Evolution of the RALF Gene Family in Plants: Gene Duplication and Selection Patterns

被引:77
作者
Cao, Jun [1 ]
Shi, Feng [2 ]
机构
[1] Jiangsu Univ, Inst Life Sci, Zhenjiang 212013, Jiangsu, Peoples R China
[2] Shandong Lvdu Biotech Ind, Binzhou 256600, Shandong, Peoples R China
来源
EVOLUTIONARY BIOINFORMATICS | 2012年 / 8卷
基金
美国国家科学基金会;
关键词
RALF; tandem duplication; evolution; selection; PEPTIDE SIGNAL; PHYTOSULFOKINE-ALPHA; SELF-INCOMPATIBILITY; ARABIDOPSIS; EXPRESSION; GROWTH; OVEREXPRESSION; IDENTIFICATION; SUBSTITUTIONS; CONSEQUENCES;
D O I
10.4137/EBO.S9652
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Rapid alkalinization factors (RALFs) are plant small peptides that could induce a rapid pH increase in the medium of plant cell suspension culture and play a critical role in plant development. The evolutionary process of the RALF gene family remains unclear. To obtain details of the phylogeny of these genes, this study characterized RALF genes in Arabidopsis, rice, poplar and maize. Phylogenetic trees, evolutionary patterns and molecular evolutionary rates were used to elucidate the evolutionary process of this gene family. In addition, the different signatures of selection, expression patterns, and subcellular localization of RALFs were also analyzed. We found that the RALF gene family had a rapid birth process after the separation of the eudicot and monocot species about 145 million years ago, that tandem duplication played a dominant role in the expansion of Arabidopsis and rice RALF gene family, and that RALFs were under purifying selection according to estimations of the substitution rates of these genes. We also identified a diverse expression pattern of RALF genes and predominant extracellular localization feature of RALF proteins. Our findings shed light on several key differences in RALF gene family evolution among the plant species, which may provide a scaffold for future functional analysis of this family.
引用
收藏
页码:271 / 292
页数:22
相关论文
共 67 条
[1]   Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].
Kaul, S ;
Koo, HL ;
Jenkins, J ;
Rizzo, M ;
Rooney, T ;
Tallon, LJ ;
Feldblyum, T ;
Nierman, W ;
Benito, MI ;
Lin, XY ;
Town, CD ;
Venter, JC ;
Fraser, CM ;
Tabata, S ;
Nakamura, Y ;
Kaneko, T ;
Sato, S ;
Asamizu, E ;
Kato, T ;
Kotani, H ;
Sasamoto, S ;
Ecker, JR ;
Theologis, A ;
Federspiel, NA ;
Palm, CJ ;
Osborne, BI ;
Shinn, P ;
Conway, AB ;
Vysotskaia, VS ;
Dewar, K ;
Conn, L ;
Lenz, CA ;
Kim, CJ ;
Hansen, NF ;
Liu, SX ;
Buehler, E ;
Altafi, H ;
Sakano, H ;
Dunn, P ;
Lam, B ;
Pham, PK ;
Chao, Q ;
Nguyen, M ;
Yu, GX ;
Chen, HM ;
Southwick, A ;
Lee, JM ;
Miranda, M ;
Toriumi, MJ ;
Davis, RW .
NATURE, 2000, 408 (6814) :796-815
[2]   MEME SUITE: tools for motif discovery and searching [J].
Bailey, Timothy L. ;
Boden, Mikael ;
Buske, Fabian A. ;
Frith, Martin ;
Grant, Charles E. ;
Clementi, Luca ;
Ren, Jingyuan ;
Li, Wilfred W. ;
Noble, William S. .
NUCLEIC ACIDS RESEARCH, 2009, 37 :W202-W208
[3]   RALFs Peptide regulators of plant growth [J].
Bedinger, Patricia A. ;
Pearce, Gregory ;
Covey, Paul A. .
PLANT SIGNALING & BEHAVIOR, 2010, 5 (11) :1342-1346
[4]   Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes [J].
Blanc, G ;
Wolfe, KH .
PLANT CELL, 2004, 16 (07) :1667-1678
[5]   A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome [J].
Blanc, G ;
Hokamp, K ;
Wolfe, KH .
GENOME RESEARCH, 2003, 13 (02) :137-144
[6]   Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events [J].
Bowers, JE ;
Chapman, BA ;
Rong, JK ;
Paterson, AH .
NATURE, 2003, 422 (6930) :433-438
[7]   INFLORESCENCE DEFICIENT IN ABSCISSION controls floral organ abscission in arabidopsis and identifies a novel family of putative ligands in plants [J].
Butenko, MA ;
Patterson, SE ;
Grini, PE ;
Stenvik, GE ;
Amundsen, SS ;
Mandal, A ;
Aalen, RB .
PLANT CELL, 2003, 15 (10) :2296-2307
[8]   Dynamics of arginase gene evolution in metazoans [J].
Cao, Jun ;
Shi, Feng .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2012, 30 (04) :407-418
[9]   Analyses of the oligopeptide transporter gene family in poplar and grape [J].
Cao, Jun ;
Huang, Jinling ;
Yang, Yongping ;
Hu, Xiangyang .
BMC GENOMICS, 2011, 12
[10]   Genome-Wide Identification and Evolutionary Analysis of Arabidopsis Sm Genes Family [J].
Cao, Jun ;
Shi, Feng ;
Liu, Xiaoguang ;
Jia, Jinli ;
Zeng, Jun ;
Huang, Guang .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2011, 28 (04) :535-544