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All Journal HAYATI Journal of Biosciences Natural Science: Journal of Science and Technology Biospecies Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences METAMORFOSA Journal of Biological Sciences Jurnal Pendidikan Matematika dan IPA AL KAUNIYAH Biogenesis: Jurnal Ilmiah Biologi Jurnal Biologi Universitas Andalas Indonesian Journal of Biotechnology TREUBIA JMPM (Jurnal Material dan Proses Manufaktur) Jurnal Biologi Tropis JURNAL KESEHATAN PERINTIS Majalah Kedokteran Andalas Menara Ilmu International Journal of Agricultural Sciences Sainstek : Jurnal Sains dan Teknologi Best Journal (Biology Education, Sains and Technology) Jurnal Ners Journal of Ocean, Mechanical and Aerospace -science and engineering- (JOMAse) Makara Journal of Science
Djong Hon Tjong
Universitas Andalas
Aerospace Engineering Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Nursing Physics Public Health Social Sciences Other

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Phylogenetic Study of Bufonidae (Amphibia: Anura) from Sumatera and Asia Based on Cytochrome B Gene Tjong, Djong Hon; Roesma, Dewi Imelda; Indra, Silvia
Journal of Tropical Life Science Vol 11, No 3 (2021)
Publisher : Journal of Tropical Life Science

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Abstract

Bufonidae is widely distributed amphibian family around the world, including Indonesia (Sumatra) and Asia. Sumatra is an island which has separated because of sea level increase and create gene flows barrier for amphibian in Sumatra and Asia. The purpose of this research is to analyse Bufonidae phylogenetic which exist in several locations in Sumatra and Asia based on gene cytochrome b analysis. Samples were collected from six localities in West Sumatra. DNA extraction and amplification has been done in Genetics and Cell Biology Laboratory, Andalas University, whereas DNA sequencing were analyzed at MacroGen USA DNA Sequencing Laboratory, South Korea. About 14 tissue samples of Bufonidae from West Sumatra has been analyzed. The relationship of Bufonidae phylogenetics in Sumatra and Asia were divided into three main clusters. Duttaphrynus melanostictus in Sumatra is closer to Duttaphrynus melanostictus from India with 0,3-0,5% sequence divergence and it is a group of paraphyletic with Duttaphrynus melanostictus from Vietnam, Taiwan, and China.
Phylogenetic Study of Bufonidae (Amphibia: Anura) from Sumatera and Asia Based on Cytochrome B Gene Djong Hon Tjong; Dewi Imelda Roesma; Silvia Indra
Journal of Tropical Life Science Vol. 11 No. 3 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.03.15

Abstract

Bufonidae is widely distributed amphibian family around the world, including Indonesia (Sumatra) and Asia. Sumatra is an island which has separated because of sea level increase and create gene flows barrier for amphibian in Sumatra and Asia. The purpose of this research is to analyse Bufonidae phylogenetic which exist in several locations in Sumatra and Asia based on gene cytochrome b analysis. Samples were collected from six localities in West Sumatra. DNA extraction and amplification has been done in Genetics and Cell Biology Laboratory, Andalas University, whereas DNA sequencing were analyzed at MacroGen USA DNA Sequencing Laboratory, South Korea. About 14 tissue samples of Bufonidae from West Sumatra has been analyzed. The relationship of Bufonidae phylogenetics in Sumatra and Asia were divided into three main clusters. Duttaphrynus melanostictus in Sumatra is closer to Duttaphrynus melanostictus from India with 0,3-0,5% sequence divergence and it is a group of paraphyletic with Duttaphrynus melanostictus from Vietnam, Taiwan, and China.
Authentication of Barbonymus spp. From Lake Singkarak Using DNA Barcoding: Authentication of Barbonymus spp. From Lake Singkarak using DNA Barcoding Salis, Viola Mutiara; Roesma, Dewi Imelda; Tjong, Djong Hon; Syaifullah; Aadrean; Dahelmi
Journal of Tropical Life Science Vol. 14 No. 3 (2024)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.14.03.15

Abstract

The local community distinguishes between Barbonymus belinka (Balingka) and Barbonymus schwanefeldii (Kapiek) in Lake Singkarak based on size due to the morphological similarities between the two species. From previous reports, B. belinka (Balingka) is a fish endemic to Lake Singkarak, West Sumatra, while B. schwanefeldii has a wider distribution, including Sumatra, Kalimantan, and Java. Consequently, molecular identification is necessary to discern between the species and to understand the DNA barcode characteristics of fish belonging to the genus Barbonymus in Lake Singkarak. One molecular technique utilized for species identification is DNA barcoding, which focuses on the COI (Cytochrome Oxidase Subunit I) gene. Liver tissue samples from Balingka and Kapiek fish from Lake Singkarak were used in the study. Based on 585 bp of COI gene sequences and 30 comparison sequences from BOLD system and GenBank NCBI, seven samples from Lake Singkarak show a genetic distance of 0–1.2% from B. schwanefeldii populations elsewhere, with 15 differing nucleotide bases. Moreover, samples from Lake Singkarak show a genetic distance of 7.7–8.2% from B. belinka in the BOLD system from Aceh, with 42 differing nucleotide bases. Furthermore, two specific bases are present in B. schwanefeldii from Lake Singkarak. Based on the results of this research, it is known that all samples from Lake Singkarak, including Balingka and Kapiek, belong to the same species, namely B. schwanefeldii.
DNA Barcoding and eDNA Metabarcoding for Identification Species: A Case Study (West Sumatra): DNA barcoding and eDNA metabarcoding Roesma, Dewi Imelda; Tjong, Djong Hon; Syaifullah, Syaifullah; Nofrita, Nofrita; Janra, Muhammad Nazri; Aidil, Dyta Rabbani; Prawira, Furqan Dwiki Lintang; Salis, Viola Mutiara
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Abstract

The biodiversity of freshwater fish is important to study because there is data and information that remain undiscovered. The waters of Sumatra, especially West Sumatra, are areas with high freshwater fish diversity but have limited information. Providing information and genetic data has become one of the important things to conduct. DNA barcoding and eDNA metabarcoding have become molecular methods for identifying species and providing information about the presence of species in a region. A study using DNA barcoding and eDNA metabarcoding was conducted on freshwater fish in several locations in West Sumatra. Isolation and amplification of DNA were performed directly on individual samples and sequenced using conventional methods (Sanger sequencing) to generate DNA barcodes. Water samples were collected (2 liters) at each location using a sterile bottle. The water samples were filtrated, isolated, and amplified using universal primer and sequenced with next-generation sequencing techniques. The study successfully collected 25 species belonging to 14 genera, 2 families, and 1 order. A total of 134 sequences from West Sumatra with a length of 648-670 bp were analyzed. All DNA barcodes were submitted to the BOLD System and GenBank, NCBI. The mean Kimura two-parameter model (K2P) genetic distances within species, genera, families, and orders were 0.7%, 8.3%, 15.8%, and 21.3%, respectively. The eDNA metabarcoding technique has successfully detected three native fish species in the waters of West Sumatra (Barbonymus schwanefeldii, Mystacoleucus padangensis, and Rasbora jacobsoni). The availability of fish DNA barcodes in reference databases is crucial for the success of identification using eDNA metabarcoding. Combining identification using conventional methods and eDNA metabarcoding can provide more reliable results and become a reference for future freshwater monitoring.
Co-Authors - Jumawita - Syaifullah Aadrean Aidil, Dyta Rabbani Aldino Fauzil Fanani Almurdi Almurdi Amir Hamidy AMIR HAMIDY Anggraini, Debie Annisya Fitri Anthoni Agustien Anugrah Viona Agesi Arum Setiawan Asnul Fitria Aurora, Dhea Apriano Dahelmi Dahelmi Dahelmi David Gusman Dewi Imelda Roesma Dharmayanthi, Anik Budhi Dian Juliadmi Djoko T. Iskandar Djoko T. Iskandar, Djoko T. Dwitya Elvira, Dwitya Dyta Rabbani Aidil Elli Firdamila fachrul reza, fachrul Fauzan . Feskaharny Alamsjah Firdamila, Elli Fuji Astuti Febria G Gunawarman, G Gusman, David Hadi Addaha, Hadi Hadi Kurniawan Henny Herwina Hirowati Ali Hirowati Ali, Hirowati Ida Ayu Putu Sri Widnyani Ilhamdi, Ilhamdi Indra Junaidi Zakaria Irawati Chaniago Irvan Fadli Wanda Jamsari Jamsari Janra, Muhammad Nazri Jon Affi, Jon Juliadmi, Dian Kevin Origia Kevin Origia Kharisma Putra Liza Aulia Yusfi Mahmudul Hasan Mahmudul Hasan, Mahmudul Marlina Marlina Masayuki Sumida Masayuki Sumida, Masayuki Maulana, Imron Melinda, Annisa Menkher Manjas Meri Wulandari Muhamad Irsyad Muhammad Silmi Nelmi Fitria Netty Marusin Netty Marusin Nia Kurniawan Nia Kurniawan Nofrita Nofrita Nofrita Nofrita Nurul Aida Nurvalinda, Nurvalinda Nuswantoro, Nuzul Ficky Nuzulia Irawati Oktaviana, Dili Padilla, Putri Rahma Prawira, Furqan Dwiki Lintang Putri, Emilya Putri, Fanny Adhy Rahmadina, Shovinda Ravelino Nesty Resti Rahayu Ridho Hendrikos Rifka Rahmat Riska Mayori Rita Permatasari Rivi Hamdani Rizaldi Rizaldi Rizia Irsa Salis, Viola Mutiara Saputri, Rahmi Agu Silvia Indra Sisca Dwi Yarni Sri Wahyuni Handayani Sri Wahyuni Handayani, Sri Wahyuni Syaifullah Syaifullah Syaifullah Syaifullah Syaifullah Syandri, Hafrijal Takeshi Igawa Takeshi Igawa, Takeshi Tesri Maideliza Tofrizal Wilson Novarino Yarni, Sisca Dwi Yelvita Sari Yeni Gusma Yanti Yuliarni Syafrita Yurike Nova Edlin Zil Fadhillah Rahma Zozy Aneloi Noli