Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes

Abstract

RNA-binding glycine-rich (RBG) proteins play diverse roles in plant growth, development, protection and genome organization. An overly broad definition for class IV glycine-rich proteins (GRPs), namely RNA-binding activity and a glycine-rich C-terminus, has resulted in many distantly related and/or non-related proteins being grouped into this class of RBGs. This definition has hampered the study of RBG evolution. In this study, we used a comparative genomic approach consisting of ortholog, homolog, synteny and phylogenetic analyses to legitimately exclude all distantly/non-related proteins from class IV GRPs and to identify 15, 22, 12 and 18 RBG proteins in Arabidopsis, Chinese cabbage, rice and maize genomes, respectively. All identified RBGs could be divided into three subclasses, namely RBGA, RBGB and RBGD, which may be derived from a common ancestor. We assigned RBGs excluded from class IV GRPs to a separate RBG superfamily. RBGs have evolved and diversified in different species via different mechanisms; segmental duplication and recombination have had major effects, with tandem duplication, intron addition/deletion and domain recombination/deletion playing minor roles. Loss and retention of duplicated RBGs after polyploidization has been species and subclass specific. For example, following recent whole-genome duplication and triplication in maize and Chinese cabbage, respectively, most duplicated copies of RBGA have been lost in maize while RBGD duplicates have been retained; in Chinese cabbage, in contrast, RBGA duplicates have been retained while RBGD duplicates have been lost. Our findings reveal fundamental information and shed new light on the structural characteristics and evolutionary dynamics of RBGs.

Genomic Identification and Comparative Expansion Analysis of the Non-Specific Lipid Transfer Protein Gene Family in Gossypium

“…In addition, G. arboreum lost all the Type III and Type IX nsLTPs (Fig. S2), suggesting that the evolution of plants not only involves gene retentions, but also is accompanied by gene losses and mutations428. Meanwhile, the proportion of nsLTPs in each subfamily indicated that Type I seemed to have contracted while Type VIII expanded in G. hirsutum compared with its diploid progenitors (Fig.…”

Genome-wide identification and expression analysis of glycine-rich protein genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

“…Anyway, 15, 22, 12, and 18 glycine-rich RNA-binding proteins (RBGs) have been identified in Arabidopsis, Chinese cabbage, rice and maize genomes, respectively [22,24], furthermore, 9 and 51 GRP genes have been identified in sweet potato and Curcuma longa L., respectively [21,23]. In this paper, 141 BrGRP genes were preliminarily identified in Chinese cabbage based on the BRAD genome sequence.…”

“…Although the research of GRP genes has been reported in many plants [21][22][23][24], the GRP gene has seldom reported in Chinese cabbage so far. In previous study, we found that an Oleosin-GRP gene BcGRP17 showed higher expression levels in flower buds of male fertile plant than in sterile plant but the detail function is still unknown [25].…”

A Plant SMALL RNA-BINDING PROTEIN 1 Family Mediates Cell-to-Cell Trafficking of RNAi Signals

“…To ascertain whether CsSRBP1 has homologs in the model plant, Arabidopsis thaliana, a phylogenetic analysis was performed and we identified four potential CsSRBP1 homologs, AtSRBP1-4 ( Figure 2A), also identified as AtRBP7/8/2/4 (Krishnamurthy et al, 2015). As with CsSRBP1, all four homologs had a highly conserved RRM domain, but, by contrast, the GR domain was of variable length for these Arabidopsis family members ( Figure 2B and Supplemental Figure 1B We next assessed whether AtSRBP1-4 could also interdict ZYMV infection.…”