Genome-wide identification and characterization of WUSCHEL-related homeobox (WOX) genes in Salix suchowensis

Members of the WUSCHEL-related homeobox (WOX) transcription factor family are essential for determining cell fate and regulating diverse developmental processes in plants. Many WOX genes have been systematically investigated in woody plants such as Populus trichocarpa, but not in Salix suchowensis. Whole-genome sequence data for S. suchowensis is now available for comprehensive study of WOX genes in S. suchowensis. We thus surveyed the genome of S. suchowensis and demonstrated active expression of 15 WOX genes. In a phylogenetic analysis of WOX genes, the 15 SsWOX genes clustered among the modern/WUS, intermediate and ancient clades similar to the WOX genes of Arabidopsis thaliana. Based on the conserved intron/exon structure, SsWOX genes in the same subgroup had similar conserved exon–intron structures and motif domains. Furthermore, among several SsWOX subgroups, WUS (Wuschel)-box and EAR (the ERF-associated amphiphilic repression)-like motifs were conserved. Expression profiles of WOX genes in roots, stems and leaves indicate that SsWOX genes have various conserved roles in the tissues. Comparative analysis of the expression patterns in Salix suchowensis with that of Arabidopsis suggests that different shoot regeneration abilities are controlled by different WOX genes in plants. The analysis provide an overview of differentially expressed SsWOX genes during shoot regeneration, but also contribute to understanding the evolution of WOX genes in Salicaceae and the interrelations of WOX genes and other transcription factors, providing targets for further study.