MC, Van Lammeren AAM, Kreis M, The Plant Journal 2000 21 419 429 10.1046/j.1365-313x.2000.00691.x 10758494 (Pubitemid 30181271)
7. Glycogen synthase kinase 3/SHAGGY-like kinases in plants: an emerging family with novel functions. Jonak C, Hirt H, Trends Plant Sci 2002 7 457 461 10.1016/S1360-1385(02)02331-2 12399181 (Pubitemid 36726480)
8. Organization and expression of the GSK3/shaggy kinase gene family in the moss Physcomitrella patens suggest early gene multiplication in land plants and an ancestral response to osmotic stress. Richard O, Paquet N, Haudecoeur E, Charrier B, J Mol Evol 2005 61 99 113 10.1007/s00239-004-0302-6 16007489 (Pubitemid 41188513)
9. Expression Profiling of the Whole Arabidopsis Shaggy-Like Kinase Multigene Family by Real-Time Reverse Transcriptase-Polymerase Chain Reaction. Charrier B, Champion A, Henry Y, Kreis M, Plant Physiol 2002 130 577 590 10.1104/pp.009175 12376626 (Pubitemid 35235282)
10. Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants. Yoo M-J, Albert V, Soltis P, Soltis D, BMC Plant Biology 2006 6 3 10.1186/1471-2229-6-3 16504046 (Pubitemid 44139063)
11. Increased taxon sampling greatly reduces phylogenetic error. Zwickl DJ, Hillis DM, Syst Biol 2002 51 588 598 10.1080/10635150290102339 12228001 (Pubitemid 35180690)
12. Phytozome: a comparative platform for green plant genomics. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS, Nucleic Acids Res 2012 40 1178 1186 10.1093/nar/gkr944
13. The Amborella genome: an evolutionary reference for plant biology. Soltis DE, Albert VA, Leebens-Mack J, Palmer JD, Wing RA, de Pamphilis CW, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis PS, Genome Biol 2008 9 402 10.1186/gb-2008-9-3-402 18341710 (Pubitemid 351944020)
14. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Nickrent DL, Parkinson CL, Palmer JD, Duff RJ, Mol Biol Evol 2000 17 1885 1895 10.1093/oxfordjournals.molbev.a026290 11110905
15. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS, Sipes SD, Nature 2001 409 618 622 10.1038/35054555 11214320 (Pubitemid 32154813)
16. Records of Cooksonia-type sporangia from late Wenlock strata in Ireland. Edwards D, Feehan J, Nature 1980 287 41 42 10.1038/287041a0
17. An Approximately Unbiased Test of Phylogenetic Tree Selection. Shimodaira H, Syst Biol 2002 51 492 508 10.1080/10635150290069913 12079646 (Pubitemid 35180700)
18. 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, dePamphilis CW, Nature 2011 473 97 100 10.1038/nature09916 21478875
19. The frequency of polyploid speciation in vascular plants. Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH, PNAS 2009 106 13875 13879 10.1073/pnas.0811575106 19667210
20. 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)
21. Paleopolyploidy and gene duplication in soybean and other legumes. Shoemaker RC, Schlueter J, Doyle JJ, Curr Opin Plant Biol 2006 9 104 109 10.1016/j.pbi.2006.01.007 16458041 (Pubitemid 43292366)
22. Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years. Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH, Mol Biol Evol 2008 25 2445 2455 10.1093/molbev/msn187 18728074
23. Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome. Cenci A, Combes M-C, Lashermes P, Mol Genet Genomics 2010 283 493 501 10.1007/s00438-010-0534-7 20361338
24. 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, Fabbro CD, Alaux M, Gaspero GD, Dumas V, et al. Nature 2007 449 463 467 10.1038/nature06148 17721507 (Pubitemid 47509545)
25. A genome triplication associated with early diversification of the core eudicots. Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers J, McKain M, McNeal J, Rolf M, Ruzicka D, Wafula E, Wickett N, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter E, Deyholos M, Kutchan T, Chanderbali A, Soltis P, Stevenson D, McCombie R, Pires J, Wong G, Soltis D, dePamphilis C, Genome Biol 2012 13 3 10.1186/gb-2012-13-1-r3 22280555
26. CSN1 N-terminal-dependent activity is required for Arabidopsis development but not for Rub1/Nedd8 deconjugation of cullins: a structure-function study of CSN1 subunit of COP9 signalosome. Wang X, Kang D, Feng S, Serino G, Schwechheimer C, Wei N, Mol Biol Cell 2002 13 646 655 10.1091/mbc.01-08-0427 11854419 (Pubitemid 34165090)
27. A gene expression map of Arabidopsis thaliana development. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU, Nat Genet 2005 37 501 506 10.1038/ng1543 15806101 (Pubitemid 40617278)
28. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A, Geneious v5.4 2011 Available from http://www.geneious.com
29. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Katoh K, Misawa K, Kuma K, Miyata T, Nucl Acids Res 2002 30 3059 3066 10.1093/nar/gkf436 12136088 (Pubitemid 34851225)
30. Evolutionary trees from DNA sequences: A maximum likelihood approach. Felsenstein J, J Mol Evol 1981 17 368 376 10.1007/BF01734359 7288891 (Pubitemid 11016207)
31. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Stamatakis A, Bioinformatics 2006 22 2688 2690 10.1093/bioinformatics/btl446 16928733 (Pubitemid 44642609)
32. CONSEL: for assessing the confidence of phylogenetic tree selection. Shimodaira H, Hasegawa M, Bioinformatics 2001 17 1246 1247 10.1093/ bioinformatics/17.12.1246 11751242 (Pubitemid 33735360)
33. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, Nat Meth 2008 5 621 628 10.1038/nmeth.1226 (Pubitemid 351911867)