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Kumar V, Sharma H, Saini L, Tyagi A, Jain P, Singh Y, Balyan P, Kumar S, Jan S, Mir RR, Djalovic I, Singh KP, Kumar U, Malik V. Phylogenomic analysis of 20S proteasome gene family reveals stress-responsive patterns in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1037206. [PMID: 36388569 PMCID: PMC9659873 DOI: 10.3389/fpls.2022.1037206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The core particle represents the catalytic portions of the 26S proteasomal complex. The genes encoding α- and β-subunits play a crucial role in protecting plants against various environmental stresses by controlling the quality of newly produced proteins. The 20S proteasome gene family has already been reported in model plants such as Arabidopsis and rice; however, they have not been studied in oilseed crops such as rapeseed (Brassica napus L.). In the present study, we identified 20S proteasome genes for α- (PA) and β-subunits (PB) in B. napus through systematically performed gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 82 genes, comprising 35 BnPA and 47 BnPB of the 20S proteasome, were revealed in the B. napus genome. These genes were distributed on all 20 chromosomes of B. napus and most of these genes were duplicated on homoeologous chromosomes. The BnPA (α1-7) and BnPB (β1-7) genes were phylogenetically placed into seven clades. The pattern of expression of all the BnPA and BnPB genes was also studied using RNA-seq datasets under biotic and abiotic stress conditions. Out of 82 BnPA/PB genes, three exhibited high expression under abiotic stresses, whereas two genes were overexpressed in response to biotic stresses at both the seedling and flowering stages. Moreover, an additional eighteen genes were expressed under normal conditions. Overall, the current findings developed our understanding of the organization of the 20S proteasome genes in B. napus, and provided specific BnPA/PB genes for further functional research in response to abiotic and biotic stresses.
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Affiliation(s)
- Vivek Kumar
- Department of Botany, Chaudhary Charan Singh University, Meerut, UP, India
| | - Hemant Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP, India
| | - Lalita Saini
- Department of Botany, Chaudhary Charan Singh University, Meerut, UP, India
| | - Archasvi Tyagi
- Department of Botany, Chaudhary Charan Singh University, Meerut, UP, India
| | - Pooja Jain
- Department of Botany, Chaudhary Charan Singh University, Meerut, UP, India
| | - Yogita Singh
- Department of Molecular Biology & Biotechnology, College of Biotechnology, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri Post Graduate (PG) College, Chaudhary Charan Singh (CCS) University, Meerut, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, UP, India
| | - Sofora Jan
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST)-Kashmir, Wadura, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST)-Kashmir, Wadura, India
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki, Novi Sad, Serbia
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences & Humanities, Govind Ballabh (GB) Pant University of Agriculture & Technology, Pantnagar, India
- Vice-Chancellor’s Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, India
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology, College of Biotechnology, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Vijai Malik
- Department of Botany, Chaudhary Charan Singh University, Meerut, UP, India
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