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

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.