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

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.

Genome-wide identification and characterization of polycomb repressive complex 2 core components in upland cotton (Gossypium hirsutum L.)

“…These cereal E(z) homologs are orthologs of Arabidopsis CLF and SWN, and the Su(z)12 homologs fall into the EMF2 clade [ 49 ]. A recent study in M. truncatula identified 31 PRC2 core components, containing two MEA ortholog and one VRN2 ortholog [ 24 ], which is distinct from those in cereals.…”

“…The orthologs of Arabidopsis MEA and FIS2 are also absent in cotton species, in line with that in cereals [ 17 – 20 , 23 ]. Nevertheless, the VRN2 orthologs have been identified, similar to M. truncatula [ 24 ]. Unsurprisingly, different cotton PRC2 members of the same clade display good collinearity, identical gene and protein structures, and similar subcellular localizations (Fig.…”

“…Using RNA-seq data, a study in bread wheat revealed that the PcG homologs within the A, B and D subgenomes show highly similar transcriptional profiles, whereas members in different clades display variable transcriptional activities [ 23 ]. Another work in M. truncatula explored various types of expression of PcG genes and predicted their functions in the regulation of development and response to various environmental stimuli [ 24 ]. A very recent study in rice indicated that PcG genes are differentially expressed in different tissues, and responded variably in different environmental stress [ 63 ].…”

“…The duplication enables alternative combinations of these four subunits to form at least three distinct PRC2 complexes, named FIS-PRC2 (FIS2, MEA, FIE, MSI1), EMF2-PRC2 (EMF2, CLF/SWN, FIE, MSI1), and VRN2-PRC2 (VRN2, CLF/SWN, FIE, MSI1) [ 1 – 3 , 15 , 16 ]. PRC2 components have been also identified in other plant species, including rice [ 17 ], maize [ 18 , 19 ], green lineage [ 20 ], Brachypodium distachyon [ 21 ], barley [ 22 ], bread wheat [ 23 ] and Medicago truncatula [ 24 ]. Notably, the composition of PRC2 complexes displays considerable variability in different species.…”

Identification and Characterization of Abiotic Stress–Responsive NF-YB Family Genes in Medicago

“…Previous studies have shown that the NF-YB subfamily plays key role in improving drought tolerance in plants such as Arabidopsis [13], tobacco [18], and maize [19]. Gene families such as P450 [23], HD-ZIP [24], SRS [25], and PcG [26] in Medicago have been identified. These families are related to abiotic stress and growth, but the NF-YB gene family has not yet been reported.…”