Optimization of PCR Protocols for ITS rDNA Amplification of Yeasts Isolated from Apis mellifera Honeycomb
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Abstract
Yeast is a microorganism that can be found in honeycomb. Yeast identification is a process to find and identify new species. One of which is molecular identification of yeast with rDNA sequences in the ITS region. Before carrying out molecular identification, it is necessary to optimize yeast DNA amplification methods to obtain good DNA sequences that ease the yeast identification process. The purpose of this study was to discover the optimum PCR (Polymerase Chain Reaction)protocols for the identification of yeasts isolated from Apis mellifera honeycomb based on the ITS rDNA. This study used 3 PCR (Polymerase Chain Reaction) protocols, i.e., from Kanti et al. (2018), Ediningsari (2008), and Maulana (2011). This results study shows that the optimum PCR protocol was from Maulana (2011), which produced clear and whole DNA fragment luminescences.
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Optimization of PCR Protocols for ITS rDNA Amplification of Yeasts Isolated from Apis mellifera Honeycomb. (2022). Jurnal Biota, 8(2), 78-87. https://doi.org/10.19109/Biota.v8i2.10181
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How to Cite
Optimization of PCR Protocols for ITS rDNA Amplification of Yeasts Isolated from Apis mellifera Honeycomb. (2022). Jurnal Biota, 8(2), 78-87. https://doi.org/10.19109/Biota.v8i2.10181
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Cindy. 2017. Optimization and Validasi Kondisi Polymerase Chain Reaction pada Identifikasi CYP2A6*9. Skripsi. Universitas Sanata Dharma, Yogyakarta.
Citra, Yoda Ikke F. 2019. Isolasi dan Identifikasi Khamir pada Bunga Pisang Klutuk (Musa balbisiana) serta Kemampuannya dalam Fermentasi karbohidrat. Skripi. UIN Maulana Malik Ibrahim, Malang.
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Nur’utami, Dwi Aryanti. 2011. Metode Analisis Isolasi and Identifikasi Salmonella typhimurium pada Susu dengan Metode Real-Time PCR (Polymerase Chain Reaction). Skripsi. Institut Pertanian Bogor, Bogor.
Prasetyo, B. A., Sri Minarti., and Nur Cholis. 2014. Perbandingan Mutu Madu Lebah Apis mellifera berdasarkan Kandungan Gula Pereduksi and Non Pereduksi di Kawasan Karet (Hevea brasilliensis) and Rambutan (Nephelium lappaceum). 1–7.
Rahayu, F., Saryono., Titania T. N. 2015. Isolasi DNA dan Amplifikasi PCR Daerah ITS rDNA Fungi Endofit Umbi Tanaman Dahlia (Dahlia variabilis) LBKURCC69. JOM FMIPA. 2(1): 100-106.
Rahman, M.T., Uddin M. S., Sultana R., Mone A., and Setu. 2013. Polymerase Chain Reaction (PCR): A Short Review. Anwer Khan Modern Medical College Journal. 4(1): 30-36.
Rakhmana, Senjavi., Saryono., and Titania T. Nugroho. 2015. Extraction DNA and Amplifikasi ITS rDNA Isolat Fungi Endofit LBKURCC67 Umbi Tanaman Dahlia (Dahlia variabilis). JOM FMIPA. 2(1): 145-151.
Savitri, N. P. T., E. D. Hastuti., and S. W. A. Suedy. 2017. Kualitas Madu Lokal dari Beberapa Wilayah di Kabupaten Temanggung. Buletin Anatomi and Fisiologi. 2(1).
Sulastri, Winda. 2019. Jumlah Cemaran and Identifikasi Yeast pada Jajanan Jubede yang Dijual di Pasar Kapedi Kecamatan Bluto Kabupaten Sumenep sebagai Source Belajar Biologi. Skripsi. Universitas Muhammadiyah Malang, Malang.
Sunarno, Fauzal M., Nyoman F., Amarila M., Anis K., and Amin S. 2014. Metode Cepat Ektraksi DNA Corynebacterium diphtheria untuk Pemeriksaan PCR. Bul. Penelit. Kesehat. 42(2): 85-92.
Suryaningsih, V., Rejeki S. F., Endang K. 2018. Karakteristik Morfologi, Biokimia, dan Moekuler Isolat Khamir IK-2 Hasil Isolasi dari Jus Buah Sirsak (Annona muricata L.). Jurnal Biologi. 7(1): 18-25.
Syafaruddin and Tri Joko Santoso. 2011. Optimization Teknik Extraction and Purifikasi DNA yang Efisien and Efektif pada Kemiri Sunan (Reutalistrisperma (Blanco) Airy Shaw). Jurnal Littri.17(1): 11-17.
Thacker, E. 2012. The Honey Book. Ohio: James Direct.
Walker, G. M. 2009. Yeasts In: Schaechter M-Desk Encyclopedia of Microbiology. 2nd ed. London: Elsevier.
White, T. J., Bruns, T., Lee, S., Taylor, J. 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. PCR Protocols: A Guide to Methods and Applications.
Amalia, Ulfah. 2013. Optimization Polymerase Chain Reaction (PCR) untuk Deteksi Salmonella spp. pada Uandg Segar. Tesis. Institut Pertanian Bogor, Bogor.
Anggraini, Ika., Rejeki Siti Ferniah., and Enandg Kusdiyantini. 2019. Extraction Yeast Fermentatif dari Batang Tanaman Tebu (Saccharum officinarum L.) and Hasil Identifikasinya Berdasarkan Sequences Internal Transcribed Spacer. Berkala Bioteknologi. 2(2): 12-22.
Ashliha, I. N. and Nur Hidayatul Alami. 2014. Karakterisasi Yeast dari Pulau Poteran Madura. JURNAL SAINS AND SENI POMITS. 3(2): 2337–3520.
Candra, R. P. 2015. Keragaman Yeast dari Sarang Lebah Madu Hutan. Skripsi. Universitas Gadjah Mada, Yogyakarta.
Cindy. 2017. Optimization and Validasi Kondisi Polymerase Chain Reaction pada Identifikasi CYP2A6*9. Skripsi. Universitas Sanata Dharma, Yogyakarta.
Citra, Yoda Ikke F. 2019. Isolasi dan Identifikasi Khamir pada Bunga Pisang Klutuk (Musa balbisiana) serta Kemampuannya dalam Fermentasi karbohidrat. Skripi. UIN Maulana Malik Ibrahim, Malang.
Deekshit, V. K., Ballamoole K.K., Praveen R., Anusha R., andIndrani K., 2013. Simultaneous Detection of Salmonella Pathogenicity Island 2 and Itsantibiotic Resistance Genes from Seafood. Journal of Microbiological Methods. 93: 233-238.
Ediningsari, A. R. 2008. Identifikasi Yeast dari Perairan Mangrove and laut Cagar Alam Pulau Rambut Berdasarkan Daerah Internal Transcribed Spacer (ITS). Skripsi. Universitas Indonesia, Depok.
Fajarningsih, Nurrahmi D. 2016. Internal Transcribed Spacer (ITS) as DNA Barcoding to Identify Fungal Species: a Review. Squallen Bull of Mar. and Fish. Postharvest and Biotech. 11(2): 37-44.
Hikmatyar, M. F., Royani J. I., and Dasumiati. 2015. Isolasi and Amplifikasi DNA Keladi Tikus (Thyponium flagelliform) untuk Identifikasi Keragaman Genetik. J. Bioteknol Bios Indon. 2(2): 42-48.
Joko, Tri., Nanda Kusumandari., and Sedyo Hartono. 2011. Optimization Metode PCR untuk Deteksi Pectobacterium carotovorum, Penyebab Penyakit Busuk Lunak Anggrek. Jurnal Perlindungan Tanaman Indonesia. 17(2): 54-59.
Kanti, A. and H.J.D. Latupapua. 2011. Identifikasi Keragaman Yeast yang Diextraction dari Tanah Kebun Biologi Wamena Kabupaten Jayawijaya, Propinsi Papua. J. Biol .Indon. 3(2): 150–160.
Kanti, A., M. Ilyas, Arif N., Tri Ratna S., and Siti Meliah. 2018. Panduan Pengelolaan Koleksi Mikroorganisme Indonesian Culture Collection (InaCC). Jakarta: Lipi Press.
Katsu, M., S. Kidd, A. Ando, M. L. Moretti-Branchimi, Y. Mikami, K. Nishimura & W. Meyer. 2003. The Internal Transcribed Spacers and 5.8S rRNA Gen Show Extensive Diversity Among Isolates of the Cryptococcus neformans Species Complex. FEMS Yeast Res. 1608: 1-12.
Kurtzman, C. P. et al. 2011. Methods for Isolation, Phenotypic Characterization and Maintenance of Yeast. USA: Elsevier B.V.
Maknunah, Jauharoh. 2017. Eksplorasi Yeast and Bakteri sebagai Agens Antagonis terhadap Penyebab Penyakit Blas pada Padi (Pyricularia oryzae). Skrispi. Institut Pertanian Bogor, Bogor.
Maulana, I. 2011. Identifikasi Isolat-isolat Yeast dari Saluran Pencernaan Apis cerana (FABRICIUS, 1793) di Apiari berdasarkan Data Sequence Daerah ITS rDNA. Skripsi. Universitas Indonesia, Depok.
Muladno. 2010. Teknologi Rekayasa Genetika. Edisi Kedua. Penerbit IPB Press.
Nugroho, Titania Tjandrawati., Evariati Rambe., Arfa Dewi., Reni M. Fitri., Harni Sepryani., Fajar Restuhadi., and Yuli Haryani. 2013. Optimization Extraction and Amplifikasi ITS DNA Ribosomal Fungi Karbolitik Isolat Zona Inti Cagar Biosfer Giam Siak Kecil-Bukit Batu. Prosiding Semirata FMIPA Universitas Lampung.
Nur’utami, Dwi Aryanti. 2011. Metode Analisis Isolasi and Identifikasi Salmonella typhimurium pada Susu dengan Metode Real-Time PCR (Polymerase Chain Reaction). Skripsi. Institut Pertanian Bogor, Bogor.
Prasetyo, B. A., Sri Minarti., and Nur Cholis. 2014. Perbandingan Mutu Madu Lebah Apis mellifera berdasarkan Kandungan Gula Pereduksi and Non Pereduksi di Kawasan Karet (Hevea brasilliensis) and Rambutan (Nephelium lappaceum). 1–7.
Rahayu, F., Saryono., Titania T. N. 2015. Isolasi DNA dan Amplifikasi PCR Daerah ITS rDNA Fungi Endofit Umbi Tanaman Dahlia (Dahlia variabilis) LBKURCC69. JOM FMIPA. 2(1): 100-106.
Rahman, M.T., Uddin M. S., Sultana R., Mone A., and Setu. 2013. Polymerase Chain Reaction (PCR): A Short Review. Anwer Khan Modern Medical College Journal. 4(1): 30-36.
Rakhmana, Senjavi., Saryono., and Titania T. Nugroho. 2015. Extraction DNA and Amplifikasi ITS rDNA Isolat Fungi Endofit LBKURCC67 Umbi Tanaman Dahlia (Dahlia variabilis). JOM FMIPA. 2(1): 145-151.
Savitri, N. P. T., E. D. Hastuti., and S. W. A. Suedy. 2017. Kualitas Madu Lokal dari Beberapa Wilayah di Kabupaten Temanggung. Buletin Anatomi and Fisiologi. 2(1).
Sulastri, Winda. 2019. Jumlah Cemaran and Identifikasi Yeast pada Jajanan Jubede yang Dijual di Pasar Kapedi Kecamatan Bluto Kabupaten Sumenep sebagai Source Belajar Biologi. Skripsi. Universitas Muhammadiyah Malang, Malang.
Sunarno, Fauzal M., Nyoman F., Amarila M., Anis K., and Amin S. 2014. Metode Cepat Ektraksi DNA Corynebacterium diphtheria untuk Pemeriksaan PCR. Bul. Penelit. Kesehat. 42(2): 85-92.
Suryaningsih, V., Rejeki S. F., Endang K. 2018. Karakteristik Morfologi, Biokimia, dan Moekuler Isolat Khamir IK-2 Hasil Isolasi dari Jus Buah Sirsak (Annona muricata L.). Jurnal Biologi. 7(1): 18-25.
Syafaruddin and Tri Joko Santoso. 2011. Optimization Teknik Extraction and Purifikasi DNA yang Efisien and Efektif pada Kemiri Sunan (Reutalistrisperma (Blanco) Airy Shaw). Jurnal Littri.17(1): 11-17.
Thacker, E. 2012. The Honey Book. Ohio: James Direct.
Walker, G. M. 2009. Yeasts In: Schaechter M-Desk Encyclopedia of Microbiology. 2nd ed. London: Elsevier.
White, T. J., Bruns, T., Lee, S., Taylor, J. 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. PCR Protocols: A Guide to Methods and Applications.