Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 101; no. 7; pp. 1910 - 1915
• Main Authors: Nam, J, Kim, J, Lee, S, An, G, Ma, H, Nei, M
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 17.02.2004; National Acad Sciences
• Subjects: Angiosperms; Arabidopsis - genetics; Arabidopsis thaliana; Biological Sciences; Birth rate; Datasets; Evolution; Evolution, Molecular; Flowers & plants; Genes; Genes, Plant - genetics; Genome, Plant; Genomes; Genomics; MADS box; MADS Domain Proteins - genetics; Magnoliopsida - genetics; Mortality; Oryza - genetics; Oryza sativa; Phylogenetics; Phylogeny; Plant Proteins - genetics; Plants; Protein Structure, Tertiary; Pseudogenes; Pseudogenes - genetics; Rice
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0308430100

Plant MADS-box genes form a large gene family for transcription factors and are involved in various aspects of developmental processes, including flower development. They are known to be subject to birth-and-death evolution, but the detailed features of this mode of evolution remain unclear. To have a deeper insight into the evolutionary pattern of this gene family, we enumerated all available functional and nonfunctional (pseudogene) MADS-box genes from the Arabidopsis and rice genomes. Plant MADS-box genes can be classified into types I and II genes on the basis of phylogenetic analysis. Conducting extensive homology search and phylogenetic analysis, we found 64 presumed functional and 37 nonfunctional type I genes and 43 presumed functional and 4 nonfunctional type II genes in Arabidopsis. We also found 24 presumed functional and 6 nonfunctional type I genes and 47 presumed functional and 1 nonfunctional type II genes in rice. Our phylogenetic analysis indicated there were at least about four to eight type I genes and ≈ 15-20 type II genes in the most recent common ancestor of Arabidopsis and rice. It has also been suggested that type I genes have experienced a higher rate of birth-and-death evolution than type II genes in angiosperms. Furthermore, the higher rate of birth-and-death evolution in type I genes appeared partly due to a higher frequency of segmental gene duplication and weaker purifying selection in type I than in type II genes.