Gene Structures, Evolution and Transcriptional Profiling of the WRKY Gene Family in Castor Bean (Ricinus communis L.)

PLoS One. 2016 Feb 5;11(2):e0148243. doi: 10.1371/journal.pone.0148243. eCollection 2016.

Abstract

WRKY proteins comprise one of the largest transcription factor families in plants and form key regulators of many plant processes. This study presents the characterization of 58 WRKY genes from the castor bean (Ricinus communis L., Euphorbiaceae) genome. Compared with the automatic genome annotation, one more WRKY-encoding locus was identified and 20 out of the 57 predicted gene models were manually corrected. All RcWRKY genes were shown to contain at least one intron in their coding sequences. According to the structural features of the present WRKY domains, the identified RcWRKY genes were assigned to three previously defined groups (I-III). Although castor bean underwent no recent whole-genome duplication event like physic nut (Jatropha curcas L., Euphorbiaceae), comparative genomics analysis indicated that one gene loss, one intron loss and one recent proximal duplication occurred in the RcWRKY gene family. The expression of all 58 RcWRKY genes was supported by ESTs and/or RNA sequencing reads derived from roots, leaves, flowers, seeds and endosperms. Further global expression profiles with RNA sequencing data revealed diverse expression patterns among various tissues. Results obtained from this study not only provide valuable information for future functional analysis and utilization of the castor bean WRKY genes, but also provide a useful reference to investigate the gene family expansion and evolution in Euphorbiaceus plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Conserved Sequence
  • Evolution, Molecular*
  • Exons / genetics
  • Gene Expression Profiling*
  • Molecular Sequence Data
  • Phylogeny
  • Plant Proteins / chemistry
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Ricinus communis / genetics*
  • Transcription Factors / chemistry
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism

Substances

  • Plant Proteins
  • Transcription Factors

Grants and funding

The Funding should be the National Natural Science Foundation of China (31371556), the Fundamental Research Funds for Rubber Research Institute, CATAS (1630022015004) and the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-34-GW5).