/
| 〈 |
|
〉 |
Comparative evolutionary analysis of MADS-box genes in Arabidopsis thaliana and A. lyrata
Received date: 2009-11-11
Accepted date: 2009-12-16
Online published: 2010-03-20
MADS-box genes encode a family of transcription factors. In angiosperms, MADS-box genes play key roles in vegetative growth and reproductive development, and are indispensable for the formation of inflorescences, flowers and fruits. To understand the evolution of MADS-box genes on a relatively small time scale, we conducted comparative genomic studies of a pair of closely related plant species, Arabidopsis thaliana and A. lyrata. A total of 106 and 115 MADS-box genes were identified from the two species, respectively, and phylogenetic analyses suggested that these genes correspond to Types I and II MADS-box genes. Type I genes have been duplicated and lost extensively in the lineages leading to the two species, whereas the number of Type II genes has not changed very much during the same period. Comparisons of the locations of orthologous gene pairs not only detected chromosomal regions that showed clear microsynteny between the two genomes, but also found evidence that most newly gained genes were generated through tandem and dispersed duplications rather than segmental duplication. Molecular evolutionary studies further suggested that different clades of MADS-box genes have experienced significantly different patterns of evolution, with functional constraints being less stringent for Type I genes than for Type II genes. Our results will help better understand the genetic differences between closely related species, and stimulate additional studies on the mechanisms that underlie speciation and biodiversification.
Haoyue Xue, Guixia Xu, Chunce Guo, Hongyan Shan, Hongzhi Kong . Comparative evolutionary analysis of MADS-box genes in Arabidopsis thaliana and A. lyrata[J]. Biodiversity Science, 2010 , 18(2) : 109 -119 . DOI: 10.3724/SP.J.1003.2010.109
| [1] | Alvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C, Ditta GS, Vergara-Silva F, Yanofsky MF (2000) MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. The Plant Journal, 24,457-466. |
| [2] | Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics, 8,242. |
| [3] | Beaulieu J, Jean M, Belzile F (2007) Linkage maps for Arabidopsis lyrata subsp. lyrata and Arabidopsis lyrata subsp. petraea combining anonymous and Arabidopsis thaliana-derived markers . Genome, 50,142-150. |
| [4] | Becker A, Theissen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Molecular Phylogenetics and Evolution, 29,464-489. |
| [5] | Coen ES, Meyerowitz EM (1991) The war of whorls: genetic interactions controlling flower development. Nature, 353,31-37. |
| [6] | Das S, Nikolaidis N, Klein J, Nei M (2008) Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers. Proceedings of the National Academy of Sciences, USA, 105,16647-16652. |
| [7] | Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52,696-704. |
| [8] | Hernandez-Hernandez T, Martinez-Castilla LP, Alvarez-Buylla ER (2007) Functional diversification of B MADS-box homeotic regulators of flower development: adaptive evolution in protein-protein interaction domains after major gene duplication events. Molecular Biology and Evolution, 24,465-481. |
| [9] | Kianian SF, Quiros CF (1992) Generation of a Brassica oleracea composite RFLP map: linkage arrangements among various populations and evolutionary implications . Theoretical and Applied Genetics, 84,544-554. |
| [10] | Kim S, Yoo M-J, Albert VA, Farris JS, Soltis PS, Soltis DE (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implication of a 260-million-year-old duplication. American Journal of Botany, 91,2102-2118. |
| [11] | Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis , Arabis, and related genera (Brassicaceae). Molecular Biology and Evolution, 17,1483-1498. |
| [12] | Kramer EM, Jaramillo MA,Di Stilio VS (2004) Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms . Genetics, 166,1011-1023. |
| [13] | Kuittinen H, de Haan AA, Vogl C, Oikarinen S, Leppala J, Koch M, Mitchell-Olds T, Langley CH, Savolainen O (2004) Comparing the linkage maps of the close relatives Arabidopsis lyrata and A . thaliana. Genetics, 168,1575-1584. |
| [14] | Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25,1451-1452. |
| [15] | Martinez-Castilla LP, Alvarez-Buylla ER (2003) Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny . Proceedings of the National Academy of Sciences, USA, 100,13407-13412. |
| [16] | Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Current Opinion in Plant Biology, 8,122-128. |
| [17] | Nam J, Kim J, Lee S, An GH, Ma H, Nei MS (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proceedings of the National Academy of Sciences, USA, 101,1910-1915. |
| [18] | Nei M, Niimura Y, Nozawa M (2008) The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nature Reviews Genetics, 9,951-963. |
| [19] | Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution, 3,418-426. |
| [20] | Nicholas KB, Nicholas HB Jr, Deerfield II (1997) GeneDoc: a tool for editing and annotating multiple sequence alignments. EMBNEW NEWS, 4,1-4. |
| [21] | Nozawa M, Kawahara Y, Nei M (2007) Genomic drift and copy number variation of sensory receptor genes in humans. Proceedings of the National Academy of Sciences, USA, 104,20421-20426. |
| [22] | Nozawa M, Nei M (2008) Genomic drift and copy number variation of chemosensory receptor genes in humans and mice. Cytogenetic and Genome Research, 123,263-269. |
| [23] | Parenicova L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram RM, Kater MM, Davies B, Angenent GC, Colombo L (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world . The Plant Cell, 15,1538-1551. |
| [24] | Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14,817-818. |
| [25] | Purugganan MD, Suddith JI (1998) Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function . Proceedings of the National Academy of Sciences, USA, 95,8130-8134. |
| [26] | Riechmann JL, Meyerowitz EM (1997) MADS domain proteins in plant development. Biological Chemistry, 378,1079-1101. |
| [27] | Shan H, Zahn L, Guindon S, Wall PK, Kong H, Ma H, dePamphilis CW, Leebens-Mack J (2009) Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Molecular Biology and Evolution, 26,2229-2244. |
| [28] | Shan H, Zhang N, Liu C, Xu G, Zhang J, Chen Z, Kong H (2007) Patterns of gene duplication and functional diversification during the evolution of the AP1/ SQUA subfamily of plant MADS-box genes . Molecular Phylogenetics and Evolution, 44,26-41. |
| [29] | Shore P, Sharrocks AD (1995) The MADS-box family of transcription factors. European Journal of Biochemistry, 229,1-13. |
| [30] | Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24,1596-1599. |
| [31] | Theissen G (2001) Development of floral organ identity: stories from the MADS house. Current Opinion in Plant Biology, 4,75-85. |
| [32] | Theissen G, Becker A, Di Rosa A, Kanno A, Kim JT, Munster T, Winter KU, Saedler H (2000) A short history of MADS-box genes in plants. Plant Molecular Biology, 42,115-149. |
| [33] | 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 Research, 25,4876-4882. |
| [34] | Veron AS, Kaufmann K, Bornberg-Bauer E (2007) Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins. Molecular Biology and Evolution, 24,670-678. |
| [35] | Wapinski I, Pfeffer A, Friedman N, Regev A (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature, 449,54-61. |
| [36] | Xu GX, Kong HZ (2007) Duplication and divergence of floral MADS-box genes in grasses: evidence for the generation and modification of novel regulators. Journal of Integrative Plant Biology, 49,927-939. |
| [37] | Zahn LM, Kong H, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis DE, Depamphilis CW, Ma H (2005) The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history . Genetics, 169,2209-2223. |
| [38] | Zahn LM, Leebens-Mack JH, Arrington JM, Hu Y, Landherr LL, dePamphilis CW, Becker A, Theissen G, Ma H (2006) Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events . Evolution and Development, 8,30-45. |
| [39] | Zhang JZ (2003a) Evolution by gene duplication: an update. Trends in Ecology and Evolution, 18,292-298. |
| [40] | Zhang JZ (2003b) Overexpression analysis of plant transcription factors. Current Opinion in Plant Biology, 6,430-440. |
/
| 〈 |
|
〉 |