Molecular evolution analysis of WUSCHEL-related homeobox transcription factor family reveals functional divergence among the clades in the homeobox region

Development Genes and Evolution

A. L. A. Segatto, C. E. Thompson, L. B. Freitas

Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, PO Box 15053, Porto Alegre, RS 91501-970, Brazil

Fig. S2 Species phylogenetic tree, the whole genome duplication events are indicated by the yellow asterisk. Estimated genome size in mega bases and number of WUSCHEL-related homeobox genes in each species are indicated in the right side. The red superscript numbers indicate the references used, as follow:1The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:795-815;2Hu TT, Pattyn P, Bakker EG, Cao J, Cheng J, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H et al (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature 43:476-481;3The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature 43:1035-1039;4Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo Y, Steige K, Platts AE, Escobar JS, Newman LK, et al (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature 45:831-835;5Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Pavel Senin P, Wang W, Ly BV, Lewis KLT et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-995;6Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S et al (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44:1098-1103;7Argout X, Salse J, Aury J, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN et al (2011) The genome of Theobroma cacao. Nature 43:101-108; 8Xu Q, Chen L, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao W, Hao B, Lyon MP et al (2013) The draft genome of sweet orange (Citrus sinensis). Nature 45:59-66; 9Myburg A, Grattapaglia D, Tuskan G, Jenkins J, Schmutz J, Mizrachi E, Hefer C, Pappas G, Sterck L, Van De Peer Y et al (2011) The Eucalyptus grandis Genome Project: Genome and transcriptome resources for comparative analysis of woody plant biology. BMC Proceedings 5:I20; 10The French–Italian Public Consortium for Grapevine Genome Characterization (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463-467;11Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178-183;12Blair MW, Cortés AJ, Penmetsa RV, Farmer A, Carrasquilla-Garcia N, Cook DR (2013) A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet 126:535-548;13Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480:22-29;14Huang S , Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P et a. (2009) The genome of the cucumber, Cucumis sativus L. Nature 41:1275 -1281;15Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP et al (2011) The genome of woodland strawberry (Fragaria vesca). Nature 43:109-114;16The International Peach Genome Initiative (2013) The high-quality draft genome of peach (Prunus ­persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature 45:487-494;17Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R et al (2012)The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant Journal 72:461-473;18Tuskan GA,DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al (2006) The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-160;19Fregene M, Angel F, Gomez R, Rodriguez F, Chavarriaga P, Roca W, Tohme J, Bonierbale M (1997) A molecular genetic map of cassava (Manihot esculenta Crantz). Theor Appl Genet 95:431-441;20Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G et al (2010) Draft genome sequence of the oil seed species Ricinus communis. Nature 28:951-959;21The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635- 641;22Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 29:551-556;23Schnablea JC, Springerb NM, Freelinga M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. PNAS 108:4069-4074; 24Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. N. biotechnology 30:549-554; 25Sharma MK, Sharma R, Cao P, Jenkins J, Bartley LE, Qualls M, Grimwood J, Schmutz J, Rokhsar D, Ronald PC (2012) A Genome-Wide Survey of Switchgrass Genome Structure and Organization. Plos One 7:e33892;26Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD et al (2008) The nuclear genome of Brachypodiumdistachyon: analysis of BAC end sequences. Funct Integr Genomics 8:135-147;27Goff SA, Ricke D, Lan T, Presting G,Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al (2002) A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica). Science 296:92-100;28Wang W, Tanurdzic M, Luo M, Sisneros N, Kim HR, Weng J, Kudrna D, Mueller C, Arumuganathan K, Carlson J et al (2005) Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Biol 5:10;29Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P, Lindquist EA, Kamisugi Y et al (2008) The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 319:64-69;30Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S et al (2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol 13:R39; 31Peers Gand and Niyogi KK (2008) Pond Scum Genomics: The Genomes of Chlamydomonas and Ostreococcus. Plant Cell 20:502-507; 32Huang S, Su X, Haselkorn R, Gornicki P (2003) Evolution of switchgrass (Panicum virgatum L.) based on sequences of the nuclear gene encoding plastid acetyl-CoA carboxylase. Plant Science 164:43-49;33Missaoui AM, Paterson AH, Bouton JH (2005) Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers. Theor Appl Genet 110:1372-1383;34Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433-438.