Genome-wide analysis of the RING finger gene family in apple

Abstract

The RING finger protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for apple (Malus × domestica L. Borkh) due to the limited information on whole genome sequences. In this study, 688 RING domains in 663 predicted proteins were identified in apple. Based on the spacing between metal ligands or substitutions at one or more of the metal ligand positions, nine RING types were identified: RING-H2, RING-HC, RING-C2, RING-v, RING-D, RING-S/T, RING-G, RING-mH2, and RING-mHC, in which the first seven types were described previously in Arabidopsis, while the latter two were newly identified in apple. Proteins containing RING finger motifs were further classified into 57 groups according to the different known or unknown domains outside the RING domains. A total of 643 retrieved proteins appear to be distributed over all 17 linkage groups with different densities. Microarray and expressed sequence tag data revealed that only a few of these RING finger proteins may be involved in fruit development. As a first step towards genome-wide analyses of the RING-containing genes in apple, our results provide valuable information for understanding the classification and putative functions of the RING finger gene family in higher plants.

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development, and phytohormone and abiotic stress responses

“…Our investigation of gene duplication indicated that the G. hirsutum RH2FE3 gene family expanded through tandem as well as segmental duplication events. The RH2FE3 genes had the same duplication patterns in Arabidopsis (Serrano et al 2006), rice (Lim et al 2010), apple (Li et al 2011), and poplar (Liu et al 2015). Thus, we consider the complexity of RH2FE3 genes is the result of diverse duplication events.…”

“…RING proteins are responsive to various biological processes (Lyzenga and Stone 2012), including plant growth and development (Li et al 2011;Schwechheimer et al 2009;Zhang et al 2008), hormone signaling pathways (Bu et al 2009), cell cycle, embryogenesis, and biotic and abiotic stress responses (Lee and Kim 2011;Santner and Estelle 2010;Vierstra 2009). The diversified regulatory functions of RING proteins means they are involved in nearly every aspect of plant life, which makes them distinct from other proteins.…”

Genome-Wide Identification and Analysis of bZIP Family and their Expression in Response to Multiple Abiotic Stresses in Malus domestica

“…For the first method, all of the identified sequences of bZIP proteins from Arabidopsis and rice were used as queries to search the Golden Delicious peptide database (GDR http://www.rosaceae.org/) using software BLASTp [21]. Trying not to miss potential proteins and taking account of credible results, the E value cutoff was set to 0.001 as in references of similar investigations [22]. From this method, about 700 proteins were screened out.…”

“…Presumably these nine genes could be localized to unassembled genomic sequence scaffolds [22]. The number of M.bZIP genes on different chromosomes was variable.…”

“…Based on this result, we hypothesized that the tandem duplication of genes was one reason for the expansion of the M.bZIP genes. In addition to gene tandem duplication, a genome-wide duplication (GWD) event also occurred in apple and formed several intra-genomic homologous regions [22]. Large numbers of M.bZIP genes were located in homologous regions (gray shadow region in Figure 1) on different chromosomes, which suggest that genome duplication was another important way for expansion of M.bZIP genes.…”