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Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot

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Abstract

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.

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Abbreviations

DAS:

Days after sowing

DD:

Dispersed gene duplication

HD:

Homeodomain

HD-ZIP:

HD-leucine zipper

LD:

Luminidependens

LS-WGDs:

Lineage-specific WGDs

PD:

Proximal duplication

RT-qPCR:

Quantitative real-time PCR

TD:

Tandem duplication

TSD:

DNA-transposed duplication

WGD:

Whole genome duplication

WOX:

WUSCHEL-like homeobox

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Acknowledgements

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).

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Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China

    Feng Que, Guang-Long Wang, Tong Li, Ya-Hui Wang, Zhi-Sheng Xu & Ai-Sheng Xiong

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  1. Feng Que
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  2. Guang-Long Wang
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  3. Tong Li
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  4. Ya-Hui Wang
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  5. Zhi-Sheng Xu
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Contributions

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.

Corresponding author

Correspondence to Ai-Sheng Xiong.

Electronic supplementary material

ESM 1

S1 Figure. Multiple sequence alignment of homedomain sequence of all carrot homeobox genes. (PDF 22517 kb)

ESM 2

S2 Figure. Phylogenetic tree of KNOX genes from carrot and Arabidopsis. (PDF 914 kb)

ESM 3

S1 Table. List of 130 carrot homeobox genes and their related information. (XLSX 28 kb)

ESM 4

S2 Table. Pfam domain of the 130 carrot homeobox genes. (XLSX 15 kb)

ESM 5

S3 Table. List of homeobox genes from Arabidopsis thaliana, Oryza sativa and carrot. (XLSX 25 kb)

ESM 6

S4 Table. Ka/Ks values of gene pairs from different duplication modes. (XLSX 27 kb)

ESM 7

S5 Table. List of Gene Ontology (GO) ID of carrot homeobox genes. (XLSX 14 kb)

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Que, F., Wang, GL., Li, T. et al. Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Funct Integr Genomics 18, 685–700 (2018). https://doi.org/10.1007/s10142-018-0624-x

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