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All Journal Jurnal Ilmu Lingkungan Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Biosfer: Jurnal Tadris Biologi Jurnal Biologi Tropis Journal Of Agriculture Sciences (Agrosci)
Susanto, Alvin Wiwiet
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Education Environmental Science Immunology & microbiology Social Sciences Other

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Phylogenetic Construction of Stingless Bees in Bandar Lampung based on 16S rRNA Gene Priyambodo, Priyambodo; Rustiati, Elly Lestari; Pratiwi, Dian Neli; Susanto, Alvin Wiwiet; Srihanto, Eko Agus; Saswiyanti, Enny
Biosfer: Jurnal Tadris Biologi Vol 15 No 2 (2024): Biosfer: Jurnal Tadris Biologi
Publisher : UNIVERSITAS ISLAM NEGERI RADEN INTAN LAMPUNG

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24042/biosfer.v15i2.24589

Abstract

Stingless bees are one of the honey-producing groups that are currently in increasing demand. The significant rise in honey demand necessitates research into the variety of stingless bee species that have the potential to produce high-quality honey in large quantities. This study aims to determine the genetic relationship of stingless bees from two colonies in Rajabasa, Bandar Lampung. Samples were collected from two different colonies in Rajabasa, Bandar Lampung. Molecular analysis was conducted, including DNA extraction, amplification, DNA sequencing, and phylogenetic analysis using the 16S rRNA gene. The study assessed homology values, genetic distance, and the phylogenetic map. The results indicated that the individual samples, GB1 and GB2, found in Bandar Lampung, were closely related to the species Heterotrigona itama. This was confirmed by the query value of both samples being 100%, with similarity values of 96.99% and 97.20%, respectively. The genetic distance analysis, visualized in the phylogenetic map, also shows that the two samples are close relatives of Heterotrigona itama.ABSTRAK: Lebah tanpa sengat menjadi salah satu kelompok penghasil madu yang saat ini makin banyak diminati masyarakat. Peningkatan kebutuhan madu yang signifikan, memerlukan penelitian tentang ragam spesies lebah tanpa sengat yang potensial dalam menghasilkan madu yang berkualitas prima dalam jumlah yang melimpah. Penelitian ini telah dilakukan dengan tujuan untuk mengetahui kedekatan genetik lebah tanpa sengat dari dua koloni di Rajabasa, Bandar Lampung. Sampel diambil dari dua koloni yang berbeda di Rajabasa, Bandar Lampung. Analisis molekuler telah dilakukan dengan tahapan ekstraksi DNA, amplifikasi DNA, sekuensing DNA, dan dilanjutkan dengan analisis filogenetik dengan menggunakan gen 16S rRNA. Analisis dilakukan untuk mengetahui nilai homologi, jarak genetik, dan peta filogenetik. Hasil menunjukkan bahwa individu sampel GB1 dan GB2 yang ditemukan di Bandar Lampung mempunyai kedekatan dengan spesies Heterotrigona itama. Hal ini ditunjukkan dengan nilai query keduanya sebesar 100% dan nilai similarity masing-masing adalah 96,99% dan 97,20%. Analisis jarak geneti yang divisualisasi dalam peta filogenetik juga menunjukkan bahwa kedua sampel yang diperoleh merupakan kerabat dekat dari Heterotrigona itama.
Species Confirmation for Robusta Coffee in Sedayu, Semaka, Tanggamus: Social Forestry Data Base Management Rustiati, Elly Lestari; Priyambodo, Priyambodo; Srihanto, Eko Agus; Pratiwi, Dian Neli; Susanto, Alvin Wiwiet; Febriansyah, Muhammad; Kusuma, Andriyani Wijaya; Saswiyanti, Enny
Jurnal Ilmu Lingkungan Vol 23, No 4 (2025): July 2025
Publisher : School of Postgraduate Studies, Diponegoro Univer

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jil.23.4.1149-1154

Abstract

Lampung, including the Register 31 Pematang Arahan area which is next to the Bukit Barisan Selatan National Park, is known for its high biodiversity, and its coffee production. Gapoktanhut Lestari Sejahtera, consisting of 13 Forest Farmer Groups (KTH), practiced community-based forest coffee under the KPH Kotaagung Utara, Tanggamus, Lampung. To support the development of biodiversity data base for KPH Kotaagung Utara, molecular-based species identification for robusta coffee has been carried out under BLU LPPM Unila grant year 2023 and in collaboration with the Lampung Disease Investigation Center. Robusta coffee leaf samples from six KTH areas (Bumi Mulyo, Sido Makmur 1, Sido Makmur 2, Sido Makmur 3, Mandiri Jaya, and Murah Rejeki) were collected for molecular species confirmation based on the N-methyl transferase genetic marker. Molecular analysis included DNA extraction, amplification, and electrophoresis conducted at the Lampung Disease Investigation Center. Sequencing was based on the Coffea canephora CAF2 genetic marker. Bioinformatics analysis was performed using the Basic Local Alignment Search Tool (BLAST) and Molecular Evolutionary Genetics Analysis (MEGA) software version 6. Identical sequence lengths of samples in 6 KTH are varied in base pair length and nitrogen base sequences, ranging from 163-530 bp, with 5 out of 6 KTH having a genetic distance of 0.000%, while 1 sample had a genetic distance of 0.006%. It indicates that robusta coffee samples from 6 KTH areas are genetically closely related. It is supported by its phylogenetic tree, the coffee species cultivated by Gapoktanhut Lestari Sejahtera is molecularly confirmed to be robusta coffee, Coffea canephora.
Qualitative Analysis of Partial 16S rRNA Amplicon of Mitochondrial Gene of Stingless Bees in Pesawaran Priyambodo, Priyambodo; Rustiati, Elly Lestari; Pratiwi, Dian Neli; Susanto, Alvin Wiwiet; Imtitsal, Aulia; Fahrezi, Aditya; Febriansyah, Muhammad; Kusuma, Andriyani Wijaya; Srihanto, Eko Agus; Saswiyanti, Enny; Sidik, Mahfud; Sa'uddah, Lousanja D.; Lestari, Indah Ayu; Yani, Ani Andri; Ramadhan, Viki
Jurnal Biologi Tropis Vol. 23 No. 1 (2023): Special Issue
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v23i1.6470

Abstract

Pesawaran is one of the areas that has the potential to cultivate stingless bees as producers of honey and propolis. This study was aimed at qualitatively analysing partial amplicons of the 16S rRNA gene from individuals found at the research site. The research was performed from April to September 2023 in an explorative approach. Based on the exploration that has been done in Harapan Jaya Village, Way Ratai District, Pesawaran Regency, individual stingless bees were obtained from 5 different colonies. Individual samples of stingless bees were further extracted and amplified by commercial kits. Each individual from 5 different colonies has successfully obtained its DNA amplicons. Based on qualitative analysis using 1% agarose gel, the size of the partial gene ranged from 400bp to 500bp. This result is in accordance with the data contained in the genbank, where the 16S rRNA gene size is more than 500bp. Therefore, it has been concluded that the size of the partial amplicons of the 16S rRNA gene of individual stingless bees from the 5 colonies that were obtained is actually in range of the size of the 16S rRNA gene of stingless bees that have been recorded in the genbank.
Konstruksi Filogenetik Spesies Lebah Tanpa Sengat di Lampung Timur Berdasarkan Gen 16S rRNA Imtitsal, Aulia; Priyambodo; Rustiati, Elly Lestari; Pratiwi, Dian Neli; Susanto, Alvin Wiwiet; Ramadhan, Viki; Fahrezi, Aditya; Febriansyah, Muhammad; Kusuma, Andriyani Wijaya; Srihanto, Eko Agus; Saswiyanti, Enny
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 10, No 3 (2025): October 2025
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v10i3.9506

Abstract

Keanekaragaman flora dan fauna Indonesia sangat beragam. Jenis fauna yang terkenal di Indonesia adalah lebah tanpa sengat yang tersebar di seluruh wilayah di Indonesia. Informasi keragaman lebah tanpa sengat dan hubungan kekerabatan masing-masing kelompok lebah akan memberikan informasi terkait data populasi. Analisis molekuler berguna sebagai ilmu dan alat untuk melakukan identifikasi spesies. Analisis molekuler keragaman lebah tanpa sengat dapat menggunakan DNA mitokondria (mtDNA) pada lebah. Salah satu gen pengkode DNA mitokondria adalah gen 16S rRNA. Penelitian ini bertujuan untuk menganalisis sekuen sampel lebah tanpa sengat secara molekuler dan menyusun peta kekerabatan sehingga dapat menjadi data genetik dan informasi keanekaragaman spesie lebah tanpa sengat di Kabupaten Lampung Timur. Metode yang digunakan adalah  isolasi dan amplifikasi gen DNA, elektroforesis dan visualisasi, sekuensing dan analisis hasil sekuensing  menggunakan Basic Local Alignment Search Tool (BLAST), dan  konstruksi pohon filogenetik menggunakan Molecular Evolution Genetic Analysis (MEGA11). Berdasarkan penelitian ini 3 sampel lebah tanpa sengat yang didapatkan dari eksplorasi di Kabupaten Lampung Timur terdeteksi sebagai spesies Heterotrigona itama dan memiliki kekerabatan yang dekat dengan spesies sundatrigona sp dan paling jauh dengan Paratrigona lineatifrons. Hal ini sesuai dengan hasil uji BLAST dan analisis data molekuler menggunakan software Mega 11.
Oral Swab-Based DNA Extraction Of Cynopterus Brachyotis: An Initial Step For Species Confirmation Rhamadaningtyas, Nabila Aulia; Rustiati, Elly Lestari; Priyambodo, Priyambodo; Srihanto, Eko Agus; Saswiyanti, Enny; Pratiwi, Dian Neli; Susanto, Alvin Wiwiet
Jurnal Agrosci Vol 3 No 3 (2026): Vol 3 No 3 January 2026
Publisher : Ann Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.62885/agrosci.v3i3.1025

Abstract

Background. Identifying bat species based on morphological characteristics often faces challenges due to character overlap among species, especially within cryptic species groups. Cynopterus brachyotis is one of the fruit bats with high genetic diversity but relatively uniform morphology. Aims. Therefore, a molecular approach is needed to support accurate species confirmation. Under the HETI Research Grant of Innovation and Collaboration Batch 3- II Year 2025, this study aims to obtain genomic DNA from C. brachyotis bats caught at the Lampung Disease Investigation Center as the initial step of molecular species confirmation. Methods. Samples were obtained by taking oral swabs on bat individuals caught using mist nets. DNA extraction is performed using silica membrane-based methods with commercial kits. Quantitative evaluation of DNA was performed using a Qubit Fluorometer, while qualitative evaluation was performed by agarose gel electrophoresis. Conclusion. The results showed that the DNA concentration was in the low range (0.1–0.7 ng/μL), with a DNA band appearing very thin on electrophoresis. Implementation. Nevertheless, the quantification results confirm that DNA was successfully extracted and remains suitable for advanced molecular analysis, with optimization at the DNA amplification stage.
DNA Extraction of Cynopterus brachyotis of Labuhan Ratu VII Based on Column Method in Supporting its Molecular Species Confirmation Maharani, Annisa Lidya; Rustiati, Elly Lestari; Priyambodo, Priyambodo; Srihanto, Eko Agus; Saswiyanti, Enny; Neli Pratiwi, Dian; Susanto, Alvin Wiwiet
Jurnal Agrosci Vol 3 No 1 (2025): Vol 3 No 1 September 2025
Publisher : Ann Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.62885/agrosci.v3i1.1043

Abstract

Background. Bats (Chiroptera) are true flying mammals and nocturnal. Ecologically, bats play important roles as pollinators, seed dispersers, guano producers, biocontrol, and hosts a range of viruses. Cynopterus brachyotis belongs to fruit-eating bats and is considered morphologically cryptic with C. sphinx. Aims. To support morphological identification, molecular species confirmation needed to be conducted. DNA extraction, as an initial step, plays a crucial role in molecular analysis. Methods. The quality and quantity of extracted DNA determine the success rate of sequencing for species confirmation in bats. In this study, oropharyngeal samples were used. Result. The research procedures included bat capture and DNA oropharyngeal swab sample collection, sample preparation, DNA extraction using a silica column-based commercial kit, DNA concentration measurement using a Qubit assay, and electrophoresis. Conclusion. The Qubit assay showed DNA concentrations of >1 ng/µL, while electrophoresis did not reveal bright DNA bands.
Co-Authors Eko Agus Srihanto, Eko Agus Elly Lestari Rustiati Fahrezi, Aditya Febriansyah, Muhammad Imtitsal, Aulia Indah Ayu Lestari, Indah Ayu Kusuma, Andriyani Wijaya Maharani, Annisa Lidya Neli Pratiwi, Dian Pratiwi, Dian Neli Priyambodo Priyambodo Priyambodo Priyambodo Priyambodo Ramadhan, Viki Rhamadaningtyas, Nabila Aulia Sa'uddah, Lousanja D. Saswiyanti, Enny Sidik, Mahfud Yani, Ani Andri