Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa

Overview & Synopsis

More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.