Genome-Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa
Xuan Yao
Shanghai Jiao Tong University-Shanghai Institute for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
School of Life Sciences, Shanghai University, Shanghai 200444, China
Search for more papers by this authorHong Ma
Shanghai Jiao Tong University-Shanghai Institute for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Search for more papers by this authorJian Wang
School of Life Sciences, Shanghai University, Shanghai 200444, China
Search for more papers by this authorCorresponding Author
Dabing Zhang
Shanghai Jiao Tong University-Shanghai Institute for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
*Author for correspondence. Tel: +86 (0)21 3420 5073; Fax:+86 (0)21 3420 4869; E-mail: <[email protected]>.Search for more papers by this authorXuan Yao
Shanghai Jiao Tong University-Shanghai Institute for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
School of Life Sciences, Shanghai University, Shanghai 200444, China
Search for more papers by this authorHong Ma
Shanghai Jiao Tong University-Shanghai Institute for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Department of Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Search for more papers by this authorJian Wang
School of Life Sciences, Shanghai University, Shanghai 200444, China
Search for more papers by this authorCorresponding Author
Dabing Zhang
Shanghai Jiao Tong University-Shanghai Institute for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
*Author for correspondence. Tel: +86 (0)21 3420 5073; Fax:+86 (0)21 3420 4869; E-mail: <[email protected]>.Search for more papers by this authorSupported by Funds from the National Key Basic Research Developments Program of the Ministry of Science and Technology, China (2006CB101700, 2005CB120802), the High-Tech Research and Development (863) Programe of China (2005AA2710330), the Shuguang Scholarship (04SG15), and the Shanghai Institutes of Biological Sciences (Reproductive Development Project).
Publication of this paper is supported by the National Natural Science Foundation of China (30624808).
Abstract
Several TCP genes have been reported to play important roles in plant development; the TCP homologs encode a plant-specific family of putative transcription factors. To understand the evolutionary relationship of TCP genes of Arabidopsis thaliana and Oryza sativa L. (hereafter called rice), we have identified 23 and 22 TCP genes in the Arabidopsis and rice genomes, respectively. Using phylogenetic analysis, we grouped these TCP genes into three classes. In addition, the motifs outside the TCP domain further support the evolutionary relationships among these genes. The genome distribution of the TCP genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the TCP gene family. The expression pattern of the TCP genes was analyzed further, providing useful clues about the function of these genes.
References
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
- Bailey PC, Martin C, Toledo-Ortiz G, Quail PH, Huq E, Heim MA et al. (2003). Update on the basic helix-loop-helix transcription factor gene family i. Arabidopsis thaliana. Plant Cell 15, 2497–2502.
- Bailey TL, Elkan C (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36.
- Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000). Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12, 1093–1101.
- Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004). The roles of segmental and tandem gene duplication in the evolution of large gene families i. Arabidopsis thaliana. BMC Plant Biol. 4, 10.
- Chomczynski P, Sacchi N (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156–159.
- Citerne HL, Luo D, Pennington RT, Coen E, Cronk QC (2003). A phylogenomic investigation of CYCLOIDEA-like TCP genes in the Leguminosae. Plant Physiol. 131, 1042–1053.
- Cubas P, Lauter N, Doebley J, Coen E (1999). The TCP domain: A motif found in proteins regulating plant growth and development. Plant J. 18, 215–222.
-
Cubas P (2002). Role of TCP genes in the evolution of morphological characters in angiosperms. In: QCB Cronk,
RM Bateman,
JA Hawkins, eds.
Developmental Genetics and Plant Evolution. Taylor & Francis,
London
. pp.
247–266.
10.1201/9781420024982.ch13 Google Scholar
- Dingwall C, Laskey RA (1991). Nuclear targeting sequences: A consensus. Trends Biochem. Sci. 16, 478–481.
- Doebley J, Stec A, Gustus C (1995). Teosinte branched1 and the origin of maize: Evidence for epistasis and the evolution of dominance. Genetics 141, 333–346.
- Doebley J, Stec A, Hubbard L (1997). The evolution of apical dominance in maize. Nature 386, 485–488.
- Faivre-Rampant O, Bryan GJ, Roberts AG, Milbourne D, Viola R, Taylor MA (2004). Regulated expression of a novel TCP domain transcription factor indicates an involvement in the control of meristem activation processes i. Solanum tuberosum. J. Exp. Bot. 55, 951–953.
- Guo A, He K, Liu D, Bai S, Gu X, Wei L et al. (2005). DATF: A database of Arabidopsis transcription factors. Bioinformatics 21, 2568–2569.
- Guyot R, Keller B (2004). Ancestral genome duplication in rice. Genome 47, 610–614.
- Heery DM, Kalkhoven E, Hoare S, Parker MG (1997). A signature motif in transcriptional co-activators mediates binding to nuclear receptors. Nature 387, 733–736.
- Howarth DG, Donoghue MJ (2006). Phylogenetic analysis of the “ECE” (CYC/TB1) clade reveals duplications predating the core eudicots. Proc. Natl. Acad. Sci. USA 103, 9101–9106.
- Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003). Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 100, 11484–11489.
- Kosugi S, Ohashi Y (1997). PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. Plant Cell 9, 1607–1619.
- Kumar S, Tamura K, Nei M (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5, 150–163.
- Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J et al. (2004). SMART 4.0: Towards genomic data integration. Nucleic Acids Res. 32, D142–144.
- Li C, Potuschak T, Colon-Carmona A, Gutierrez RA, Doerner P. (2005). Arabidopsis TCP20 links regulation of growth and cell. division control pathways. Proc. Natl. Acad. Sci. USA 102, 12978–12983.
- Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z et al. (2006). Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol. 141, 1167–1184.
- Luo D, Carpenter R, Vincent C, Copsey L, Coen E (1996). Origin of floral asymmetry i. Antirrhinum. Nature 383, 794–799.
- Mehan MR, Freimer NB, Ophoff RA (2004). A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture. Hum. Genomics 1, 335–344.
- Murre C, Bain G, Van Dijk MA, Engel I, Furnari BA, Massari ME et al. (1994). Structure and function of helix-loop-helix proteins. Biochim. Biophys. Acta 1218, 129–135.
- Reeves PA, Olmstead RG (2003). Evolution of the TCP gene family in Asteridae: Cladistic and network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. Mol. Biol. Evol. 20, 1997–2009.
- Schultz J, Milpetz F, Bork P, Ponting CP (1998). SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl. Acad. Sci. USA 95, 5857–5864.
- Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M et al. (2003). The OsTB1 gene negatively regulates lateral branching in rice. Plant J. 33, 513–520.
- Takeda T, Amano K, Ohto MA, Nakamura K, Sato S, Kato T et al. (2006). RNA interference of the Arabidopsis putative transcription factor TCP16 gene results in abortion of early pollen development. Plant Mol. Biol. 61, 165–177.
- Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882.
