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Transcriptome-wide identification of ARF gene family in medicinal plant Polygonatum kingianum and expression analysis of PkARF members in different tissues

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Abstract

Background

Polygonatum kingianum holds significant importance in Traditional Chinese Medicine due to its medicinal properties, characterized by its diverse chemical constituents including polysaccharides, terpenoids, flavonoids, phenols, and phenylpropanoids. The Auxin Response Factor (ARF) is a pivotal transcription factor known for its regulatory role in both primary and secondary metabolite synthesis. However, our understanding of the ARF gene family in P. kingianum remains limited.

Methods and results

We employed RNA-Seq to sequence three distinct tissues (leaf, root, and stem) of P. kingianum. The analysis revealed a total of 31,558 differentially expressed genes (DEGs), with 43 species of transcription factors annotated among them. Analyses via gene ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that these DEGs were predominantly enriched in metabolic pathways and secondary metabolite biosynthesis. The proposed temporal expression analysis categorized the DEGs into nine clusters, suggesting the same expression trends that may be coordinated in multiple biological processes across the three tissues. Additionally, we conducted screening and expression pattern analysis of the ARF gene family, identifying 12 significantly expressed PkARF genes in P. kingianum roots. This discovery lays the groundwork for investigations into the role of PkARF genes in root growth, development, and secondary metabolism regulation.

Conclusion

The obtained data and insights serve as a focal point for further research studies, centred on genetic manipulation of growth and secondary metabolism in P. kingianum. Furthermore, these findings contribute to the understanding of functional genomics in P. kingianum, offering valuable genetic resources.

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Data availability

The transcriptomes data of Polygonatum kingianum samples (root, stem, and leaf) in this study been deposited in NCBI under accession number BioProject: PRJNA1001864, BioSample: SAMN36822867–SAMN36822875, SRA: SRR25503077–SRR25503085.

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Funding

This work was supported by the Science and Technology Research Program of Chongqing Municipal Education Commission (KJZD-K202202701 and KJZD-K202302701), the Doctor Direct Train Project of Wanzhou District (wzstc-20220125), the Natural Science Project of Chongqing Three Gorges Medical College (XJ2021000301 and 2023gccrc07).

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Authors and Affiliations

  1. School of Pharmacy, Chongqing Three Gorges Medical College, Chongqing, 404120, China

    Wen-Xiang Wang, Ce Yang, Chun-Yu Chen & Ning Li

  2. Faculty of Basic Medical Sciences, Chongqing Three Gorges Medical College, Chongqing, 404120, China

    Wei Xiong

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  1. Wen-Xiang Wang
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CC and NL wrote the main manuscript, CY, WX, and WW prepared figures and tables; all authors have read and approved to the published version of the manuscript.

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Correspondence to Chun-Yu Chen or Ning Li.

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Wang, WX., Yang, C., Xiong, W. et al. Transcriptome-wide identification of ARF gene family in medicinal plant Polygonatum kingianum and expression analysis of PkARF members in different tissues. Mol Biol Rep 51, 648 (2024). https://doi.org/10.1007/s11033-024-09608-0

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