Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.)
Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene f...
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Elsevier
2019-02-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844018353994 |
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| author | Nehal Dubey Maitri Trivedi Suresh Varsani Vishal Vyas Manisha Farsodia Sunil Kumar Singh |
| author_facet | Nehal Dubey Maitri Trivedi Suresh Varsani Vishal Vyas Manisha Farsodia Sunil Kumar Singh |
| author_sort | Nehal Dubey |
| collection | DOAJ |
| description | Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene family in potato (Solanum tuberosum L.) and analyzed their expression pattern in various developmental tissues and stress responses of plants. There were eight metacaspase genes identified in the Peptidase (Cysteine protease) C14 family and based upon sequence alignment and phylogenetic analysis, a systematic nomenclature of potato metacaspases (SotubMCs) has been proposed. Three of the eight candidate genes showing homology with Arabidopsis thaliana type I metacaspase, AtMC1 were given name SotubMC1, SotubMC2 and SotubMC3 as per the degree of relatedness. Similarly, the next three being homologous to A. thaliana type I metacaspase, AtMC3 were named SotubMC4, SotubMC5, and SotubMC6. The remaining two were named SotubMC7 and SotubMC8, showing significant similarity with type II metacaspases of A. thaliana, AtMC4 and AtMC9, respectively. Evolutionary divergence analysis of SotubMCs from its orthologs in seven other members of Solanaceae family as well as with A. thaliana, Vitis vinifera and Oryza sativa was also carried out. The dN/dS ratios of the orthologous pairs suggested the SotubMCs were under purifying (negative) selection in course of plant evolution. Splicing patterns of potato metacaspases were also analyzed. Amongst all SotubMCs, SotubMC2, SotubMC4, SotubMC6 and SotubMC7 genes appeared to produce multiple alternative spliced variants of different lengths. Furthermore using protein modeling tools, we have predicted the protein structure of identified metacaspases. The cis-regulatory elements analysis was also performed exhibiting the presence of development, stress and hormones related cis-elements in the promoter regions of the SotubMCs. This indicates that potato metacaspases might be playing important roles in the development, stress and hormone responsive pathways. Moreover, relative expression analysis of identified genes was carried out using qRT-PCR in various developmental tissues that also include stolons and tubers. The eight metacaspases showed differential expression in different tissues. Some of the tissues such as leaf undergoing senescence among different leaf developmental stages (immature, mature and senescent) displayed higher relative expression of some of the metacaspases, implying their involvement in leaf senescence. The expression pattern of SotubMCs under various abiotic, biotic and hormonal stresses was also analysed. The results showed that many members of the potato metacaspase gene family displayed differential expression patterns under various stress conditions. Taken together, the study could provide crucial resources for further investigations to understand the functional roles of the identified metacaspases in potato. |
| first_indexed | 2024-12-11T19:03:53Z |
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| language | English |
| last_indexed | 2024-12-11T19:03:53Z |
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| spelling | doaj.art-f468973de18c482bab3b9500e2cf4abe2022-12-22T00:53:57ZengElsevierHeliyon2405-84402019-02-0152e01162Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.)Nehal Dubey0Maitri Trivedi1Suresh Varsani2Vishal Vyas3Manisha Farsodia4Sunil Kumar Singh5Plant Cell and Molecular Biology Laboratory, Department of Botany, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, IndiaPlant Cell and Molecular Biology Laboratory, Department of Botany, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, IndiaDepartment of Entomology, University of Nebraska, Lincoln, Nebraska 68583-0816, USAPlant Cell and Molecular Biology Laboratory, Department of Botany, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, IndiaPlant Cell and Molecular Biology Laboratory, Department of Botany, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, IndiaPlant Cell and Molecular Biology Laboratory, Department of Botany, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India; Corresponding author.Metacaspases are distant relatives of animal caspases found in plants, protozoa and fungi. Some recent studies have demonstrated that metacaspases are involved in regulating the developmental and environmentally induced programmed cell death in plants. In this study, we identified metacaspase gene family in potato (Solanum tuberosum L.) and analyzed their expression pattern in various developmental tissues and stress responses of plants. There were eight metacaspase genes identified in the Peptidase (Cysteine protease) C14 family and based upon sequence alignment and phylogenetic analysis, a systematic nomenclature of potato metacaspases (SotubMCs) has been proposed. Three of the eight candidate genes showing homology with Arabidopsis thaliana type I metacaspase, AtMC1 were given name SotubMC1, SotubMC2 and SotubMC3 as per the degree of relatedness. Similarly, the next three being homologous to A. thaliana type I metacaspase, AtMC3 were named SotubMC4, SotubMC5, and SotubMC6. The remaining two were named SotubMC7 and SotubMC8, showing significant similarity with type II metacaspases of A. thaliana, AtMC4 and AtMC9, respectively. Evolutionary divergence analysis of SotubMCs from its orthologs in seven other members of Solanaceae family as well as with A. thaliana, Vitis vinifera and Oryza sativa was also carried out. The dN/dS ratios of the orthologous pairs suggested the SotubMCs were under purifying (negative) selection in course of plant evolution. Splicing patterns of potato metacaspases were also analyzed. Amongst all SotubMCs, SotubMC2, SotubMC4, SotubMC6 and SotubMC7 genes appeared to produce multiple alternative spliced variants of different lengths. Furthermore using protein modeling tools, we have predicted the protein structure of identified metacaspases. The cis-regulatory elements analysis was also performed exhibiting the presence of development, stress and hormones related cis-elements in the promoter regions of the SotubMCs. This indicates that potato metacaspases might be playing important roles in the development, stress and hormone responsive pathways. Moreover, relative expression analysis of identified genes was carried out using qRT-PCR in various developmental tissues that also include stolons and tubers. The eight metacaspases showed differential expression in different tissues. Some of the tissues such as leaf undergoing senescence among different leaf developmental stages (immature, mature and senescent) displayed higher relative expression of some of the metacaspases, implying their involvement in leaf senescence. The expression pattern of SotubMCs under various abiotic, biotic and hormonal stresses was also analysed. The results showed that many members of the potato metacaspase gene family displayed differential expression patterns under various stress conditions. Taken together, the study could provide crucial resources for further investigations to understand the functional roles of the identified metacaspases in potato.http://www.sciencedirect.com/science/article/pii/S2405844018353994Molecular biologyPlant biologyBioinformaticsGenetics |
| spellingShingle | Nehal Dubey Maitri Trivedi Suresh Varsani Vishal Vyas Manisha Farsodia Sunil Kumar Singh Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.) Heliyon Molecular biology Plant biology Bioinformatics Genetics |
| title | Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.) |
| title_full | Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.) |
| title_fullStr | Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.) |
| title_full_unstemmed | Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.) |
| title_short | Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.) |
| title_sort | genome wide characterization molecular evolution and expression profiling of the metacaspases in potato solanum tuberosum l |
| topic | Molecular biology Plant biology Bioinformatics Genetics |
| url | http://www.sciencedirect.com/science/article/pii/S2405844018353994 |
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