Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula.

Yuanyuan Zhao,Junchao Zhang,Yixiong Tang,Zhanmin Sun,Yanmin Wu

doi:10.3390/ijms22147537

Abstract

Polycomb group (PcG) proteins, which are important epigenetic regulators, play essential roles in the regulatory networks involved in plant growth, development, and environmental stress responses. Currently, as far as we know, no comprehensive and systematic study has been carried out on the PcG family in Medicago truncatula. In the present study, we identified 64 PcG genes with distinct gene structures from the M. truncatula genome. All of the PcG genes were distributed unevenly over eight chromosomes, of which 26 genes underwent gene duplication. The prediction of protein interaction network indicated that 34 M. truncatula PcG proteins exhibited protein–protein interactions, and MtMSI1;4 and MtVRN2 had the largest number of protein–protein interactions. Based on phylogenetic analysis, we divided 375 PcG proteins from 27 species into three groups and nine subgroups. Group I and Group III were composed of five components from the PRC1 complex, and Group II was composed of four components from the PRC2 complex. Additionally, we found that seven PcG proteins in M. truncatula were closely related to the corresponding proteins of Cicer arietinum. Syntenic analysis revealed that PcG proteins had evolved more conservatively in dicots than in monocots. M. truncatula had the most collinearity relationships with Glycine max (36 genes), while collinearity with three monocots was rare (eight genes). The analysis of various types of expression data suggested that PcG genes were involved in the regulation and response process of M. truncatula in multiple developmental stages, in different tissues, and for various environmental stimuli. Meanwhile, many differentially expressed genes (DEGs) were identified in the RNA-seq data, which had potential research value in further studies on gene function verification. These findings provide novel and detailed information on the M. truncatula PcG family, and in the future it would be helpful to carry out related research on the PcG family in other legumes.

Highlights

A large number of studies have shown that epigenetics plays an important regulatory role throughout the life cycle from plant growth and development to senescence and death
The results showed that the ORF lengths of the M. truncatula polycomb group (PcG) genes ranged from 315 (MtVRN1;23, encodes 104 amino acids) to 3651 bp (MtFIE;4, encodes 1216 amino acids), the MW of the M. truncatula PcG proteins varied from 29.13 (MtRING1B;2) to 136.27 kDa (MtFIE;4), the pI value ranged from 3.97 (MtRING1B;2) to 9.99 (MtVRN1;24), and all of the M. truncatula PcG proteins were hydrophilic
The secondary structure analysis (Table 2) of M. truncatula PcG proteins showed that the α-helixes ranged from 3.68% (MtFIE;16) to 50.79% (MtRING1B;2), the extended strand varied from 7.34% (MtRING1A) to 45.09% (MtFIE;16), the β-sheet extended from 1.71% (MtEMF1;1) to 14.42% (MtFIE;16), and the random coil ranged from 28.28% (MtFIE;18) to 73.20% (MtEMF1;1)

Summary

Introduction

A large number of studies have shown that epigenetics plays an important regulatory role throughout the life cycle from plant growth and development to senescence and death This includes effects on the morphological architecture, physiological process, metabolic pathways, and evolutionary adaptation of plants. Numerous PcG proteins have been identified in several plants, including Arabidopsis thaliana, Oryza sativa, Zea mays, mosses, and green algae in recent years [2] These studies mainly focus on the regulation of important biological processes, such as plant flowering [4,5], growth and development [6,7,8], and stress responses [9,10,11]. It was initially considered that PRC1 acts strictly downstream of PRC2, whereas recent studies suggest that the two complexes may function together or independently in transcriptional repression [19]

Methods

Results

Conclusion