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Genome-wide analysis of HD-Zip genes in grape (Vitis vinifera)

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Abstract

Grape (Vitis vinifera) is one of the most important fruit trees worldwide, and genomics research has played an important role in grape breeding and culture. According to numerous studies in higher plants, homeodomain-leucine zipper (HD-Zip) proteins are a specific class of transcription factors that play an important role in plant development. In this study, bioinformatics methods were used to carry out genome-wide analysis of a complete set of candidate genes encoding HD-Zip proteins in grape, including analysis of the number, physical locations, and encoded amino acid sequences of grape HD-Zip genes, as well as phylogenetic analysis. We identified 31 HD-Zip genes (Vvhdz1–31) in the grape genome, which were categorized into four classes (HD-Zip I–IV). These HD-Zip proteins contain 20 conserved motifs; their amino acids sequences were deduced. Chromosomal location analysis revealed that these genes are distributed unevenly across all 18 chromosomes. The digital EST expression analyses provided a first glimpse of the expression patterns of HD-Zip genes in grape. The results of this study provide an important theoretical reference for more thorough investigations of HD-Zip genes in grape, as well as studies examining the growth, development, and breeding of grape.

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Acknowledgments

We extend our thanks to the reviewers for their careful reading and helpful comments on this manuscript. This work was supported by grants from the National Natural Science Foundation of China (grant numbers 31301324, 31101159) and the Scientific and Technological Research Plan of Anhui (grant numbers 1206c0805032, 1208085MC36).

Conflict of interest

The authors declared that they have no conflicts of interest to this work.

Data archiving statement

All identified HD-Zip gene sequences were deposited into the Phytozome database (http://www.phytozome.net/). The accession numbers are listed in Table 1.

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Authors and Affiliations

  1. Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, 230036, China

    Haiyang Jiang, Jing Jin, Huan Liu, Qing Dong, Hanwei Yan, Defang Gan, Wei Zhang & Suwen Zhu

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  1. Haiyang Jiang
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  2. Jing Jin
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  3. Huan Liu
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  4. Qing Dong
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  5. Hanwei Yan
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  7. Wei Zhang
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  8. Suwen Zhu
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Corresponding author

Correspondence to Suwen Zhu.

Additional information

Communicated by J. L. Wegrzyn

Haiyang Jiang and Jing Jin contributed equally to this work.

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Supplementary Table S1

The probes and microarray data of grape HD-ZIP genes. (XLSX 12 kb)

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Jiang, H., Jin, J., Liu, H. et al. Genome-wide analysis of HD-Zip genes in grape (Vitis vinifera). Tree Genetics & Genomes 11, 827 (2015). https://doi.org/10.1007/s11295-014-0827-9

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  • DOI: https://doi.org/10.1007/s11295-014-0827-9

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