Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides
Cochlodinium polykrikoides is one of the causative agents for harmful algal blooms occurring in the west cost of Sabah, which result in massive economic damage to the aquaculture and mariculture industries. Currently, limited information is available on the genomics of C polykrikoides. The objective...
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| Format: | Thesis |
| Language: | English English |
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2011
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| Online Access: | https://eprints.ums.edu.my/id/eprint/6670/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/6670/2/FULLTEXT.pdf |
| _version_ | 1811136321775730688 |
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| author | Kalnisha Devi |
| author_facet | Kalnisha Devi |
| author_sort | Kalnisha Devi |
| collection | UMS |
| description | Cochlodinium polykrikoides is one of the causative agents for harmful algal blooms occurring in the west cost of Sabah, which result in massive economic damage to the aquaculture and mariculture industries. Currently, limited information is available on the genomics of C polykrikoides. The objectives of this study were to develop a protocol for the construction of an expressed sequence tag (EST) library for C polykrikoides cells cultured under normalized conditions, to design gene specific primers using sequence information of related dinoflagellates and to test the gene specific primers against the DNA and RNA of C polykrikoides. Cochlodinium polykrikoides stock cultures were obtained from the Unit for Harmful Algal Blooms Studies (UHABs) of the Borneo Marine Research Institute, Universiti Malaysia Sabah and cultured in f/2 medium. Optimization of total RNA isolation from C polykrikoides was performed using five different methods. Among the five methods tried, the RNA isolation protocol using the TRIzol reagent produced the best results. Synthesis of cDNA was performed on successfully isolated RNA samples followed by cloning and direct sequencing of the purified clones. In addition, fourteen gene specific primer pairs were designed and synthesized using sequence information from other harmful algae species. Genomic DNA samples isolated from C polykrikoides cells were used as templates for the peR amplification carried out using the synthesized gene specific primers. Amplification products from three gene specific primers, psaA1 FIR, COX-l FIR and ATPsynC FIR were purified and subsequently cloned and directly sequenced. Based on the sequencing results, the cloned products were found to produce identity matches to genes encoding products from similar and related protein families, such as the oxidoreductases and cytochrome oxidases. |
| first_indexed | 2024-09-24T00:48:44Z |
| format | Thesis |
| id | ums.eprints-6670 |
| institution | Universiti Malaysia Sabah |
| language | English English |
| last_indexed | 2024-09-24T00:48:44Z |
| publishDate | 2011 |
| record_format | dspace |
| spelling | ums.eprints-66702024-05-10T01:31:27Z https://eprints.ums.edu.my/id/eprint/6670/ Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides Kalnisha Devi QK Botany Cochlodinium polykrikoides is one of the causative agents for harmful algal blooms occurring in the west cost of Sabah, which result in massive economic damage to the aquaculture and mariculture industries. Currently, limited information is available on the genomics of C polykrikoides. The objectives of this study were to develop a protocol for the construction of an expressed sequence tag (EST) library for C polykrikoides cells cultured under normalized conditions, to design gene specific primers using sequence information of related dinoflagellates and to test the gene specific primers against the DNA and RNA of C polykrikoides. Cochlodinium polykrikoides stock cultures were obtained from the Unit for Harmful Algal Blooms Studies (UHABs) of the Borneo Marine Research Institute, Universiti Malaysia Sabah and cultured in f/2 medium. Optimization of total RNA isolation from C polykrikoides was performed using five different methods. Among the five methods tried, the RNA isolation protocol using the TRIzol reagent produced the best results. Synthesis of cDNA was performed on successfully isolated RNA samples followed by cloning and direct sequencing of the purified clones. In addition, fourteen gene specific primer pairs were designed and synthesized using sequence information from other harmful algae species. Genomic DNA samples isolated from C polykrikoides cells were used as templates for the peR amplification carried out using the synthesized gene specific primers. Amplification products from three gene specific primers, psaA1 FIR, COX-l FIR and ATPsynC FIR were purified and subsequently cloned and directly sequenced. Based on the sequencing results, the cloned products were found to produce identity matches to genes encoding products from similar and related protein families, such as the oxidoreductases and cytochrome oxidases. 2011 Thesis NonPeerReviewed text en https://eprints.ums.edu.my/id/eprint/6670/1/24%20PAGES.pdf text en https://eprints.ums.edu.my/id/eprint/6670/2/FULLTEXT.pdf Kalnisha Devi (2011) Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides. Masters thesis, Universiti Malaysia Sabah. |
| spellingShingle | QK Botany Kalnisha Devi Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides |
| title | Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides |
| title_full | Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides |
| title_fullStr | Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides |
| title_full_unstemmed | Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides |
| title_short | Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides |
| title_sort | development of protocols for the genomic characterization and est library construction of cochlodinium polykrikoides |
| topic | QK Botany |
| url | https://eprints.ums.edu.my/id/eprint/6670/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/6670/2/FULLTEXT.pdf |
| work_keys_str_mv | AT kalnishadevi developmentofprotocolsforthegenomiccharacterizationandestlibraryconstructionofcochlodiniumpolykrikoides |