Phylogenetic analysis of caught rat by using cytochrome oxidase 1 fragment / Wan Muhammad Imran Wan Ismail

Wan Ismail, Wan Muhammad Imran (2018) Phylogenetic analysis of caught rat by using cytochrome oxidase 1 fragment / Wan Muhammad Imran Wan Ismail. [Student Project] (Unpublished)


The rats were widely diverse around the world. The identification of rat were difficult since most rats share common morphology characteristics. Thus, the identification through genetic material might help to identify the rat more accurately since the rat species were difficult to identify through the morphology characteristic. The aim of this study was to identify the unknown caught rats using phylogeny-based identification and further compared rat identification through morphological characteristics. Five rats’ samples were obtained from five different areas and the morphological characteristics of each sample were recorded to identify their species. The five rats’ tails were taken for DNA extractions by using high-salt method. The extracted DNA were amplified and sequenced for cytochrome oxidase 1 region. A total of 745 base pair were successfully sequenced for all samples and were aligned with 77 sequences retrieve from GenBank. Three phylogenetic trees were reconstructed Neighbor-Joining, Bayesian inferences and maximum likelihood method. Based on the morphological characteristics, the five samples were most likely identified as Rattus norgevicus for Rat 1, Rat 2 as Rattus tiomanicus, Rat 3 as Rattus andamanensis, Raat 4 as Rattus norvegicus and Rat 5 as Rattus exulans. However, further identification through phylogeny-based identification from the three phylogenetic tree shows that Rat 1 highly probably identified as Rattus norvegius, while Rat 2, Rat 3, Rat 4 and Rat 5 as Rattus kandianus and/or Rattus andamanensis.


Item Type: Student Project
Email / ID Num.
Wan Ismail, Wan Muhammad Imran
Email / ID Num.
Thesis advisor
Zakaria, Sarah Syazwani
Subjects: Q Science > Q Science (General) > Study and teaching > Laboratories. General works
Q Science > QD Chemistry > Extraction (Chemistry)
Q Science > QP Physiology > DNA. Deoxyribonucleic acids
Divisions: Universiti Teknologi MARA, Negeri Sembilan > Kuala Pilah Campus > Faculty of Applied Sciences
Programme: Bachelor of Science (Hons.) Biology
Keywords: Phylogenetic analysis, cytochrome oxidase 1 fragment
Date: 2018
Edit Item
Edit Item


[thumbnail of 34413.pdf] Text

Download (639kB)

Digital Copy

Digital (fulltext) is available at:

Physical Copy

Physical status and holdings:
Item Status:

ID Number




Statistic details