Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I
Pseudo-nitzschia is a marine and planktonic chain-forming diatom. Some Pseudo-nitzschia species produce biotoxin, domoic acid (DA) which causes Amnesic Shellfish Poisoning (ASP) in humans and marine mammals. Species of Pseudo-nitzschia are difficult to distinguish under light microscope (LM). In t...
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| Format: | Final Year Project Report / IMRAD |
| Language: | en en |
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Universiti Malaysia Sarawak, UNIMAS
2013
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| Online Access: | http://ir.unimas.my/id/eprint/7549/1/Molecular%20characterization%20of%20the%20diatom%2C%20pseudo-nitzschia%20%28bacillariophyceae%29%20using%20the%20mitochondrial%20genetic%20marker%2C%20cytochrome%20oxidase%20I%20%2824pgs%29.pdf http://ir.unimas.my/id/eprint/7549/8/Tan%20Suh%20Nih.pdf http://ir.unimas.my/id/eprint/7549/ |
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| _version_ | 1831805650509758464 |
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| author | Tan, Suh Nih |
| author_facet | Tan, Suh Nih |
| author_sort | Tan, Suh Nih |
| building | Centre for Academic Information Services (CAIS) |
| collection | Institutional Repository |
| content_provider | Universiti Malaysia Sarawak |
| content_source | UNIMAS Institutional Repository |
| continent | Asia |
| country | Malaysia |
| description | Pseudo-nitzschia is a marine and planktonic chain-forming diatom. Some Pseudo-nitzschia species produce
biotoxin, domoic acid (DA) which causes Amnesic Shellfish Poisoning (ASP) in humans and marine
mammals. Species of Pseudo-nitzschia are difficult to distinguish under light microscope (LM). In this study,
a total of 22 strains of Pseudo-nitzschia from Malaysian waters were identified based on morphological
characteristics observed under LM and transmission electron microscope (TEM). A total of 17 stains were
successfully identified; they are P. circumpora, P. cuspidata and P. pungens. A pair of genus-specific primer
targeting the mitochondrial cytochrome oxidase I (COI) gene was developed in silico to infer the molecular
phylogeny of Pseudo-nitzschia species. The primer specificity was tested using genomic DNA from clonal
cultures. The designed primer was successfully amplified with a fragment length of 450 bp. A total of 12
strains of Pseudo-nitzschia species were successfully amplified. LSU rRNA gene of the cultures were also
amplified to compare with the COI dataset. Genetic divergences of COI dataset and LSU rRNA dataset
among the Pseudo-nitzschia taxa were ranged from 0 to 20.5 % and from 0 to 5 % respectively. Phylogenetic
reconstruction revealed Pseudo-nitzschia taxa as a monophyletic group. However, the results showed
incongruence in both COI and LSU phylogenies. As conclusion, the cultures and the species identity
obtained in this study provide useful information on Pseudo-nitzschia study, and added to the database of
harmful algal blooms research in the country. |
| format | Final Year Project Report / IMRAD |
| id | my.unimas.ir-7549 |
| institution | Universiti Malaysia Sarawak |
| language | en en |
| publishDate | 2013 |
| publisher | Universiti Malaysia Sarawak, UNIMAS |
| record_format | eprints |
| spelling | my.unimas.ir-75492024-04-30T01:37:40Z http://ir.unimas.my/id/eprint/7549/ Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I Tan, Suh Nih Q Science (General) QH301 Biology QH426 Genetics Pseudo-nitzschia is a marine and planktonic chain-forming diatom. Some Pseudo-nitzschia species produce biotoxin, domoic acid (DA) which causes Amnesic Shellfish Poisoning (ASP) in humans and marine mammals. Species of Pseudo-nitzschia are difficult to distinguish under light microscope (LM). In this study, a total of 22 strains of Pseudo-nitzschia from Malaysian waters were identified based on morphological characteristics observed under LM and transmission electron microscope (TEM). A total of 17 stains were successfully identified; they are P. circumpora, P. cuspidata and P. pungens. A pair of genus-specific primer targeting the mitochondrial cytochrome oxidase I (COI) gene was developed in silico to infer the molecular phylogeny of Pseudo-nitzschia species. The primer specificity was tested using genomic DNA from clonal cultures. The designed primer was successfully amplified with a fragment length of 450 bp. A total of 12 strains of Pseudo-nitzschia species were successfully amplified. LSU rRNA gene of the cultures were also amplified to compare with the COI dataset. Genetic divergences of COI dataset and LSU rRNA dataset among the Pseudo-nitzschia taxa were ranged from 0 to 20.5 % and from 0 to 5 % respectively. Phylogenetic reconstruction revealed Pseudo-nitzschia taxa as a monophyletic group. However, the results showed incongruence in both COI and LSU phylogenies. As conclusion, the cultures and the species identity obtained in this study provide useful information on Pseudo-nitzschia study, and added to the database of harmful algal blooms research in the country. Universiti Malaysia Sarawak, UNIMAS 2013 Final Year Project Report / IMRAD NonPeerReviewed text en http://ir.unimas.my/id/eprint/7549/1/Molecular%20characterization%20of%20the%20diatom%2C%20pseudo-nitzschia%20%28bacillariophyceae%29%20using%20the%20mitochondrial%20genetic%20marker%2C%20cytochrome%20oxidase%20I%20%2824pgs%29.pdf text en http://ir.unimas.my/id/eprint/7549/8/Tan%20Suh%20Nih.pdf Tan, Suh Nih (2013) Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I. [Final Year Project Report / IMRAD] (Unpublished) |
| spellingShingle | Q Science (General) QH301 Biology QH426 Genetics Tan, Suh Nih Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I |
| title | Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I |
| title_full | Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I |
| title_fullStr | Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I |
| title_full_unstemmed | Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I |
| title_short | Molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase I |
| title_sort | molecular characterization of the diatom, pseudo-nitzschia (bacillariophyceae) using the mitochondrial genetic marker, cytochrome oxidase i |
| topic | Q Science (General) QH301 Biology QH426 Genetics |
| url | http://ir.unimas.my/id/eprint/7549/1/Molecular%20characterization%20of%20the%20diatom%2C%20pseudo-nitzschia%20%28bacillariophyceae%29%20using%20the%20mitochondrial%20genetic%20marker%2C%20cytochrome%20oxidase%20I%20%2824pgs%29.pdf http://ir.unimas.my/id/eprint/7549/8/Tan%20Suh%20Nih.pdf http://ir.unimas.my/id/eprint/7549/ |
| url_provider | http://ir.unimas.my/ |