title: Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms.
abstract: 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 approximately 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.
authors.affiliation: Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Jongmin
authors.initials: J
authors.lastname: Nam
authors.forename: Joonyul
authors.initials: J
authors.lastname: Kim
authors.forename: Shinyoung
authors.initials: S
authors.lastname: Lee
authors.forename: Gynheung
authors.initials: G
authors.lastname: An
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Nei
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant; D026161:MADS Domain Proteins / Q000235:genetics*; D019684:Magnoliopsida / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D017434:Protein Structure, Tertiary; D011544:Pseudogenes / Q000235:genetics
chemical_list: D026161:MADS Domain Proteins; D010940:Plant Proteins