Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis
Abstract Background Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation an...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43141-022-00453-x |
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| author | Borhan Ahmed Fakhrul Hasan Anika Tabassum Rasel Ahmed Rajnee Hassan Md. Ruhul Amin Mobashwer Alam |
| author_facet | Borhan Ahmed Fakhrul Hasan Anika Tabassum Rasel Ahmed Rajnee Hassan Md. Ruhul Amin Mobashwer Alam |
| author_sort | Borhan Ahmed |
| collection | DOAJ |
| description | Abstract Background Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profiling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family. Result We identified seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in different plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fiber cells providing evidence of the role of fiber formation. Conclusion This is the first comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identified in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses. |
| first_indexed | 2024-04-10T21:00:42Z |
| format | Article |
| id | doaj.art-22a033bc300e4289a55aa1bc3035eca3 |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:35:18Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-22a033bc300e4289a55aa1bc3035eca32024-04-16T17:29:54ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202023-01-0121111710.1186/s43141-022-00453-xGenome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularisBorhan Ahmed0Fakhrul Hasan1Anika Tabassum2Rasel Ahmed3Rajnee Hassan4Md. Ruhul Amin5Mobashwer Alam6Basic and Applied Research On Jute Project, Bangladesh Jute Research InstituteFaculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural UniversityAmerican International University of BangladeshBasic and Applied Research On Jute Project, Bangladesh Jute Research InstituteDepartment of Biochemistry, University of Nebraska-LincolnBasic and Applied Research On Jute Project, Bangladesh Jute Research InstituteQueensland Alliance for Agriculture and Food Innovation, The University of QueenslandAbstract Background Sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2), a plant-specific serine/threonine kinase family, is associated with metabolic responses, including abscisic acid signaling under biotic and abiotic stresses. So far, no information on a genome-wide investigation and stress-mediated expression profiling of jute SnRK2 is available. Recent whole-genome sequencing of two Corchorus species prompted to identify and characterize this SnRK2 gene family. Result We identified seven SnRK2 genes of each of Corchorus olitorius (Co) and C. capsularis (Cc) genomes, with similar physico-molecular properties and sub-group patterns of other models and related crops. In both species, the SnRK2 gene family showed an evolutionarily distinct trend. Highly variable C-terminal and conserved N-terminal regions were observed. Co- and CcSnRK2.3, Co- and CcSnRk2.5, Co- and CcSnRk2.7, and Co- and CcSnRK2.8 were upregulated in response to drought and salinity stresses. In waterlogging conditions, Co- and CcSnRk2.6 and Co- and CcSnRK2.8 showed higher activity when exposed to hypoxic conditions. Expression analysis in different plant parts showed that SnRK2.5 in both Corchorus species is highly expressed in fiber cells providing evidence of the role of fiber formation. Conclusion This is the first comprehensive study of SnRK2 genes in both Corchorus species. All seven genes identified in this study showed an almost similar pattern of gene structures and molecular properties. Gene expression patterns of these genes varied depending on the plant parts and in response to abiotic stresses.https://doi.org/10.1186/s43141-022-00453-xSnRK2sPhylogenetic analysisWaterloggingDroughtSalt toleranceExpression analysis |
| spellingShingle | Borhan Ahmed Fakhrul Hasan Anika Tabassum Rasel Ahmed Rajnee Hassan Md. Ruhul Amin Mobashwer Alam Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis Journal of Genetic Engineering and Biotechnology SnRK2s Phylogenetic analysis Waterlogging Drought Salt tolerance Expression analysis |
| title | Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis |
| title_full | Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis |
| title_fullStr | Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis |
| title_full_unstemmed | Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis |
| title_short | Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis |
| title_sort | genome wide investigation of snrk2 gene family in two jute species corchorus olitorius and corchorus capsularis |
| topic | SnRK2s Phylogenetic analysis Waterlogging Drought Salt tolerance Expression analysis |
| url | https://doi.org/10.1186/s43141-022-00453-x |
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