DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh
This thesis is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Biotechnology, 2019.
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Brac University
2020
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10361-137602020-02-16T21:01:23Z DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh Ahmed, Sajid Siddique, Romana Ahmed, Md. Sagir Department of Mathematics and Natural Sciences, Brac University Cytochrome c oxidase DNA barcoding Ray fish Marine Sharks Cytochromes This thesis is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Biotechnology, 2019. Cataloged from PDF version of thesis. Includes bibliographical references (pages 49-52). Objective: The Lack of proper identification of various sharks and ray species has been a far cry among scientists. Cytochrome c oxidase gene-based DNA barcoding is used in various species identification not only because of pinpoint accuracy but how it can be used only a small amount of sample which doesn’t have proper morphological identification scope. So a need for a strong database of these sharks and rays identifying marker Cytochrome c oxidase gene is needed to crosscheck, regulate and update for current use and future reference. Methods: Collection of samples were done from the southern region of Bangladesh in the Bay of Bengal at various points and times. To identify the species a partial portion of it was collected, in general an approximate 650bp sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene is taken in consideration for this study. Since cytochrome c oxidase gene is easy to multiply in numbers with specified primers, a good number of outcomes are taken into consideration via Sanger-Sequencing method. The raw sequences were then trimmed according to match value and uploaded to NCBI database from where a cross match is done to verify the sequences. Further analysis was done using both offline and online resources of bioinformatics tools. Results: Our study concluded results that the K2P percentage of intra species of sharks and rays cluster around a close range of 1% to 6.5% in intra species and the range is spread from 11% to a maximum of 64% between species which gives us a genetic gap of 4.5%. For sharks, the GC1, GC2, and GC3 codons were 52.52 ± 0.23, 42.89 ± 0.04, and 20.38 ± 0.31, respectively with an average GC percentage being 38.59 ± 0.12 in the 8 species of sharks. For the rays, the GC1, GC2, and GC3 codons were 53.96 ± 0.36, 43.48 ± 0.19, and 33.59 ± 0.44, respectively with an average GC percentage being 43.67 ± 0.28 among 10 species of rays. Amino acid profiling showed clear similarities among the percentage of amino acid translated from the mitochondrial COI gene of same species and a significant difference between intra and inter species which makes it a good second marker apart from the GC percentage via DNA barcoding method. Conclusion: This study proved that COI gene-based DNA barcoding is a sound technique for rapid and accurate identification of sharks and rays also amino acid profiling can also be set as possible additional identification marker. Sajid Ahmed B. Biotechnology 2020-02-16T08:34:07Z 2020-02-16T08:34:07Z 2019 2019-12 Thesis ID 16136016 http://hdl.handle.net/10361/13760 en Brac University theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. 52 pages application/pdf Brac University |
| institution |
Brac University |
| collection |
Institutional Repository |
| language |
English |
| topic |
Cytochrome c oxidase DNA barcoding Ray fish Marine Sharks Cytochromes |
| spellingShingle |
Cytochrome c oxidase DNA barcoding Ray fish Marine Sharks Cytochromes Ahmed, Sajid DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh |
| description |
This thesis is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Biotechnology, 2019. |
| author2 |
Siddique, Romana |
| author_facet |
Siddique, Romana Ahmed, Sajid |
| format |
Thesis |
| author |
Ahmed, Sajid |
| author_sort |
Ahmed, Sajid |
| title |
DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh |
| title_short |
DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh |
| title_full |
DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh |
| title_fullStr |
DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh |
| title_full_unstemmed |
DNA barcoding using Cytochrome c oxidase gene marker of Marine Sharks and Ray fish of Bangladesh |
| title_sort |
dna barcoding using cytochrome c oxidase gene marker of marine sharks and ray fish of bangladesh |
| publisher |
Brac University |
| publishDate |
2020 |
| url |
http://hdl.handle.net/10361/13760 |
| work_keys_str_mv |
AT ahmedsajid dnabarcodingusingcytochromecoxidasegenemarkerofmarinesharksandrayfishofbangladesh |
| _version_ |
1814308136108949504 |