Abstract
A transcription factor in plants encodes SQUAMOSA promoter binding protein-like (SPL) serves a broad spectrum of important roles for the plant, like, growth, flowering, and signal transduction. A gene family that encodes SPL proteins is documented in various model plant species, including Arabidopsis thaliana and Oryza sativa. Chickpea (Cicer arietinum), a leguminous crop, has not been thoroughly explored with regard to the SPL protein-encoding gene family. Chickpea SPL family genes were located and characterized computationally using a genomic database. Gene data of chickpea were obtained from the phytozome repository and was examined using bioinformatics methods. For investigating the possible roles of SPLs in chickpea, genome-wide characterization, expression, as well as structural analyses of this SPL gene family were performed. Cicer arietinum genome had 19 SPL genes, whereas, according to phylogenetic analysis, the SPLs in chickpea are segregated among four categories: Group-I has 2 introns, Group-II and IV have 1–2 introns (except CaSPL13 and CaSPL15 having 3 introns), and Group-III has 9 introns (except CaSPL1 and CaSPL11 with 1 and 8 introns, respectively). The SBP domain revealed that SPL proteins featured two zinc-binding sites, i.e., C3H and C2HC and one nuclear localization signal. All CaSPL proteins are found to contain highly conserved motifs, i.e., Motifs 1, 2, and 4, except CaSPL10 in which Motifs 1 and 4 were absent. Following analysis, it was found that Motifs 1 and 2 of the chickpea SBP domain are Zinc finger motifs, and Motif 4 includes a nuclear localization signal. All pairs of CaSPL paralogs developed by purifying selection. The CaSPL promoter investigation discovered cis-elements that are responsive to stress, light, and phytohormones. Examination of their expression patterns highlighted major CaSPLs to be evinced primarily among younger pods and flowers. Indicating their involvement in the plant’s growth as well as development, along with their capacity to react as per different situations by handling the regulation of target gene’s expression, several CaSPL genes are also expressed under certain stress conditions, namely, cold, salt, and drought. The majority of the CaSPL genes are widely expressed and play crucial roles in terms of the plant’s growth, development, and responses to the environmental-stress conditions. Our work provides extensive insight into the gene family CaSPL, which might facilitate further studies related to the evolution and functions of the SPL genes for chickpea and other plant species.
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Abbreviations
- CaSPL:
-
Chickpea SPL
- CDS:
-
Coding sequence
- HMM:
-
Hidden Markov model
- SPL:
-
SQUAMOSA promoter-binding protein-like
- NLS:
-
Nuclear localization signal
- SMART:
-
Simple Modular Architecture Research Tool
- GRAVY:
-
Grand average of hydropathicity
- pI:
-
Isoelectric point
- MW:
-
Molecular weight
- MEME:
-
Multiple Em for Motif Elicitation
- MCScanX:
-
Multiple Collinearity Scan toolbox
- PPI:
-
Protein-protein interaction
- TF:
-
Transcription factor
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The authors acknowledge the Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, U.P., India for the required facilities.
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A. P. thanks the Department of Biotechnology, Ministry of Science and Technology, Govt. of India for MK Bhan Young Researcher Fellowship Program (HRD-12/4/2020-AFS-DBT-Part (1) (13815).
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S. S. conceived and designed the research. S. S. conducted the experiments. S. S. and A. P. contributed the analytical tools. S. S. and P. B. analyzed the data. S. S. wrote the manuscript. All authors read and approved the manuscript.
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Singh, S., Praveen, A. & Bhadrecha, P. Genome-wide identification and analysis of SPL gene family in chickpea (Cicer arietinum L.). Protoplasma (2024). https://doi.org/10.1007/s00709-024-01936-z
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DOI: https://doi.org/10.1007/s00709-024-01936-z