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

Abstract

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.

Figure 1. Sequence logo of the overrepresented motif found in B. rapa RING-H2, RING-HC, RING-v and RING-C2 domains, respectively.

The asterisked letters of Cys and/or His indicate conserved metal ligands and zinc-coordinating amino acid pairs are shown. The figures were created by on-line WebLogo tool (http://weblogo.berkeley.edu/logo.cgi). The height of the letters is proportional to their frequency of the corresponding amino acid at that position.

Figure 2. Distribution of 700 RING finger protein genes on 10 chromosomes of B. rapa.

The 700 BrRING genes unevenly located on each conserved collinear blocks of the chromosomes. Chromosome number (A01-A10) is indicated at the top of each chromosome. Gene name is indicated on the right side of each chromosome. The physical position (Mb) of each mapped gene is indicated on the left side of each chromosome. The genes located on duplicated chromosomal segments are framed by same colors and connected by blue lines between the two relevant chromosomes. The tandem repeated genes are marked by red color on the different chromosomes.

Figure 3. Expression profile of 667 B. rapa RING finger genes in different tissues revealed by RNA-seq data.

The 667 genes were divided into groups (I-VII) and subgroups. The scale representing the relative signal values is shown above. The tissue types are indicated on the top. The individual gene names as well as their RING types are indicated in the Fig. S7.