Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication.

Heng Dong,Yuxue Zhao,Jiashu Cao,Sue Lin,Zhong-Hua Chen,Li Huang,Ji Sun,Dandan Liu,Tianyu Han

doi:10.1038/srep16851

Abstract

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci.

Highlights

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression
The SDG gene family is classified into seven groups in Arabidopsis thaliana: Group I, Enhancer of zeste homologs [E(z)]; Group II, Ash[1] homologs and related (Ash); Group III, trithorax homologs and related (Trx); Group IV, Arabidopsis trx related 5 (ATXR5) and ATXR6 homologs (ATXR5/6); Group V, Suppressor of variegation [Su(var)] homologs and related (Suv); Group VI, SET- and myeloid-Nervy-DEAF-1 (MYND)-domain containing HKMTases (SMYD); Group VII, RBCMT and other SET-related proteins (SETD)
Our results illustrated that the expansion of the BrSDG family was primarily due to the whole genome triplication (WGT) event, with rearrangement and tandem duplication taking place at some loci

Summary

Introduction

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. A new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. Histone lysine methylation plays critical roles in the epigenetic regulation of gene expression[1]. It participates in plant growth and development, exhibits dynamic changes to important environmental factors, such as hormones, water-stress and light[2,3,4]. ASH1-RELATED3 (ASHR3), ASHH2 in the Ash group, ATXR3 in the Trx group and ATXR6 in the ATXR5/6 group are required for sporophyte development[15,16,17,18]

Methods

Results

Conclusion