Evolutionary Conservation And Functional Divergence Of E(z) Homologous Genes In Green Plants

Histone methylation modification is major mechanism of epigenetic regulation that controls the growth and developmental processes by affecting gene transcription.Polycomb Group(PcG)protein is important epigenetic regulator,which plays vital role in the maintenance of silent states of genes and developmental regulation.E(z)(Enhancer of zeste)proteins are a component of PcG complex,and it also belongs to the SET domain family.E(z)proteins are associated with methylation of lysine residue 27 of histone(H3K27me3)and widely exist in plants and animals.In mammals,there are two E(z)homologous genes,EZHl and EZH2.In Arabidopsis,E(z)homologous genes underwent several duplication events,resulting in three copies,CLF(CURLY LEAF),SWN(SWINGER)and MEA(MEDEA).In order to deeply understand the evolutionary process of histone methylation-related genes in plants,the evolutionary history of E(z)homologous genes by comparative genomics and phylogenetic analysis.The main results are as follows:(1)Phylogenetic analysis was performed by comparative genomic analysis.The large-scale phylogenetic analysis showed that E(z)homologous genes appeared to be highly conserved only as single or low-copy genes in green algae and early land plants,whereas E(z)homologous genes underwent a duplication event,resulting in two copies in seed plants,divided into two clades:CLF and SWN.(2)Protein-conserved domain and motif architectures E(z)proteins were analyzed by SMART and MEME,respectively.The conserved domain showed that E(z)proteins contained SET domain,CXC domain and SANT domain.The motif architectures indicated that some highly differentiated motifs were identified in some species(3)The phylogenetic analysis of E(z)homologous genes in angiosperms was reconstructed.The results showed that E(z)homologous genes of Brassicaceae and Fabaceae were divided into two sub-clades.In Brassicaceae,SWN clade underwent whole genome duplications and divided into two sub-clades:SWN and MEA.Brassicaceae MEA evolved rapidly under positive selections and acquired a novel function in regulating seed development.Brassicaceae SWN probably retained its ancestral functions and evolved under purifying selection.Similar to that,the SWN clade in Fabaceae also underwent the whole genome duplication and divided into two sub-clades,SWNl and SWN2(4)Protein-conserved domain and motif architectures of Brassicaceae and Fabaceae E(z)proteins were analyzed by SMART and MEME,respectively.In Brassicaceae,compared to the SWNl sub-clade,the SWN2 sub-clade proteins lost 200 amino acids in the middle region There was a similar phenomenon in Brassicaceae,suggesting the loss of 200 amino acids may be crucial for the functional divergence of the two sub-clades.(5)The average Ka/Ks ratio of SWNl sub-clade and SWN2 sub-clade in Fabaceae were calculated with PAML.SWNl sub-clade probably retained its ancestral functions and evolved under purifying selection;SWN2 sub-clade showed evidence of positive selection(6)Based on RNA-Seq data from public databases,we analyzed temporal and spatial expression patterns of E(z)homologous genes in Glycine max.SWN1 was expressed generally in various tissues;SWN2 was only expressed in heart-shaped embryo.These results showed SWN2 may be a new gene,like Brassicaceae-specific MEA.In conclusion,we systematically analyzed the evolutionary conservation and diversification of E(z)homologous genes from lower to higher plants,elucidated the evolutionary history of E(z)homologous genes.Moreover,we speculated that SWN2 might acquire new functions,which may guide future functional characterization of these importantepigenetic regulators in plants other than Arabidopsis.