Abstract
The LIM gene (an acronym for Lin-11, Isl-1, and Mec-3 domain) is a transcription factor family widely distributed in plants. LIM proteins in plants regulate various biological processes, including cytoskeletal organization, secondary cell wall development, and cellular differentiation. They have been identified and characterized in many plant species. However, a comprehensive genome-wide study of the LIM gene family and their associated transcription factors in various important fruit species, such as grapevine (Vitis vinifera), has not been investigated. In this study, we conducted an extensive in silico genome-wide identification and characterization of LIM genes in grapevine using integrated bioinformatics tools. We analyzed the expression of identified LIM genes during early bud development in grapevines using RNA-seq samples. The analysis predicted six VvLIM genes in V. vinifera, corresponding to the LIM genes in the model plant Arabidopsis. Phylogenetic tree analysis revealed that the LIM genes in grapevine could be classified into four subfamilies: αLIM, βLIM, δLIM, and γLIM. A study of conserved motifs, domains, and gene structures (exon length and intron numbers) of VvLIM genes showed a higher similarity within the same gene family. Gene ontology analysis demonstrated that the predicted VvLIM genes are associated with various biological and molecular functions. Network analysis between transcription factors (TFs) and identified VvLIM genes revealed several important TF families, including MYB, NAC, ERF, bZIP, bHLH, C2H2, MIKC_MADS, and TCP. Furthermore, cis-acting regulatory elements related to light-responsive (LR), hormone-responsive (HR), stress-responsive (SR), and other (OT) functions were detected in the predicted VvLIM genes. In addition, we examined the expression changes of the six candidate VvLIM genes during early bud development in grapevines using RNA-seq samples. Differential expression patterns were observed for VvLIM genes involved in bud development, with specific timing coinciding with key developmental stages. Moreover, the expression of VvLIM genes associated with inflorescence primordia and endodormancy provided insights into the molecular mechanisms underlying bud development in grapevines, thus enhancing our understanding at the molecular level. This study will provide valuable information on grapevine LIM genes, laying a solid foundation for subsequent wet-lab characterization of the functional mechanisms of the identified VvLIM genes and their regulatory elements.
Key Message
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Firstly, identify the LIM gene families in the grapevine (Vitis vinifera) genome.
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Subsequently, an integrated bioinformatics approach was employed to analyze the LIM gene family.
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Additionally, the transcript levels of the six selected VvLIM gene candidates were assessed during the early stages of bud development in grapevines, utilizing pre-existing RNA-seq data.
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Finally, this study establishes an in silico foundation for the functional characterization of the LIM gene family and offers valuable insights for subsequent wet-lab investigations to further elucidate the properties of this gene family.
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Acknowledgements
The authors are very grateful to the Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh, for providing the opportunity to conduct this research. The authors acknowledge and appreciate the reviewers and the editorial panel members for their valuable comments and critical suggestions for improving the quality of this manuscript.
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Conceptualization: MARS, SMR, Supervision, project administration, resources: MARS, SMR, Investigation:, MARS, MSUI, FTZ, Methodology: MARS, MSUI, FTZ, Formal analysis: MARS, MSUI, Visualization: MARS, MSUI, Writing—original draft: MARS, SS, FTZ, Writing—review and editing: MARS, SS, FTZ.
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Sarkar, M.R., Sarkar, S., Islam, M.U. et al. Genome-Wide Identification and Characterization of LIM Gene Family in Grapevine (Vitis vinifera L.) and Their Expression Analysis at Early Bud Developmental Stages. Plant Mol Biol Rep (2023). https://doi.org/10.1007/s11105-023-01416-3
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DOI: https://doi.org/10.1007/s11105-023-01416-3