title: Molecular evolution of VEF-domain-containing PcG genes in plants.
abstract: Arabidopsis VERNALIZATION2 (VRN2), EMBRYONIC FLOWER2 (EMF2), and FERTILIZATION-INDEPENDENT SEED2 (FIS2) are involved in vernalization-mediated flowering, vegetative development, and seed development, respectively. Together with Arabidopsis VEF-L36, they share a VEF domain that is conserved in plants and animals. To investigate the evolution of VEF-domain-containing genes (VEF genes), we analyzed sequences related to VEF genes across land plants. To date, 24 full-length sequences from 11 angiosperm families and 54 partial sequences from another nine families were identified. The majority of the full-length sequences identified share greatest sequence similarity with and possess the same major domain structure as Arabidopsis EMF2. EMF2-like sequences are not only widespread among angiosperms, but are also found in genomic sequences of gymnosperms, lycophyte, and moss. No FIS2- or VEF-L36-like sequences were recovered from plants other than Arabidopsis, including from rice and poplar for which whole genomes have been sequenced. Phylogenetic analysis of the full-length sequences showed a high degree of amino acid sequence conservation in EMF2 homologs of closely related taxa. VRN2 homologs are recovered as a clade nested within the larger EMF2 clade. FIS2 and VEF-L36 are recovered in the VRN2 clade. VRN2 clade may have evolved from an EMF2 duplication event that occurred in the rosids prior to the divergence of the eurosid I and eurosid II lineages. We propose that dynamic changes in genome evolution contribute to the generation of the family of VEF-domain-containing genes. Phylogenetic analysis of the VEF domain alone showed that VEF sequences continue to evolve following EMF2/VRN2 divergence in accordance with species relationship. Existence of EMF2-like sequences in animals and across land plants suggests that a prototype form of EMF2 was present prior to the divergence of the plant and animal lineages. A proposed sequence of events, based on domain organization and occurrence of intermediate sequences throughout angiosperms, could explain VRN2 evolution from an EMF2-like ancestral sequence, possibly following duplication of the ancestral EMF2. Available data further suggest that VEF-L36 and FIS2 were derived from a VRN2-like ancestral sequence. Thus, the presence of VEF-L36 and FIS2 in a genome may ultimately be dependent upon the presence of a VRN2-like sequence.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
authors.forename: Ling-Jing
authors.initials: LJ
authors.lastname: Chen
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
authors.forename: Zhao-Yan
authors.initials: ZY
authors.lastname: Diao
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
authors.forename: Chelsea
authors.initials: C
authors.lastname: Specht
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA. Electronic address: zrsung@nature.berkeley.edu.
authors.forename: Z Renee
authors.initials: ZR
authors.lastname: Sung
mesh_terms: D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D002352:Carrier Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D004268:DNA-Binding Proteins; D019143:Evolution, Molecular; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000737:chemistry / Q000145:classification / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; C494299:EMF2 protein, Arabidopsis; C117389:FIS2 protein, Arabidopsis; D009687:Nuclear Proteins; D010940:Plant Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; C442836:VRN2 protein, Arabidopsis