Abstract
BackgroundWUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. To date, WOX genes has been identified and analyzed in many polyploids (such as cotton and tobacco), but the evolutionary analysis of them during polyploidization is rare. With the completion of genome sequencing, allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good system for studying this question.ResultsIn this study, 52, 25 and 29 WOX genes were identified in allotetraploid B. napus (2n = 4x = 38, AnCn), the An genome donor B. rapa (2n = 2x = 20, Ar) and the Cn genome donor B. oleracea (2n = 2x = 18, Co), respectively. All identified WOX genes in B. napus and its diploid progenitors were divided into three clades, and these genes were selected to perform gene structure and chromosome location analysis. The results showed that at least 70 and 67% of WOX genes maintained the same gene structure and relative position on chromosomes, respectively, indicating that WOX genes in B. napus were highly conserved at the DNA level during polyploidization. In addition, the analysis of duplicated genes and transposable elements (TEs) near WOX genes showed that whole-genome triplication (WGT) events, segmental duplication and abundant TEs played important roles in the expansion of the WOX gene family in B. napus. Moreover, the analysis of the expression profiles of WOX gene pairs with evolutionary relationships suggested that the WOX gene family may have changed at the transcriptional regulation level during polyploidization.ConclusionsThe results of this study increased our understanding of the WOX genes in B. napus and its diploid progenitors, providing a rich resource for further study of WOX genes in these species. In addition, the changes in WOX genes during the process of polyploidization were discussed from the aspects of gene number, gene structure, gene relative location and gene expression, which provides a reference for future polyploidization analysis.
Highlights
WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants
The syntenic genes were searched in the BRAD database by inputting the gene IDs of the WOX genes in Arabidopsis, which is a supplement for the first method
In this study, 52, 25 and 29 WOX genes were identified in allotetraploid B. napus, the An genome donor B. rapa and the Cn genome donor B. oleracea, respectively
Summary
WUSCHEL-related homeobox (WOX) genes encoding plant-specific homeobox (HB) transcription factors play important roles in the growth and development of plants. A common feature of proteins in this superfamily is that they contain a homeobox domain that consists of 60–66 amino acids folded into a helix-turn-helix structure, which can be recognized by specific DNA to regulate target gene expression at a precise moment [1, 2]. In this HB superfamily, WOX genes encode plant-specific HB transcription factors [3]. Previous studies have found that WOX genes are present in the genomes of many plants, ranging from lower plants, such as green algae, to higher plants, such as angiosperms [2]. The WOX genes of lower plants belong only to the ancient clade, while those of higher plants belong to all three clades [7]
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