Genomewide comparative phylogenetic and molecular evolutionary analysis of tubby-like protein family in Arabidopsis, rice, and poplar

Genomics. 2008 Oct;92(4):246-53. doi: 10.1016/j.ygeno.2008.06.001. Epub 2008 Jul 23.


Tubby-like proteins, which are characterized by a highly conserved tubby domain, play an important role in the maintenance and function of neuronal cells during postdifferentiation and development in mammals. In additional to the tubby domain, most tubby-like proteins in plants also possess an F-box domain. Plants also appear to harbor a large number of TLP genes. To gain insight into how TLP genes evolved in plants, we conducted a comparative phylogenetic and molecular evolutionary analysis of the tubby-like protein gene family in Arabidopsis, rice, and poplar. Genomewide screening identified 11 TLP genes in Arabidopsis, 14 in rice, and 11 in poplar. Phylogenetic trees, domain organizations, and intron/exon structures classified this family into three subfamilies and indicated that species-specific expansion contributed to the evolution of this family in plants. We determined that in rice and poplar, the tubby-like protein family had expanded mainly through segmental duplication events. Tissue-specific expression analysis indicated that functional diversification of the duplicated TLP genes was a major feature of long-term evolution. Our results also demonstrated that the tubby and F-box domains had co-evolved during the evolution of proteins containing both domains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Evolution, Molecular*
  • Exons / genetics
  • Gene Expression Regulation, Plant / physiology
  • Genes, Plant / physiology
  • Introns / genetics
  • Oryza / genetics*
  • Oryza / metabolism
  • Phylogeny*
  • Populus / genetics*
  • Populus / metabolism
  • Protein Structure, Tertiary / physiology


  • Arabidopsis Proteins