Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata)
Class III peroxidases are plant-specific glycoproteins and widely distributed among plant species, that play a crucial role in plant resistance to different stresses, such as salt, heat, cold and metal toxicity. The present study is the first comprehensive and systematic report to characterize the N...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1524657/full |
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| author | Wasi Ullah Khan Wasi Ullah Khan Latif Ullah Khan Noor Muhammad Khan Ji Zhang Wang Wenquan Wang Wenquan Fei Chen Fei Chen |
| author_facet | Wasi Ullah Khan Wasi Ullah Khan Latif Ullah Khan Noor Muhammad Khan Ji Zhang Wang Wenquan Wang Wenquan Fei Chen Fei Chen |
| author_sort | Wasi Ullah Khan |
| collection | DOAJ |
| description | Class III peroxidases are plant-specific glycoproteins and widely distributed among plant species, that play a crucial role in plant resistance to different stresses, such as salt, heat, cold and metal toxicity. The present study is the first comprehensive and systematic report to characterize the NcPOD gene family in water lily (Nymphaea colorata). In this study, 94 NcPOD genes in water lily were identified, each possessing a conserved POD domain, which are dispersed unevenly across the genome. Through comparative maximum-likelihood phylogenetic analysis, these genes were categorized into 10 groups, along with two other species, Arabidopsis thaliana and Nymphaea thermarum. Notably, the largest group, group-c, comprised 32 distinct types of NcPOD proteins. These genes exhibited uneven distribution on 11 of the 14 chromosomes of water lily. Exon-intron and motif analyses exhibited the structural and functional diversity among the sub-groups. The Examination of duplication patterns suggests that tandem duplication has contributed to the expansion of NcPOD genes. The analysis of promoter cis-acting elements indicated the presence of regulatory elements associated with various responses such as ABA, MeJA, light responsiveness, anaerobic conditions, and drought inducibility. Finally, the RT-qPCR based expression and enzymes activity of ten NcPOD genes depicted the dynamically differential response to NaCl, heat, cold, and heavy metals (CuSO4 and CdCl2) stresses. These findings provide valuable insights for future exploration of NcPOD functions in water lily growth and stress tolerance, laying a foundation for further comparative genomics and functional studies of this important class of antioxidant genes. |
| format | Article |
| id | doaj-art-210e2b39f8ee41518083d0e0216cca74 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-210e2b39f8ee41518083d0e0216cca742025-01-20T07:19:55ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.15246571524657Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata)Wasi Ullah Khan0Wasi Ullah Khan1Latif Ullah Khan2Noor Muhammad Khan3Ji Zhang4Wang Wenquan5Wang Wenquan6Fei Chen7Fei Chen8National Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, ChinaCollege of Tropical Agriculture and Forestry, Hainan University, Danzhou, ChinaNational Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, ChinaCollege of Tropical Agriculture and Forestry, Hainan University, Danzhou, ChinaNational Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, ChinaNational Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, ChinaCollege of Tropical Agriculture and Forestry, Hainan University, Danzhou, ChinaNational Key Laboratory for Tropical Crop Breeding, College of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya, ChinaCollege of Tropical Agriculture and Forestry, Hainan University, Danzhou, ChinaClass III peroxidases are plant-specific glycoproteins and widely distributed among plant species, that play a crucial role in plant resistance to different stresses, such as salt, heat, cold and metal toxicity. The present study is the first comprehensive and systematic report to characterize the NcPOD gene family in water lily (Nymphaea colorata). In this study, 94 NcPOD genes in water lily were identified, each possessing a conserved POD domain, which are dispersed unevenly across the genome. Through comparative maximum-likelihood phylogenetic analysis, these genes were categorized into 10 groups, along with two other species, Arabidopsis thaliana and Nymphaea thermarum. Notably, the largest group, group-c, comprised 32 distinct types of NcPOD proteins. These genes exhibited uneven distribution on 11 of the 14 chromosomes of water lily. Exon-intron and motif analyses exhibited the structural and functional diversity among the sub-groups. The Examination of duplication patterns suggests that tandem duplication has contributed to the expansion of NcPOD genes. The analysis of promoter cis-acting elements indicated the presence of regulatory elements associated with various responses such as ABA, MeJA, light responsiveness, anaerobic conditions, and drought inducibility. Finally, the RT-qPCR based expression and enzymes activity of ten NcPOD genes depicted the dynamically differential response to NaCl, heat, cold, and heavy metals (CuSO4 and CdCl2) stresses. These findings provide valuable insights for future exploration of NcPOD functions in water lily growth and stress tolerance, laying a foundation for further comparative genomics and functional studies of this important class of antioxidant genes.https://www.frontiersin.org/articles/10.3389/fpls.2024.1524657/fullplant peroxidaseswater lilyexpression patternphylogenetic analysisstresses |
| spellingShingle | Wasi Ullah Khan Wasi Ullah Khan Latif Ullah Khan Noor Muhammad Khan Ji Zhang Wang Wenquan Wang Wenquan Fei Chen Fei Chen Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) Frontiers in Plant Science plant peroxidases water lily expression pattern phylogenetic analysis stresses |
| title | Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) |
| title_full | Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) |
| title_fullStr | Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) |
| title_full_unstemmed | Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) |
| title_short | Comprehensive identification, characterization and expression analyses of the class III POD gene family in water lily (Nymphaea colorata) |
| title_sort | comprehensive identification characterization and expression analyses of the class iii pod gene family in water lily nymphaea colorata |
| topic | plant peroxidases water lily expression pattern phylogenetic analysis stresses |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1524657/full |
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