Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot
The homeobox gene family, a large family represented by transcription factors, has been implicated in secondary growth, early embryo patterning, and hormone response pathways in plants. However, reports about the information and evolutionary history of the homeobox gene family in carrot are limited. In the present study, a total of 130 homeobox family genes were identified in the carrot genome. Specific codomain and phylogenetic analyses revealed that the genes were classified into 14 subgroups. Whole genome and proximal duplication participated in the homeobox gene family expansion in carrot. Purifying selection also contributed to the evolution of carrot homeobox genes. In Gene Ontology (GO) analysis, most members of the HD-ZIP III and IV subfamilies were found to have a lipid binding (GO:0008289) term. Most HD-ZIP III and IV genes also harbored a steroidogenic acute regulatory protein-related lipid transfer (START) domain. These results suggested that the HD-ZIP III and IV subfamilies might be related to lipid transfer. Transcriptome and quantitative real-time PCR (RT-qPCR) data indicated that members of the WOX and KNOX subfamilies were likely implicated in carrot root development. Our study provided a useful basis for further studies on the complexity and function of the homeobox gene family in carrot.
KeywordsHomeobox genes Expansion Evolution GO annotation Root Daucus carota L.
Days after sowing
Dispersed gene duplication
Quantitative real-time PCR
Whole genome duplication
The research was supported by the New Century Excellent Talents in University (NCET-11-0670), Jiangsu Natural Science Foundation (BK20130027), and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).
Conceived and designed the experiments: ASX FQ. Performed the experiments: FQ GLW ZSX TL YHW. Analyzed the data: FQ. Contributed reagents/materials/analysis tools: ASX. Wrote the paper: FQ. Revised the paper: ASX GLW. All authors read and approved the final manuscript.
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