PCR Primer Spesifik Berdasarkan Gen Cytochrome b untuk Deteksi Garangan (Herpestes javanicus) secara Molekuler

https://doi.org/10.22146/jik.57463

Sena Adi Subrata(1*), Subeno Subeno(2), Atus Syahbudin(3)

(1) Departemen Konservasi Sumber Daya Hutan, Fakultas Kehutanan, Universitas Gadjah Mada
(2) Departemen Konservasi Sumber Daya Hutan, Fakultas Kehutanan, Universitas Gadjah Mada
(3) Departemen Silvikultur, Fakultas Kehutanan, Universitas Gadjah Mada
(*) Corresponding Author

Abstract


Garangan (Herpestes javanicus) merupakan salah satu spesies meso-carnivora yang berperan penting dalam ekosistem sebagai pemangsa. Kehadirannya dianggap mampu mengendalikan populasi spesies mangsa, termasuk beberapa spesies hama. Namun anggapan ini dianggap hanya anekdot karena kekurangan data ekologis pendukungnya sebagai dampak dari kesulitan pengamatan visual atas spesies ini. Penelitian ini bertujuan untuk merancang PCR primer untuk deteksi Garangan secara molekuler dari material organik yang ditinggalkan, misalnya kotoran. Perancangan PCR primer dimulai dengan memilih penanda spesifik Garangan yang melibatkan 51 sekuen DNA gen Cytochrome-b dari 19 spesies karnivora Jawa, menentukan primer forward dan reverse, dan menguji in-silico dan in vitro dari primer yang berhasil dirancang. Proses tersebut dilakukan dengan bantuan software MEGA 5 dan SP-Designer, dan memanfaatkan basis data genetik dari GenBank (NCBI). Uji in silico dan in vitro menunjukkan bahwa sekuen primer forward 5’- CAAATCACACCCACTCATTAAAATC-3’ dan reverse 5’-TGTGGGTTACTGATGAAAAGG-3’ akan mampu mendeteksi Garangan secara molekuler dari material organik spesies ini. Penelitian ini berkontribusi dalam pengumpulan data dasar kehadiran Garangan untuk mengumpulkan informasi lanjut tentang okupansi, distribusi spesies, dan pakannya. Informasi ini merupakan fondasi untuk memahami peran spesies ini dalam ekosistem.

 

Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan
Mongoose (Herpestes javanicus)

Abstract

Javan Mongoose is a meso-carnivore species that have an important role in ecosystem as a predator. It is believed that its occurrence controls prey populations including some pest species. However, the belief is an anecdote because of lacking supportive data. Difficulty in visually observing the species is a major problem preventing data collection. This study aims to design PCR primer for detecting the Mongoose molecularly from organic material remaining, such as feces. The design starts with selecting specific marker from 51 DNA sequences of cytochrome-b. The DNA sequences were of 19 Javan carnivore collected from GenBank (NCBI). PCR primers were designed and tested using both in-silico and in-vitro techniques. The sequence collection and selection, and primer design process employed MEGA 5 and SP-Designer software. We successfully designed PCR primers: forward 5’- CAAATCACACCCACTCATTAAAATC-3’ dan reverse 5’-TGTGGGTTACTGATGAAAAGG-3’. The primer is capable of detecting Javan Mongoose from remaining organic material. The study contributed to basic data collection of Javan Mongoose for advanced studies such as occupancy modeling, species distribution modeling and diet analysis. This information is fundamental for understanding the role of the Javan Mongoose in an ecosystem.


Keywords


animal; forest; Javan Mongoose; mammalian; molecular

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DOI: https://doi.org/10.22146/jik.57463

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