Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus)
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 spe...
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| Format: | Article |
| Language: | English |
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Universitas Gadjah Mada
2020-07-01
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| Series: | Jurnal Ilmu Kehutanan |
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| Online Access: | https://jurnal.ugm.ac.id/jikfkt/article/view/57463 |
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| author | Sena Adi Subrata Subeno Subeno Atus Syahbudin |
| author_facet | Sena Adi Subrata Subeno Subeno Atus Syahbudin |
| author_sort | Sena Adi Subrata |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-6ec51d3ed1e348c59ace9452a9c0e3ce |
| institution | Kabale University |
| issn | 0126-4451 2477-3751 |
| language | English |
| publishDate | 2020-07-01 |
| publisher | Universitas Gadjah Mada |
| record_format | Article |
| series | Jurnal Ilmu Kehutanan |
| spelling | doaj-art-6ec51d3ed1e348c59ace9452a9c0e3ce2025-01-27T05:38:26ZengUniversitas Gadjah MadaJurnal Ilmu Kehutanan0126-44512477-37512020-07-01141556110.22146/jik.5746327199Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus)Sena Adi Subrata0Subeno Subeno1Atus Syahbudin2Department of Forest Conservation, Universitas Gadjah Mada, IndonesiaDepartment of Forest Conservation, Universitas Gadjah Mada, IndonesiaDepartment of Silviculture, Universitas Gadjah Mada, IndonesiaJavan 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.https://jurnal.ugm.ac.id/jikfkt/article/view/57463animalforestjavan mongoosemammalianmolecular |
| spellingShingle | Sena Adi Subrata Subeno Subeno Atus Syahbudin Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus) Jurnal Ilmu Kehutanan animal forest javan mongoose mammalian molecular |
| title | Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus) |
| title_full | Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus) |
| title_fullStr | Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus) |
| title_full_unstemmed | Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus) |
| title_short | Specific PCR Primers Based on Cytochrome-b Gene for Molecular Detection of Javan Mongoose (Herpestes javanicus) |
| title_sort | specific pcr primers based on cytochrome b gene for molecular detection of javan mongoose herpestes javanicus |
| topic | animal forest javan mongoose mammalian molecular |
| url | https://jurnal.ugm.ac.id/jikfkt/article/view/57463 |
| work_keys_str_mv | AT senaadisubrata specificpcrprimersbasedoncytochromebgeneformoleculardetectionofjavanmongooseherpestesjavanicus AT subenosubeno specificpcrprimersbasedoncytochromebgeneformoleculardetectionofjavanmongooseherpestesjavanicus AT atussyahbudin specificpcrprimersbasedoncytochromebgeneformoleculardetectionofjavanmongooseherpestesjavanicus |