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Genome-Wide Analysis and Expression Profile of Nuclear Factor Y (NF-Y) Gene Family in Z. jujuba

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Abstract

Nuclear factor-Y (NF-Y) is an important transcription factor in the plant species, which potentially provides a higher level of functional diversity including for abiotic stress tolerance. The genome-wide study and expression analysis of NF-Y gene family in Ziziphus, an elite abiotic stress-tolerant species, assist bioprospecting of genes. Here, a total of 32 NF-Y (8 NF-YA, 15 NF-YB, and 9 NF-YC) genes were identified in genome-wide search of Z. jujuba genome. Physicochemical properties, cellular localization, gene structure, chromosomal location, and protein motifs were analyzed for structural and functional understanding. Identified 12 NF-Ys were responsible for the expansion of NF-Y gene family by tandem duplication in Z. jujuba. Phylogenetic and comparative physical mapping of Z. jujuba NF-Ys with its orthologs illustrated evolutionary and functional insights into NF-Y gene family. A total of 45 perfect microsatellites (20bp to 40bp) were extracted across the ZjNF-Y genes. The promoter and gene ontology study suggested that Z. jujuba NF-Y gene family is functionally diverse and could play a wide-ranging role in plant abiotic stress, development, and cellular processes. An expression study revealed that large numbers of the NF-Ys are differentially expressed in response to drought and salinity. The total 15 and 18 ZjNF-Y genes that are upregulated under drought and salinity stress, respectively, are the potential candidates for further functional analysis for development of climate-resilient crops. The present study established a base for understanding the role of NF-Ys in Z. jujuba under abiotic stress conditions and paved a way for further research.

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Acknowledgements

We gratefully acknowledge the MGM College of Agricultural Biotechnology, Aurangabad, India, for providing space for growing plants and SDMVM College of Agriculture, Georai Tanda, India, for providing technical support.

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Authors and Affiliations

  1. Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Maharashtra, 431002, India

    Kishor Prabhakar Panzade

  2. Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, Maharashtra, 431007, India

    Sonam S. Kale

  3. Thiruvananthapuram, India

    M. L. Manoj

  4. Ellora Natural Seeds Pvt Ltd., Aurangabad, Maharashtra, 431136, India

    Sonali P. Kothawale

  5. Central Sugarcane Research Station, Padegaon, Mahatma Phule Agriculture University, Rahuri, Maharashtra, 415521, India

    Dipak N. Damse

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Contributions

KPP conceived, designed experiments, conducted the most of analysis and experiments, and wrote the manuscript; MLL and SSK conducted some analysis and help in manuscript writing; SPK and DND help in analysis and experiments.

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Correspondence to Kishor Prabhakar Panzade.

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Supplementary Information

Table S1

Orthologous amino acid sequences of the NF-Y gene family used for phylogenetic relationship analysis (XLSX 18 kb)

Table S2

Summary of all NF-Y gene sequences, functional domains, and physicochemical characteristics in Z. jujuba (XLSX 87 kb)

Table S3

List of primers used for the expression analysis of NF-Y gene family (XLSX 12 kb)

Table S4

Identified conserved motif sequences of ZjNF-Y protein family in Z. jujuba (XLSX 10 kb)

Table S5

Identified paralogous and orthologous pairs of NF-Y genes of Z. jujuba, P. mume and A. thaliana (XLSX 16 kb)

Table S6

SSRs loci identified in ZjNF-Y genes (XLSX 11 kb)

Table S7

The GO analysis of ZjNF-Y family protein in Z. jujuba (XLS 112 kb)

Table S8

Details of cis-regulatory elements observed in the NF-Y gene family in Z. jujuba (XLSX 21 kb)

Fig. S1

Alignments of NF-Y domains. The sequences of Z. jujuba (A) NF-YAs (B) NF-YBs and (C) NF-YCs were aligned (PNG 6532 kb)

High Resolution Image (TIF 1637 kb)

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Panzade, K.P., Kale, S.S., Manoj, M.L. et al. Genome-Wide Analysis and Expression Profile of Nuclear Factor Y (NF-Y) Gene Family in Z. jujuba. Appl Biochem Biotechnol 194, 1373–1389 (2022). https://doi.org/10.1007/s12010-021-03730-6

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