28S RRNA GENETIC MARKERS FOR THE IDENTIFICATION OF MICROALGAE

• Main Author: Saemena, Ita
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/52265
• Institution: Institut Teknologi Bandung

Indonesia is an archipelago with a large water area, which reaches 70% of its total area. The Indonesian ocean has a high level of biodiversity and is home to various organisms, one of which is microalgae. Microalgae are microscopic photosynthetic organisms that live in water, especially in tropical waters. Microalgae are interesting research objects because of their wide range of use, such as in biodiesel production, pharmaceutical products, cosmetics, food supplements, and many other bioactive compounds. The widespread use of microalgae is still constrained by the lack of a database of microalgae species diversity along with information on their uses, therefore it is necessary to improve identification efforts for Indonesian microalgae. The difficulty in identifying microalgae species is that there is no clear morphological structure that can differentiate distinct species or even genus. Identification of microalgae using genetic markers is an attractive option because it is more likely to differentiate microalgae down to the genus and species levels. The objectives of this study are: (i) identifying a marine microalgae sample from Muara Cilincing, Jakarta Bay, Indonesia, and (ii) finding genetic marker candidates based on Single Nucleotide Polymorphism (SNP) in the 28s rRNA gene area for microalgae at the genus and species level. Pure microalgal sample of strain code B5 taken from Muara Cilincing, Jakarta Bay has been cultivated in the laboratory. The B5 microalgal cells were then observed under a light microscope to obtain morphological information. Morphologically, sample B5 is similiar to Chaetoceros decipiens and Chaetoceros cf. neogracilis. In the computational research, microalgae 28s rRNA marker gene sequences were collected from various public databases, grouped by genus and species, and were aligned at the genus and species level using the ClustalW software. The alignment results were analyzed to find SNPs that could be used as genetic markers. From this study, diagnostic SNPs were found for 245 species and 26 genera of microalgae as well as genetic markers for green and red microalgae groups in the 28S rRNA marker gene area. The diagnostic SNP marker for the genus Chaetoceros (C at 192), can be used as a candidate for genetic marker for sample B5 at the genus level. At the species level, SNPs of the species Chaetoceros decipiens and Chaetoceros cf. neogracilis can be used to identify the B5 sample. Identification of Chaetoceros decipiens can be done by using a combination of 3 SNPs at positions 270 (G), 411 (del), and 430 (C). Chaetoceros cf. neogracilis can be identified using 2 single diagnostic SNP alternatives (C at 531 or 560).