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

Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1910-5. doi: 10.1073/pnas.0308430100. Epub 2004 Feb 5.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Evolution, Molecular*
  • Genes, Plant / genetics*
  • Genome, Plant
  • MADS Domain Proteins / genetics*
  • Magnoliopsida / genetics*
  • Oryza / genetics
  • Phylogeny
  • Plant Proteins / genetics
  • Protein Structure, Tertiary
  • Pseudogenes / genetics

Substances

  • MADS Domain Proteins
  • Plant Proteins