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All Journal Agrin : Jurnal Penelitian Pertanian Menara Perkebunan
Dini Astika SARI
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Agriculture, Biological Sciences & Forestry

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Molecular identification and phylogenetic analysis of Chlorella isolates from Indonesia using rbcL gene Fauziatul FITRIYAH; Yora FARAMITHA; Dini Astika SARI; Irma KRESNAWATY; Tri PANJI; Djoko SANTOSO
E-Journal Menara Perkebunan Vol 89, No 1 (2021): April, 2021
Publisher : INDONESIAN RESEARCH INSTITUTE FOR BIOTECHNOLOGY AND BIOINDUSTRY

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v89i1.408

Abstract

Identifying the newly isolated species is crucial to establishing a reliable algal database with successful commercial applications for different biotechnological applications. Morphological identification does not give sufficient description, especially for tiny unicellular microalgae. The rbcL gene encodes the large unit of ribulose-1, 5-bisphosphate carboxylase /oxygenase (Rubisco) has been widely known for barcoding in plants and developed for microalgae molecular identification. In this study, we examined the local strains of green microalgae from Indonesia using the rbcL partial gene sequence to identify the strains. Green microalgae isolates originated from Yogyakarta, Serayu, Gondol, Ancol, Cilegon, and Teluk Jakarta were cultured in f/2 media and harvested for DNA extraction. The DNA extracted was proceeded to PCR using 1AB_rbcL primer pair to amplify the sequences of rbcL gene with target band located at 582 bp, followed by the sequencing of the PCR product was conducted. Molecular identification of local green microalgae isolates was successfully carried out using primers 1AB_rbcL with a genetic similarity of 99% toward identified species in the NCBI database. Among six isolates, TJ, G, S, C, and A isolates were identified as C. pyrenoidosa. Only CP isolate from Yogyakarta identified as C. sorokiniana. Nannochloropsis gaditana rbcL sequence was selected as an outgroup. The phylogenetic analysis indicated that the five isolates of Chlorella belong to one clade and clearly distinguished from C. sorokiniana isolate from Yogyakarta.
OPTIMASI DAN EFISIENSI TEKNIK ISOLASI RNA DAUN DAN AKAR KELAPA SAWIT (Elaeis guineensis Jacq) Dini Astika Sari; Irfan Martiansyah; Restu Prasetya Mukmin; Sapto Nugroho Hadi; Indra Syahputra; Dadang Afandi; Riza Arief Putranto
Agrin Vol 23, No 2 (2019): Agrin
Publisher : Jenderal Soedirman University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (191.431 KB) | DOI: 10.20884/1.agrin.2019.23.2.500

Abstract

Tanaman kelapa sawit memiliki kandungan polisakarida dan polifenol yang tinggi. Kontaminasi polisakarida dan polifenol menyebabkan sulitnya proses isolasi RNA dari jaringan tanaman kelapa sawit. Penelitian ini dilakukan untuk mengoptimasi beberapa protokol isolasi RNA tanaman kelapa sawit yang efektif dan efisien. Penelitian dilaksanakan selama tiga bulan, pada bulan Oktober-Desember 2018 di Laboratorium Biokimia dan Biologi Molekuler, Pusat Penelitian Bioteknologi dan Bioindustri Indonesia (PPBBI), Jalan Taman Kencana No. 1 Bogor 16128. Penelitian dilakukan dengan melaksanakan teknik isolasi RNA menggunakan tiga protokol, yaitu modifikasi Cetyl Trimethyl Ammonium Bromide (CTAB), kit isolasi RNA RNeasy Plant Mini Kit (Qiagen), dan kit isolasi NucleoSpin RNAPlant (Macherey-Nagel). Sampel yang digunakan adalah daun dan akar tanaman kelapa sawit berumur kurang dari tiga bulan dengan bobot 0,1 gram dan 2,5 gram yang disesuaikan untuk tiap protokol. Variabel yang diamati adalah konsentrasi (ng/µl), kemurnian (rasio A260/A280 dan A260/A230), dan pita RNA pada elektroforesis gel agarosa. Hasil penelitian menunjukkan, RNA total hasil isolasi protokol NucleoSpin RNAPlant (Macherey-Nagel) memiliki kualitas paling tinggi. Konsentrasi RNA total daun dan akar kelapa sawit yang didapatkan melalui protokol NucleoSpin RNAPlant (Macherey-Nagel) sebesar 338 ng/µl dan 184,4 ng/µl dengan rasio A260/A280 RNA total daun dan akar kelapa sawit sebesar 2,13 dan 2,18 serta rasio A260/A230 sebesar 2,09 dan 2,20. Hasil elektroforesis gel agarosa menunjukkan integritas yang bagus dari RNA total hasil isolasi RNeasy Plant Mini Kit (Qiagen) dan NucleoSpin RNAPlant (Macherey-Nagel), namun terdapat kontaminasi dan smear pada RNA total hasil isolasi CTAB modifikasi 1 dan 2. Kata kunci: kelapa sawit, isolasi RNA, spektrofotometer, elektroforesis gel agarosa
Molecular identification and phylogenetic analysis of Chlorella isolates from Indonesia using rbcL gene Fauziatul FITRIYAH; Yora FARAMITHA; Dini Astika SARI; Irma KRESNAWATY; Tri PANJI; Djoko SANTOSO
Menara Perkebunan Vol. 89 No. 1 (2021): 89 (1), 2021
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v89i1.408

Abstract

Identifying the newly isolated species is crucial to establishing a reliable algal database with successful commercial applications for different biotechnological applications. Morphological identification does not give sufficient description, especially for tiny unicellular microalgae. The rbcL gene encodes the large unit of ribulose-1, 5-bisphosphate carboxylase /oxygenase (Rubisco) has been widely known for barcoding in plants and developed for microalgae molecular identification. In this study, we examined the local strains of green microalgae from Indonesia using the rbcL partial gene sequence to identify the strains. Green microalgae isolates originated from Yogyakarta, Serayu, Gondol, Ancol, Cilegon, and Teluk Jakarta were cultured in f/2 media and harvested for DNA extraction. The DNA extracted was proceeded to PCR using 1AB_rbcL primer pair to amplify the sequences of rbcL gene with target band located at 582 bp, followed by the sequencing of the PCR product was conducted. Molecular identification of local green microalgae isolates was successfully carried out using primers 1AB_rbcL with a genetic similarity of 99% toward identified species in the NCBI database. Among six isolates, TJ, G, S, C, and A isolates were identified as C. pyrenoidosa. Only CP isolate from Yogyakarta identified as C. sorokiniana. Nannochloropsis gaditana rbcL sequence was selected as an outgroup. The phylogenetic analysis indicated that the five isolates of Chlorella belong to one clade and clearly distinguished from C. sorokiniana isolate from Yogyakarta.
Co-Authors Dadang Afandi Djoko Santoso Fauziatul FITRIYAH Indra Syahputra Irfan Martiansyah Irma KRESNAWATY Restu Prasetya Mukmin Riza Arief Putranto Sapto Nugroho Hadi Tri Panji Yora FARAMITHA