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Genome-wide identification of the Carya illinoinensis bZIP transcription factor and the potential function of S1-bZIPs in abiotic stresses

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Abstract 

The basic leucine zipper (bZIP) is a transcription factor broadly found in higher plants and is involved in numerous crucial physiological processes: growth and development, stress responses, etc. The pecan (Carya illinoinensis) is a highly ornamental and economical woody plant that is popular in landscape and economic forestry. However, the identification and analysis of the bZIP TF system in pecan have not been reported. To acquire information on the bZIP gene family in pecan, we appraised 77 members of the bZIP gene family from the pecan genome and categorized them into 12 subfamilies (S, B, A, D, F, E, G, I, J, H, K, and C) using bioinformatics methods. Analysis in terms of gene structure and conserved motif composition revealed that each subtribe shares a comparable number of introns-exons and functions. Ka/Ks results suggested that bZIP evolution was influenced by purifying selection. The promoter cis-acting element analysis revealed a huge number of abscisic acid–responsive elements, light-responsive elements, and jasmonic acid–responsive elements in pecan bZIPs. Furthermore, the protein interaction network predicted a possible role for S1-bZIPs in abiotic stress, and the qRT-PCR results further demonstrated that this subpopulation responds to abiotic stress. Meanwhile, the results of subcellular localization and transcriptional activity indicated that CibZIP38, CibZIP55, and CibZIP43 are all nuclear-localized transcriptional activators. The report of the pecan bZIP gene family in this work can further improve our understanding of CibZIPs as a genetic resource for the genetic engineering breeding of pecan.

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Data availability

Genomic information of Carya illinoinensis was obtained from (GIGA)nDB (http://gigadb.org/) and the identified gene IDs are available in Table 1 of the article. A. thaliana genomes were obtained from the TAIR (https://www.arabidopsis.org/index.jsp). The genome sequence of C. paliurus was downloaded from Genome Warehouse in the National Genomics Data Center Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation (https://ngdc.cncb.ac.cn/gwh). Walnut whole genome data were downloaded from the NCBI database (http://www.ncbi.nlm.nih.gov/). Grape cds and protein sequences were downloaded from (http://genomes.cribi.unipd.it/). And all primer sequences can be found in the Appendix.

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Acknowledgements

We thank the members of Anhui Provincial Key Laboratory of Forest Resources and Silviculture for their assistance in this study.

Funding

This work was supported by the Key Project of Scientific Research of Anhui Provincial Education Department (Grant no. 2022AH050903).

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Authors and Affiliations

  1. Anhui Provincial Key Laboratory of Forest Resources and Silviculture, Anhui Agricultural University, Hefei, 230036, China

    Nianqin Jiang, Linna Wang, Yangang Lan, Hongxia Liu, Xiaoyue Zhang, Wei He, Min Wu, Hanwei Yan & Yan Xiang

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  1. Nianqin Jiang
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  2. Linna Wang
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  4. Hongxia Liu
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  8. Hanwei Yan
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  9. Yan Xiang
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Contributions

NQJ designed and conducted the experiments, wrote the manuscript, and processed the figures. XYZ and WH assisted with part of the experiment. LNW and YGL helped to handle figures and tables. HWY and MW helped to revise the manuscript. YX provided financial support for the article and designed the way and frame of this study. All the authors read and approved the final manuscript.

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Correspondence to Yan Xiang.

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Jiang, N., Wang, L., Lan, Y. et al. Genome-wide identification of the Carya illinoinensis bZIP transcription factor and the potential function of S1-bZIPs in abiotic stresses. Tree Genetics & Genomes 19, 47 (2023). https://doi.org/10.1007/s11295-023-01622-w

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