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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Main Author:	Kalnisha Devi
Format:	Thesis
Language:	English English
Published:	2011
Subjects:	QK Botany
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
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spelling	my-ums-ep.66702024-05-10T01:31:27Z Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides 2011 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 https://eprints.ums.edu.my/id/eprint/6670/ https://eprints.ums.edu.my/id/eprint/6670/1/24%20PAGES.pdf text en public https://eprints.ums.edu.my/id/eprint/6670/2/FULLTEXT.pdf text en validuser masters Universiti Malaysia Sabah Institut Penyelidikan Bioteknologi
institution	Universiti Malaysia Sabah
collection	UMS Institutional Repository
language	English English
topic	QK Botany
spellingShingle	QK Botany Kalnisha Devi Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides
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.
format	Thesis
qualification_level	Master's degree
author	Kalnisha Devi
author_facet	Kalnisha Devi
author_sort	Kalnisha Devi
title	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_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_sort	development of protocols for the genomic characterization and est library construction of cochlodinium polykrikoides
granting_institution	Universiti Malaysia Sabah
granting_department	Institut Penyelidikan Bioteknologi
publishDate	2011
url	https://eprints.ums.edu.my/id/eprint/6670/1/24%20PAGES.pdf https://eprints.ums.edu.my/id/eprint/6670/2/FULLTEXT.pdf
_version_	1804890332829057024

Development of protocols for the genomic characterization and EST library construction of Cochlodinium polykrikoides

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