TY - JOUR AU - Jones, R. L. AU - Varner, J. E. PY - 1966 DA - 1966// TI - The bioassay of gibberellins JO - Planta VL - 72 UR - https://doi.org/10.1007/BF00387479 DO - 10.1007/BF00387479 ID - Jones1966 ER - TY - JOUR AU - Pharis, R. P. AU - King, R. W. PY - 1985 DA - 1985// TI - Gibberellins and reproductive development in seed plants JO - Annu Rev Plant Physiol VL - 36 UR - https://doi.org/10.1146/annurev.pp.36.060185.002505 DO - 10.1146/annurev.pp.36.060185.002505 ID - Pharis1985 ER - TY - JOUR AU - Hooley, R. PY - 1994 DA - 1994// TI - Gibberellins: perception, transduction and responses JO - Plant Mol Biol VL - 26 UR - https://doi.org/10.1007/BF00016489 DO - 10.1007/BF00016489 ID - Hooley1994 ER - TY - JOUR AU - Blázquez, M. A. AU - Green, R. AU - Nilsson, O. AU - Sussman, M. R. AU - Weigel, D. PY - 1998 DA - 1998// TI - Gibberellins promote flowering of Arabidopsis by activating the LEAFY promoter JO - Plant Cell VL - 10 UR - https://doi.org/10.1105/tpc.10.5.791 DO - 10.1105/tpc.10.5.791 ID - Blázquez1998 ER - TY - JOUR AU - MacMillan, J. PY - 1997 DA - 1997// TI - Biosynthesis of the gibberellin plant hormones JO - Nat Prod Rep VL - 14 UR - https://doi.org/10.1039/np9971400221 DO - 10.1039/np9971400221 ID - MacMillan1997 ER - TY - JOUR AU - MacMillan, J. PY - 2001 DA - 2001// TI - Occurrence of gibberellins in vascular plants, fungi, and bacteria JO - J Plant Growth Regul VL - 20 UR - https://doi.org/10.1007/s003440010038 DO - 10.1007/s003440010038 ID - MacMillan2001 ER - TY - JOUR AU - Hedden, P. AU - Phillips, A. L. PY - 2000 DA - 2000// TI - Gibberellin metabolism: new insights revealed by the genes JO - Trends Plant Sci VL - 5 UR - https://doi.org/10.1016/S1360-1385(00)01790-8 DO - 10.1016/S1360-1385(00)01790-8 ID - Hedden2000 ER - TY - JOUR AU - Graebe, J. E. PY - 1987 DA - 1987// TI - Gibberellin biosynthesis and control JO - Annu Rev Plant Physiol VL - 38 UR - https://doi.org/10.1146/annurev.pp.38.060187.002223 DO - 10.1146/annurev.pp.38.060187.002223 ID - Graebe1987 ER - TY - JOUR AU - Olszewski, N. AU - Sun, T. P. AU - Gubler, F. PY - 2002 DA - 2002// TI - Gibberellin signaling: biosynthesis, catabolism, and response pathways JO - Plant Cell VL - 14 ID - Olszewski2002 ER - TY - JOUR AU - Sakamoto, T. AU - Miura, K. AU - Itoh, H. AU - Tatsumi, T. AU - Ueguchi-Tanaka, M. AU - Ishiyama, K. PY - 2004 DA - 2004// TI - An overview of gibberellin metabolism enzyme genes and their related mutants in rice JO - Plant Physiol VL - 134 UR - https://doi.org/10.1104/pp.103.033696 DO - 10.1104/pp.103.033696 ID - Sakamoto2004 ER - TY - JOUR AU - Yamaguchi, S. PY - 2008 DA - 2008// TI - Gibberellin metabolism and its regulation JO - Annu Rev Plant Biol VL - 59 UR - https://doi.org/10.1146/annurev.arplant.59.032607.092804 DO - 10.1146/annurev.arplant.59.032607.092804 ID - Yamaguchi2008 ER - TY - JOUR AU - Phillips, A. L. AU - Ward, D. A. AU - Uknes, S. AU - Appleford, N. E. J. AU - Lange, T. AU - Huttly, A. K. PY - 1995 DA - 1995// TI - Isolation and expression of three gibberellin 20-oxidase cDNA clones from Arabidopsis JO - Plant Physiol VL - 108 UR - https://doi.org/10.1104/pp.108.3.1049 DO - 10.1104/pp.108.3.1049 ID - Phillips1995 ER - TY - JOUR AU - Kawai, Y. AU - Ono, E. AU - Mizutani, M. PY - 2014 DA - 2014// TI - Evolution and diversity of the 2-oxoglutarate‐dependent dioxygenase superfamily in plants JO - Plant J VL - 78 UR - https://doi.org/10.1111/tpj.12479 DO - 10.1111/tpj.12479 ID - Kawai2014 ER - TY - JOUR AU - Carrera, E. AU - Jackson, S. D. AU - Prat, S. PY - 1999 DA - 1999// TI - Feedback control and diurnal regulation of gibberellin 20-oxidase transcript levels in potato JO - Plant Physiol VL - 119 UR - https://doi.org/10.1104/pp.119.2.765 DO - 10.1104/pp.119.2.765 ID - Carrera1999 ER - TY - JOUR AU - Itoh, H. AU - Tanaka-Ueguchi, M. AU - Kawaide, H. AU - Chen, X. AU - Kamiya, Y. AU - Matsuoka, M. PY - 1999 DA - 1999// TI - The gene encoding tobacco gibberellins 3beta-hydroxylase is expressed at the site of GA action during stem elongation and flower organ development JO - Plant J VL - 20 UR - https://doi.org/10.1046/j.1365-313X.1999.00568.x DO - 10.1046/j.1365-313X.1999.00568.x ID - Itoh1999 ER - TY - JOUR AU - Oikawa, T. AU - Koshioka, M. AU - Kojima, K. AU - Yoshida, H. AU - Kawata, M. PY - 2004 DA - 2004// TI - A role of OsGA20ox1, encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice JO - Plant Mol Biol VL - 55 UR - https://doi.org/10.1007/s11103-004-1692-y DO - 10.1007/s11103-004-1692-y ID - Oikawa2004 ER - TY - JOUR AU - Davidson, S. E. AU - Swain, S. M. AU - Reid, J. B. PY - 2005 DA - 2005// TI - Regulation of the early GA biosynthesis pathway in pea JO - Planta VL - 222 UR - https://doi.org/10.1007/s00425-005-0045-7 DO - 10.1007/s00425-005-0045-7 ID - Davidson2005 ER - TY - JOUR AU - Schomburg, F. M. AU - Bizzell, C. M. AU - Lee, D. J. AU - Zeevaart, J. A. AU - Amasino, R. M. PY - 2003 DA - 2003// TI - Overexpression of a novel class of gibberellin 2-oxidases decreases gibberellin levels and creates dwarf plants JO - Plant Cell VL - 15 UR - https://doi.org/10.1105/tpc.005975 DO - 10.1105/tpc.005975 ID - Schomburg2003 ER - TY - JOUR AU - Thomas, S. G. AU - Phillips, A. L. AU - Hedden, P. PY - 1999 DA - 1999// TI - Molecular cloning and functional expression of gibberellin 2- oxidases, multifunctional enzymes involved in gibberellin deactivation JO - Proc Natl Acad Sci U S A VL - 96 UR - https://doi.org/10.1073/pnas.96.8.4698 DO - 10.1073/pnas.96.8.4698 ID - Thomas1999 ER - TY - JOUR AU - Lee, D. J. AU - Zeevaart, J. A. D. PY - 2005 DA - 2005// TI - Molecular cloning of GA2-oxidase3 from spinach and its ectopic expression in Nicotianasylvestris JO - Plant Physiol VL - 138 UR - https://doi.org/10.1104/pp.104.056499 DO - 10.1104/pp.104.056499 ID - Lee2005 ER - TY - JOUR AU - Pimenta Lange, M. J. AU - Liebrandt, A. AU - Arnold, L. AU - Chmielewska, S. M. AU - Felsberger, A. AU - Freier, E. PY - 2013 DA - 2013// TI - Functional characterization of gibberellin oxidases from cucumber, Cucumis sativus L JO - Phytochemistry VL - 90 UR - https://doi.org/10.1016/j.phytochem.2013.02.006 DO - 10.1016/j.phytochem.2013.02.006 ID - Pimenta Lange2013 ER - TY - JOUR AU - Yang, Y. AU - Zhang, F. AU - Ge, S. PY - 2009 DA - 2009// TI - Evolutionary rate patterns of the Gibberellin pathway genes JO - BMC Evol Biol VL - 9 UR - https://doi.org/10.1186/1471-2148-9-206 DO - 10.1186/1471-2148-9-206 ID - Yang2009 ER - TY - JOUR AU - Han, F. AU - Zhu, B. PY - 2011 DA - 2011// TI - Evolutionary analysis of three gibberellin oxidase genes in rice, Arabidopsis, and soybean JO - Gene VL - 473 UR - https://doi.org/10.1016/j.gene.2010.10.010 DO - 10.1016/j.gene.2010.10.010 ID - Han2011 ER - TY - JOUR AU - Giacomelli, L. AU - Rota-Stabelli, O. AU - Masuero, D. AU - Acheampong, A. K. AU - Moretto, M. AU - Caputi, L. PY - 2013 DA - 2013// TI - Gibberellin metabolism in Vitis vinifera L. during bloom and fruit-set: functional characterization and evolution of grapevine gibberellin oxidases JO - J Exp Bot VL - 64 UR - https://doi.org/10.1093/jxb/ert251 DO - 10.1093/jxb/ert251 ID - Giacomelli2013 ER - TY - JOUR AU - Johri, M. M. PY - 2004 DA - 2004// TI - Possible origin of hormonal regulation in green plants JO - Proc Indian Natl Sci Acad VL - 70 ID - Johri2004 ER - TY - JOUR AU - Johri, M. M. PY - 2008 DA - 2008// TI - Hormonal regulation in green plant lineage families JO - Physiol Mol Biol Plants VL - 14 UR - https://doi.org/10.1007/s12298-008-0003-5 DO - 10.1007/s12298-008-0003-5 ID - Johri2008 ER - TY - JOUR AU - Yasumura, Y. AU - Crumpton-Taylor, M. AU - Fuentes, S. AU - Harberd, N. P. PY - 2007 DA - 2007// TI - Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land-plant evolution JO - Curr Biol VL - 17 UR - https://doi.org/10.1016/j.cub.2007.06.037 DO - 10.1016/j.cub.2007.06.037 ID - Yasumura2007 ER - TY - JOUR AU - Rensing, S. A. AU - Lang, D. AU - Zimmer, A. D. AU - Terry, A. AU - Salamov, A. AU - Shapiro, H. PY - 2008 DA - 2008// TI - The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants JO - Science VL - 319 UR - https://doi.org/10.1126/science.1150646 DO - 10.1126/science.1150646 ID - Rensing2008 ER - TY - JOUR AU - Hayashi, K. AU - Kawaide, H. AU - Notomi, M. AU - Sakigi, Y. AU - Matsuo, A. AU - Nozaki, H. PY - 2006 DA - 2006// TI - Identification and functional analysis of bifunctionalent-kaurene synthase from the moss Physcomitrella patens JO - FEBS Lett VL - 580 UR - https://doi.org/10.1016/j.febslet.2006.10.018 DO - 10.1016/j.febslet.2006.10.018 ID - Hayashi2006 ER - TY - JOUR AU - Anterola, A. AU - Shanle, E. K. PY - 2008 DA - 2008// TI - Genomic insights in moss gibberellin biosynthesis JO - The Bryologist VL - 111 UR - https://doi.org/10.1639/0007-2745(2008)111[218:GIIMGB]2.0.CO;2 DO - 10.1639/0007-2745(2008)111[218:GIIMGB]2.0.CO;2 ID - Anterola2008 ER - TY - JOUR AU - Hedden, P. AU - Phillips, A. L. AU - Rojas, M. C. AU - Carrera, E. AU - Tudzynski, B. PY - 2001 DA - 2001// TI - Gibberellin biosynthesis in plants and fungi: a case of convergent evolution? JO - J Plant Growth Regul VL - 20 UR - https://doi.org/10.1007/s003440010037 DO - 10.1007/s003440010037 ID - Hedden2001 ER - TY - JOUR AU - Tudzynski, B. PY - 2005 DA - 2005// TI - Gibberellin biosynthesis in fungi: genes, enzymes, evolution, and impact on biotechnology JO - Appl Microbiol Biotechnol VL - 66 UR - https://doi.org/10.1007/s00253-004-1805-1 DO - 10.1007/s00253-004-1805-1 ID - Tudzynski2005 ER - TY - JOUR AU - Pimenta Lange, M. J. AU - Lange, T. PY - 2006 DA - 2006// TI - Gibberellin biosynthesis and the regulation of plant development JO - Plant Biol VL - 8 UR - https://doi.org/10.1055/s-2006-923882 DO - 10.1055/s-2006-923882 ID - Pimenta Lange2006 ER - TY - JOUR AU - Aravind, L. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases JO - Genome Biol VL - 2 UR - https://doi.org/10.1186/gb-2001-2-3-research0007 DO - 10.1186/gb-2001-2-3-research0007 ID - Aravind2001 ER - TY - JOUR AU - Chiang, H. H. AU - Hwang, I. AU - Goodman, H. M. PY - 1995 DA - 1995// TI - Isolation of the Arabidopsis GA4 locus JO - Plant Cell VL - 7 UR - https://doi.org/10.1105/tpc.7.2.195 DO - 10.1105/tpc.7.2.195 ID - Chiang1995 ER - TY - JOUR AU - Xu, Y. L. AU - Li, L. AU - Wu, K. AU - Peeterst Anton, J. M. AU - Gage, D. A. AU - Zeevaart, J. A. D. PY - 1995 DA - 1995// TI - The GA5 locus of Arabidopsis thaliana encodes a multifunctional gibberellin 20-oxidase: molecular cloning and functional expression JO - Proc Natl Acad Sci U S A VL - 92 UR - https://doi.org/10.1073/pnas.92.14.6640 DO - 10.1073/pnas.92.14.6640 ID - Xu1995 ER - TY - JOUR AU - Wu, K. AU - Li, L. AU - Gage, D. A. AU - Zeevaart, J. A. D. PY - 1996 DA - 1996// TI - Molecular cloning and photoperiod-regulated expression of gibberellin 20-oxidase from the long-day plant spinach JO - Plant Physiol VL - 110 UR - https://doi.org/10.1104/pp.110.2.547 DO - 10.1104/pp.110.2.547 ID - Wu1996 ER - TY - JOUR AU - Toyomasu, T. AU - Kawaide, H. AU - Sekimoto, H. AU - Numers, C. AU - Phillips, A. L. AU - Hedden, P. PY - 1997 DA - 1997// TI - Cloning and characterization of a cDNA encoding gibberellin 20‐oxidase from rice (Oryza sativa) seedlings JO - Physiol Plant VL - 99 UR - https://doi.org/10.1111/j.1399-3054.1997.tb03438.x DO - 10.1111/j.1399-3054.1997.tb03438.x ID - Toyomasu1997 ER - TY - JOUR AU - Kang, H. G. AU - Jun, S. H. AU - Kim, J. AU - Kawaide, H. AU - Kamiya, Y. AU - An, G. PY - 1999 DA - 1999// TI - Cloning and molecular analyses of a gibberellin 20-oxidase gene expressed specifically in developing seeds of watermelon JO - Plant Physiol VL - 121 UR - https://doi.org/10.1104/pp.121.2.373 DO - 10.1104/pp.121.2.373 ID - Kang1999 ER - TY - JOUR AU - Lo, S. F. AU - Yang, S. Y. AU - Chen, K. T. AU - Hsing, Y. I. AU - Zeevaart, J. A. D. AU - Chen, L. J. PY - 2008 DA - 2008// TI - A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice JO - Plant Cell VL - 20 UR - https://doi.org/10.1105/tpc.108.060913 DO - 10.1105/tpc.108.060913 ID - Lo2008 ER - TY - JOUR AU - Lange, T. AU - Hedden, P. AU - Graebe, J. E. PY - 1994 DA - 1994// TI - Expression cloning of a gibberellin 20-oxidase, a multifunctional enzyme involved in gibberellin biosynthesis JO - Proc Natl Acad Sci U S A VL - 91 UR - https://doi.org/10.1073/pnas.91.18.8552 DO - 10.1073/pnas.91.18.8552 ID - Lange1994 ER - TY - JOUR AU - Huerta, L. AU - Garcia-Lor, A. AU - Garcia-Martinez, J. L. PY - 2009 DA - 2009// TI - Characterization of gibberellin 20-oxidases in the citrus hybrid Carrizo citrange JO - Tree Physiol VL - 29 UR - https://doi.org/10.1093/treephys/tpn049 DO - 10.1093/treephys/tpn049 ID - Huerta2009 ER - TY - JOUR AU - Busov, V. B. AU - Meilan, R. AU - Pearce, D. W. AU - Ma, C. AU - Rood, S. B. AU - Strauss, S. H. PY - 2003 DA - 2003// TI - Activation tagging of a dominant gibberellin catabolism gene (GA2-oxidase) frompoplar regulates tree stature JO - Plant Physiol VL - 132 UR - https://doi.org/10.1104/pp.103.020354 DO - 10.1104/pp.103.020354 ID - Busov2003 ER - TY - JOUR AU - Itoh, H. AU - Ueguchi-Tanaka, M. AU - Sentoku, N. AU - Kitano, H. AU - Matsuoka, M. AU - Kobayashi, M. PY - 2001 DA - 2001// TI - Cloning and functional analysis of two gibberellin 3β-hydroxylase genes that are differently expressed during the growth of rice JO - Proc Natl Acad Sci U S A VL - 98 UR - https://doi.org/10.1073/pnas.141239398 DO - 10.1073/pnas.141239398 ID - Itoh2001 ER - TY - JOUR AU - Sakamoto, T. AU - Kobayashi, M. AU - Itoh, H. AU - Tagiri, A. AU - Kayano, T. AU - Tanaka, H. PY - 2001 DA - 2001// TI - Expression of a gibberellin 2-oxidase gene around the shoot apex is related to phase transition in rice JO - Plant Physiol VL - 125 UR - https://doi.org/10.1104/pp.125.3.1508 DO - 10.1104/pp.125.3.1508 ID - Sakamoto2001 ER - TY - JOUR AU - Lee, D. J. AU - Zeevaart, J. A. D. PY - 2002 DA - 2002// TI - Differential regulation of RNA levels of gibberellin dioxygenases by photoperiod in spinach JO - Plant Physiol VL - 130 UR - https://doi.org/10.1104/pp.008581 DO - 10.1104/pp.008581 ID - Lee2002 ER - TY - JOUR AU - Lester, D. R. AU - Ross, J. J. AU - Davies, P. J. AU - Reid, J. B. PY - 1997 DA - 1997// TI - Mendel’s stem length gene (Le) encodes a gibberellin 3 beta-hydroxylase JO - Plant Cell VL - 9 ID - Lester1997 ER - TY - JOUR AU - Martin, D. N. AU - Proebsting, W. M. AU - Hedden, P. PY - 1997 DA - 1997// TI - Mendel’s dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins JO - Proc Natl Acad Sci U S A VL - 94 UR - https://doi.org/10.1073/pnas.94.16.8907 DO - 10.1073/pnas.94.16.8907 ID - Martin1997 ER - TY - JOUR AU - Innan, H. AU - Kondrashov, F. PY - 2010 DA - 2010// TI - The evolution of gene duplications: classifying and distinguishing between models JO - Nature Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2689 DO - 10.1038/nrg2689 ID - Innan2010 ER - TY - JOUR AU - Semon, M. AU - Wolfe, K. H. PY - 2007 DA - 2007// TI - Consequences of genome duplication JO - Curr Opin Genetics Dev VL - 17 UR - https://doi.org/10.1016/j.gde.2007.09.007 DO - 10.1016/j.gde.2007.09.007 ID - Semon2007 ER - TY - JOUR AU - Sun, H. Z. AU - Ge, S. PY - 2010 DA - 2010// TI - Molecular evolution of the duplicated TFIIAγgenes in Oryzeae and its relatives JO - BMC Evol Biol VL - 10 UR - https://doi.org/10.1186/1471-2148-10-128 DO - 10.1186/1471-2148-10-128 ID - Sun2010 ER - TY - BOOK AU - Ohno, S. PY - 1970 DA - 1970// TI - Evolution by gene duplication. London: George Alien & Unwin Ltd PB - Springer CY - Berlin, Heidelberg and New York UR - https://doi.org/10.1007/978-3-642-86659-3 DO - 10.1007/978-3-642-86659-3 ID - Ohno1970 ER - TY - CHAP AU - Li, W. -. H. ED - Otha, T. ED - Aoki, K. PY - 1985 DA - 1985// TI - Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy BT - Population genetics and molecular evolution PB - Japan Scientific Press CY - Tokyo ID - Li1985 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2000 DA - 2000// TI - The evolutionary fate and consequences of duplicate genes JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5494.1151 DO - 10.1126/science.290.5494.1151 ID - Lynch2000 ER - TY - JOUR AU - Liu, P. L. AU - Wan, J. N. AU - Guo, Y. P. AU - Ge, S. AU - Rao, G. Y. PY - 2012 DA - 2012// TI - Adaptive evolution of the chrysanthemyl diphosphate synthase gene involved in irregular monoterpene metabolism JO - BMC Evol Biol VL - 12 UR - https://doi.org/10.1186/1471-2148-12-214 DO - 10.1186/1471-2148-12-214 ID - Liu2012 ER - TY - JOUR AU - Zhang, J. AU - Rosenberg, H. F. AU - Nei, M. PY - 1998 DA - 1998// TI - Positive Darwinian selection after gene duplication in primate ribonuclease genes JO - Proc Natl Acad Sci U S A VL - 95 UR - https://doi.org/10.1073/pnas.95.7.3708 DO - 10.1073/pnas.95.7.3708 ID - Zhang1998 ER - TY - JOUR AU - Shiu, S. H. AU - Byrnes, J. K. AU - Pan, R. AU - Zhang, P. AU - Li, W. H. PY - 2006 DA - 2006// TI - Role of positive selection in the retention of duplicate genes in mammalian genomes JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0510388103 DO - 10.1073/pnas.0510388103 ID - Shiu2006 ER - TY - JOUR AU - Dykhuizen, D. AU - Hartl, D. L. PY - 1980 DA - 1980// TI - Selective neutrality of 6pgd allozymes in E. COLI and the effects of genetic background JO - Genetics VL - 96 ID - Dykhuizen1980 ER - TY - JOUR AU - Zhang, J. PY - 2003 DA - 2003// TI - Evolution by gene duplication: an update JO - Trends Ecol Evolut VL - 18 UR - https://doi.org/10.1016/S0169-5347(03)00033-8 DO - 10.1016/S0169-5347(03)00033-8 ID - Zhang2003 ER - TY - JOUR AU - Gaston, D. AU - Susko, E. AU - Roger, A. J. PY - 2011 DA - 2011// TI - A Phylogenetic Mixture Model for the Identification of Functionally Divergent Protein Residues JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr470 DO - 10.1093/bioinformatics/btr470 ID - Gaston2011 ER - TY - JOUR AU - Capra, J. A. AU - Singh, M. PY - 2008 DA - 2008// TI - Characterization and prediction of residues determining protein functional specificity JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn214 DO - 10.1093/bioinformatics/btn214 ID - Capra2008 ER - TY - JOUR AU - Gaston, D. AU - Roger, A. J. PY - 2013 DA - 2013// TI - Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of diverse eukaryotic algae JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0070396 DO - 10.1371/journal.pone.0070396 ID - Gaston2013 ER - TY - JOUR AU - Valegård, K. AU - Scheltinga, A. C. T. AU - Lloyd, M. D. AU - Hara, T. AU - Ramaswamy, S. AU - Perrakis, A. PY - 1998 DA - 1998// TI - Structure of a cephalosporin synthase JO - Nature VL - 394 UR - https://doi.org/10.1038/29575 DO - 10.1038/29575 ID - Valegård1998 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. H. AU - Zhang, Z. AU - Miller, W. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: A new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Hall, T. A. PY - 1999 DA - 1999// TI - BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT JO - Nucleic Acids Symp Ser VL - 41 ID - Hall1999 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - JOUR AU - Thompson, J. D. AU - Gibson, T. J. AU - Plewniak, F. AU - Jeanmougin, F. AU - Higgins, D. G. PY - 1997 DA - 1997// TI - The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.24.4876 DO - 10.1093/nar/25.24.4876 ID - Thompson1997 ER - TY - JOUR AU - Xia, X. AU - Xie, Z. PY - 2001 DA - 2001// TI - DAMBE: software package for data analysis in molecular biology and evolution JO - J Hered VL - 92 UR - https://doi.org/10.1093/jhered/92.4.371 DO - 10.1093/jhered/92.4.371 ID - Xia2001 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl446 DO - 10.1093/bioinformatics/btl446 ID - Stamatakis2006 ER - TY - JOUR AU - Darriba, D. AU - Taboada, G. L. AU - Doallo, R. AU - Posada, D. PY - 2011 DA - 2011// TI - ProtTest 3: fast selection of best-fit models of protein evolution JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr088 DO - 10.1093/bioinformatics/btr088 ID - Darriba2011 ER - TY - JOUR AU - Bailey, T. L. AU - Boden, M. AU - Buske, F. A. AU - Frith, M. AU - Grant, C. E. AU - Clementi, L. PY - 2009 DA - 2009// TI - MEME SUITE: tools for motif discovery and searching JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp335 DO - 10.1093/nar/gkp335 ID - Bailey2009 ER - TY - JOUR AU - Marchler-Bauer, A. AU - Anderson, J. B. AU - Cherukuri, P. F. AU - DeWeese-Scott, C. AU - Geer, L. Y. AU - Gwadz, M. PY - 2005 DA - 2005// TI - CDD: a Conserved Domain Database for protein classification JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki069 DO - 10.1093/nar/gki069 ID - Marchler-Bauer2005 ER - TY - JOUR AU - Schwede, T. AU - Kopp, J. AU - Guex, N. AU - Peitsch, M. C. PY - 2003 DA - 2003// TI - SWISS-MODEL: an automated protein homology-modeling server JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg520 DO - 10.1093/nar/gkg520 ID - Schwede2003 ER - TY - JOUR AU - Biasini, M. AU - Bienert, S. AU - Waterhouse, A. AU - Arnold, K. AU - Studer, G. AU - Schmidt, T. PY - 2014 DA - 2014// TI - SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku340 DO - 10.1093/nar/gku340 ID - Biasini2014 ER - TY - JOUR AU - Benkert, P. AU - Kunzli, M. AU - Schwede, T. PY - 2009 DA - 2009// TI - QMEAN server for protein model quality estimation JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp322 DO - 10.1093/nar/gkp322 ID - Benkert2009 ER - TY - JOUR AU - Seeliger, D. AU - Groot, B. L. PY - 2010 DA - 2010// TI - Ligand docking and binding site analysis with PyMOL and Autodock/Vina JO - J Comput Aided Mol Des VL - 24 UR - https://doi.org/10.1007/s10822-010-9352-6 DO - 10.1007/s10822-010-9352-6 ID - Seeliger2010 ER - TY - JOUR AU - Clark, A. G. AU - Eisen, M. B. AU - Smith, D. R. AU - Bergman, C. M. AU - Oliver, B. AU - Markow, T. A. PY - 2007 DA - 2007// TI - Evolution of genes and genomes on the Drosophila phylogeny JO - Nature VL - 450 UR - https://doi.org/10.1038/nature06341 DO - 10.1038/nature06341 ID - Clark2007 ER - TY - JOUR AU - Löytynoja, A. AU - Goldman, N. PY - 2005 DA - 2005// TI - An algorithm for progressive multiple alignment of sequences with insertions JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0409137102 DO - 10.1073/pnas.0409137102 ID - Löytynoja2005 ER - TY - JOUR AU - Löytynoja, A. AU - Goldman, N. PY - 2008 DA - 2008// TI - Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis JO - Science VL - 320 UR - https://doi.org/10.1126/science.1158395 DO - 10.1126/science.1158395 ID - Löytynoja2008 ER - TY - JOUR AU - Markova-Raina, P. AU - Petrov, D. PY - 2011 DA - 2011// TI - High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.115949.110 DO - 10.1101/gr.115949.110 ID - Markova-Raina2011 ER - TY - JOUR AU - Penn, O. AU - Privman, E. AU - Ashkenazy, H. AU - Landan, G. AU - Graur, D. AU - Pupko, T. PY - 2010 DA - 2010// TI - GUIDANCE: a web server for assessing alignment confidence scores JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq443 DO - 10.1093/nar/gkq443 ID - Penn2010 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: Phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 2000 DA - 2000// TI - Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026236 DO - 10.1093/oxfordjournals.molbev.a026236 ID - Yang2000 ER - TY - JOUR AU - Bielawski, J. P. AU - Yang, Z. PY - 2004 DA - 2004// TI - A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution JO - J Mol Evol VL - 59 UR - https://doi.org/10.1007/s00239-004-2597-8 DO - 10.1007/s00239-004-2597-8 ID - Bielawski2004 ER - TY - JOUR AU - Bay, R. A. AU - Bielawski, J. P. PY - 2013 DA - 2013// TI - Inference of functional divergence among proteins when the evolutionary process is non-stationary JO - J Mol Evol VL - 76 UR - https://doi.org/10.1007/s00239-013-9549-0 DO - 10.1007/s00239-013-9549-0 ID - Bay2013 ER - TY - JOUR AU - Zhang, J. AU - Nielsen, R. AU - Yang, Z. PY - 2005 DA - 2005// TI - Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi237 DO - 10.1093/molbev/msi237 ID - Zhang2005 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 2002 DA - 2002// TI - Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004148 DO - 10.1093/oxfordjournals.molbev.a004148 ID - Yang2002 ER - TY - JOUR AU - Nielsen, R. AU - Yang, Z. PY - 1998 DA - 1998// TI - Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene JO - Genetics VL - 148 ID - Nielsen1998 ER - TY - JOUR AU - Yang, Z. AU - Swanson, W. J. PY - 2002 DA - 2002// TI - Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003981 DO - 10.1093/oxfordjournals.molbev.a003981 ID - Yang2002 ER - TY - JOUR AU - Yang, Z. AU - Wong, W. S. W. AU - Nielsen, R. PY - 2005 DA - 2005// TI - Bayes empirical Bayes inference of amino acid sites under positive selection JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi097 DO - 10.1093/molbev/msi097 ID - Yang2005 ER - TY - JOUR AU - Wang, H. C. AU - Li, K. AU - Susko, E. AU - Roger, A. J. PY - 2008 DA - 2008// TI - A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-331 DO - 10.1186/1471-2148-8-331 ID - Wang2008 ER - TY - JOUR AU - Hirano, K. AU - Nakajima, M. AU - Asano, K. AU - Nishiyama, T. AU - Sakakibara, H. AU - Kojima, M. PY - 2007 DA - 2007// TI - The GID1-mediated gibberellin perception mechanism is conserved in the lycophyte Selaginella moellendorffii but not in the bryophyte Physcomitrella patens JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.107.051524 DO - 10.1105/tpc.107.051524 ID - Hirano2007 ER - TY - JOUR AU - Bomke, C. AU - Tudzynski, B. PY - 2009 DA - 2009// TI - Diversity, regulation, and evolution of the gibberellin biosynthetic pathway in fungi compared to plants and bacteria JO - Phytochemistry VL - 70 UR - https://doi.org/10.1016/j.phytochem.2009.05.020 DO - 10.1016/j.phytochem.2009.05.020 ID - Bomke2009 ER - TY - JOUR AU - Evans, M. M. S. AU - Poethig, R. S. PY - 1995 DA - 1995// TI - Gibberellins promote vegetative phase change and reproductive maturity in maize JO - Plant Physiol VL - 108 UR - https://doi.org/10.1104/pp.108.2.475 DO - 10.1104/pp.108.2.475 ID - Evans1995 ER - TY - JOUR AU - Cho, G. AU - Doolittle, R. F. PY - 1997 DA - 1997// TI - Intron distribution in ancient paralogs supports random insertion and not random loss JO - J Mol Evol VL - 44 UR - https://doi.org/10.1007/PL00006180 DO - 10.1007/PL00006180 ID - Cho1997 ER - TY - JOUR AU - Boudet, N. AU - Aubourg, S. AU - Toffano-Nioche, C. AU - Kreis, M. AU - Lecharny, A. PY - 2001 DA - 2001// TI - Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.200801 DO - 10.1101/gr.200801 ID - Boudet2001 ER - TY - JOUR AU - Babenko, V. N. AU - Rogozin, I. B. AU - Mekhedov, S. L. AU - Koonin, E. V. PY - 2004 DA - 2004// TI - Prevalence of intron gain over intron loss in the evolution of paralogous gene families JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh686 DO - 10.1093/nar/gkh686 ID - Babenko2004 ER - TY - JOUR AU - Trotman, C. A. N. PY - 1998 DA - 1998// TI - Introns-early: Slipping lately? JO - Trends Genet VL - 14 UR - https://doi.org/10.1016/S0168-9525(98)01400-0 DO - 10.1016/S0168-9525(98)01400-0 ID - Trotman1998 ER - TY - JOUR AU - Pichersky, E. AU - Gang, D. R. PY - 2000 DA - 2000// TI - Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective JO - Trends Plant Sci VL - 5 UR - https://doi.org/10.1016/S1360-1385(00)01741-6 DO - 10.1016/S1360-1385(00)01741-6 ID - Pichersky2000 ER - TY - JOUR AU - Ober, D. PY - 2005 DA - 2005// TI - Seeing double: gene duplication and diversification in plant secondary metabolism JO - Trends Plant Sci VL - 10 UR - https://doi.org/10.1016/j.tplants.2005.07.007 DO - 10.1016/j.tplants.2005.07.007 ID - Ober2005 ER - TY - JOUR AU - Benderoth, M. AU - Textor, S. AU - Windsor, A. J. AU - Mitchell-Olds, T. AU - Gershenzon, J. AU - Kroymann, J. PY - 2006 DA - 2006// TI - Positive selection driving diversification in plant secondary metabolism JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0601738103 DO - 10.1073/pnas.0601738103 ID - Benderoth2006 ER - TY - JOUR AU - Kroymann, J. PY - 2011 DA - 2011// TI - Natural diversity and adaptation in plant secondary metabolism JO - Curr Opin Plant Biol VL - 14 UR - https://doi.org/10.1016/j.pbi.2011.03.021 DO - 10.1016/j.pbi.2011.03.021 ID - Kroymann2011 ER - TY - STD TI - Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 1999;151(4):1531-45. ID - ref103 ER - TY - JOUR AU - Zhang, J. PY - 2004 DA - 2004// TI - Frequent false detection of positive selection by the likelihood method with branch-site models JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh117 DO - 10.1093/molbev/msh117 ID - Zhang2004 ER - TY - JOUR AU - Bielawski, J. P. AU - Yang, Z. PY - 2003 DA - 2003// TI - Maximum likelihood methods for detecting adaptive evolution after gene duplication JO - J Struct Funct Genomics VL - 3 UR - https://doi.org/10.1023/A:1022642807731 DO - 10.1023/A:1022642807731 ID - Bielawski2003 ER - TY - JOUR AU - Yang, Z. AU - Bielawski, J. P. PY - 2000 DA - 2000// TI - Statistical methods for detecting molecular adaptation JO - TREE VL - 15 ID - Yang2000 ER - TY - JOUR AU - Wong, W. S. AU - Yang, Z. AU - Goldman, N. AU - Nielsen, R. PY - 2004 DA - 2004// TI - Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites JO - Genetics VL - 168 UR - https://doi.org/10.1534/genetics.104.031153 DO - 10.1534/genetics.104.031153 ID - Wong2004 ER - TY - JOUR AU - Jordan, G. AU - Goldman, N. PY - 2012 DA - 2012// TI - The effects of alignment error and alignment filtering on the sitewise detection of positive selection JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/msr272 DO - 10.1093/molbev/msr272 ID - Jordan2012 ER - TY - JOUR AU - Privman, E. AU - Penn, O. AU - Pupko, T. PY - 2012 DA - 2012// TI - Improving the performance of positive selection inference by filtering unreliable alignment regions JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/msr177 DO - 10.1093/molbev/msr177 ID - Privman2012 ER - TY - JOUR AU - Levy Karin, E. AU - Susko, E. AU - Pupko, T. PY - 2014 DA - 2014// TI - Alignment errors strongly impact likelihood-based tests for comparing topologies JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/msu231 DO - 10.1093/molbev/msu231 ID - Levy Karin2014 ER -