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Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.)

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Abstract

Auxin response factor (ARF) is an important transcription factor that regulates the expression of auxin-responsive genes by direct binding to their promoters, which play a central role in plant growth, development, and response to abiotic stresses. The availability of the entire Coix (Coix lacryma-jobi L.) genome sequence provides an opportunity to investigate the characteristics and evolutionary history of the ARF gene family in this medicine and food homology plant for the first time. In this study, a total of 27 ClARF genes were identified based on the genome-wide sequence of Coix. Twenty-four of the 27 ClARF genes were unevenly distributed on 8 chromosomes except Chr 4 and 10, and the remaining three genes (ClARF25-27) were not assigned to any chromosome. Most of the ClARF proteins were predicted to be localized to the nucleus, except ClARF24, which was localized to both the plasma membrane and nucleus. Twenty-seven ClARFs were clustered into six subgroups based on the phylogenetic analysis. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the ClARF gene family. Synteny analysis showed that purifying selection might have been a primary driving force in the development of the ARF gene family in Coix and other investigated cereal plants. The prediction of the cis element of the promoter showed that 27 ClARF genes contain several stress response elements, suggesting that ClARFs might be involved in the abiotic stress response. Expression profile analysis shows that 27 ClARF genes were all expressed in the root, shoot, leaf, kernel, glume, and male flower of Coix with varying expression levels. Furthermore, qRT-PCR analyses revealed that the majority of ClARFs members were upregulated or downregulated in response to hormone treatment and abiotic stress. The current study expands our understanding of the functional roles of ClARFs in stress responses and provides basic information for the ClARF genes.

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Data availability

All data and materials used in this research are publicly available. Other supporting data are provided as supplementary files with the manuscript.

Abbreviations

ARF:

Auxin response factor

DBD:

DNA-binding domain

AuxREs:

Auxin-responsive elements

qRT-PCR:

Reverse transcription-quantitative PCR

Aux/IAA:

Auxin/indole-3-acetic acid

MW:

Molecular weight

PI:

Isoelectric point

ABA:

Abscisic acid

SA:

Salicylic acid

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Funding

This research work is financially supported by Key project at central government level: The ability to establish sustainable use for valuable Chinese medicine resources (2060302), the Zhejiang Key Scientific and Technological Grant to Breed New Agricultural Varieties (2021C02074), and the Zhejiang Sci-Tech University scientific research fund (19042142-Y).

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Author notes

  1. Yufeng Zhai and Xiaoxia Shen contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China

    Yufeng Zhai, Qiao Liu, Nan Ma, Xiaodan Zhang, Qiaojun Jia, Zongsuo Liang & Dekai Wang

  2. Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China

    Xiaoxia Shen & Yimin Sun

  3. Songyang Institute of Zhejiang Chinese Medical University, Lishui, 323400, China

    Xiaoxia Shen

  4. State Key Laboratory of Dao-Di Herbs, Beijng, 100700, China

    Xiaodan Zhang & Zongsuo Liang

Authors
  1. Yufeng Zhai
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  2. Xiaoxia Shen
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Contributions

YZ, XS, YS, and DW conceived and designed the experiments. YZ, QL, and NM performed the experiments; YZ, XZ, QJ, and ZL validated the data; QJ and ZS revised the manuscript. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Dekai Wang.

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Zhai, Y., Shen, X., Sun, Y. et al. Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.). Protoplasma 260, 1389–1405 (2023). https://doi.org/10.1007/s00709-023-01855-5

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