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Genome-wide survey, characterization, and expression analysis of RING finger protein genes in Brassica oleracea and their syntenic comparison to Brassica rapa and Arabidopsis thaliana

Yang, Yan-Qing, Lu, Yun-Hai
Genome 2018 v.61 no.9 pp. 685-697
Arabidopsis thaliana, Brassica oleracea, Brassica rapa, chromosomes, eukaryotic cells, gene deletion, genes, growth and development, ligases, plant development, proteins, sequence analysis, surveys
The ubiquitin-mediated post-translational regulatory pathway regulates a broad range of cell functions in all eukaryotes. It requires the involvement of a large number of E3 ligases, of which more than one third belongs to the RING protein family as in Arabidopsis thaliana. In this study, a total of 756 RING domains in 734 predicted proteins were identified in Brassica oleracea. Their encoding genes were characterized by RING domain type, additional domain, and expression pattern, and mapped on the nine chromosomes of B. oleracea. Comparison of these results with B. rapa and A. thaliana revealed some common as well as species-specific features. Our results showed that the differential gene loss following the whole genome triplication has largely contributed to the RING protein gene number variation among these species, although other factors such as tandem duplication, RING domain loss, or modification had also contributed to this variation. Analysis of RNA-seq data showed that these RING protein genes were functionally diversified and involved in all the stages of plant growth and development, and that the triplicated members were also diverged in expression with one member often more dominantly expressed over the two others in the majority of cases. Our study lays the foundation for further functional determination of each RING protein gene among species of the genus Brassica.