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All Journal Biosaintifika: Journal of Biology & Biology Education
Agus Nuryanto
Faculty of Biology, Jenderal Soedirman University. Jl. dr. Soeparno 63 Grendeng, Purwokerto 53122, Central Java, Indonesia
Agriculture, Biological Sciences & Forestry

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DNA Barcoding of Ornamental Crab Geosesarma in South-Slope Mount Slamet Central Java, Indonesia Elly Tuti Winarni; Aswi Andriasari Rofiqoh; Dian Bhagawati; Anastasia Endang Pulungsari; Hanan Hassan Alsheikh Mahmoud; Agus Nuryanto
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 2 (2024): August 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v16i2.2376

Abstract

Geosesarma shows intraspecific carapace color variation, which might lead to species misidentification. The problem can be solved using DNA barcoding. There is one research about Geoserarma from the southern slopes of Mount Slamet, but samples were only collected from the Banjaran River for morphological identification. Here, we collected samples from wider areas covering south slope and applied molecular identification. This research aims to assess Geosesarma diversity in south-slope Mount Slamet Central Java, Indonesia based on the cytochrome c oxidase 1 gene barcoding. Surveys were carried out at six sites. Taxonomic identification was done using the barcoding technique. Four morphotypes were obtained during the research. Three morphotypes with the square carapace were identified as Geosesarma, while the remaining one morphotype was included in Parathelphusa. The three Geosesarma morphotypes were barcoded as Geosersarma dennerle because their genetic identity was more than 97% of the G. dennerle sequence in Boldsystems. In contrast, the Parathelphusa morphotype was barcoded as P. convexa with a genetic identity of 97.50%. It can be concluded that the Geosesarma crab on the south-slope Mount Slamet only consists of one species but has carapace and claw color variations. The data are essential for Geosesarma market development and conservation in the region.
Genetic Diversity of Pacific Seabream, Acanthopagrus pacificus in South-Coast Java, Indonesia Agus Nuryanto; Dian Bhagawati; Elly Tuti Winarni; Dwi Nugroho Wibowo; Mohammed Abdalla Mohammed
Biosaintifika: Journal of Biology & Biology Education Vol. 16 No. 2 (2024): August 2024
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v16i2.3627

Abstract

Pacific Seabream, Acanthopagrus pacificus, is a popular marine fish from the Sparidae family. This species is an economically essential fisheries commodity in the south-coast Java, Indonesia. However, limited studies are available on A. pacificus in Indonesia. Only two studies reported the presence of A. pacificus in South-Coast Java. No study has been carried out on the biology of A. pacificus from south-coast Java. Therefore, biological studies of A. pacificus are needed, including genetic diversity studies. This study aimed to evaluate the genetic diversity of A. pacificus in South-Coast Java using the cytochrome c oxidase gene. Fish samples were bought from Bantul Fishing Harbor, Yogyakarta, Panganadaran Fishing Port, Bojongsalawe Fish Auction Center, West Java, and Binuangeun Fishing Harbor in Lebak Regency, Banten. The genetic marker was processed in PT. Genetika Science Indonesia follows the company procedure. Haplotype and nucleotide diversity were calculated mathematically using Arlequin software. The result showed that polymorphic loci were only 1.3%, indicating low polymorphisms. A. pacificus showed haplotype and nucleotide diversities of 0.511±0.110 and 0.15%±0.12%, respectively. Those values indicated low genetic diversity. This study concluded that the A. pacificus population in South-Coast Java showed low genetic diversity. This study provides the first data about the genetic diversity of A. pacificus in South-Coast Java, which is essential data for fisheries management.
Comparison of Two Isolation Methods for Naturally Preserved DNA in Ambergris Fabian Rizky Fathurahman; Ali Suman; Hanan Hassan Alsheikh Mahmoud; Agus Nuryanto
Biosaintifika: Journal of Biology & Biology Education Vol. 17 No. 1 (2025): April 2025
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v17i1.14302

Abstract

DNA extraction is a fundamental initial step in numerous molecular research studies. Different extraction methods are required for different biological samples to obtain high-quality DNA. Therefore, this step is one of the limiting factors for the success of molecular analysis. There has been no research evaluating an appropriate method to extract DNA from ambergris jetsam samples. This study aims to determine an appropriate method for extracting DNA from whale ambergris samples. The ambergris sample was collected from the southern coast of Cilacap. DNA extraction was performed using a commercial DNA isolation kit and the Chelex® 100 method. The extracted DNA was visualized using agarose gel electrophoresis followed by quantification with a UV Nanodrop spectrophotometer. The data were analyzed descriptively to determine the most effective extraction method. The success of the extraction was also assessed by measuring the DNA concentration using the Nanodrop spectrophotometer. The results showed that the commercial isolation kit failed to produce genomic DNA from whale ambergris, as indicated by the absence of stained DNA bands on the agarose gel. In contrast, the Chelex® 100 method successfully produced genomic DNA from ambergris, as evidenced by the presence of stained DNA bands on the agarose gel and a high quantity of genomic DNA after a Nanodrop measurement. It can be concluded that the Chelex® 100 method is more suitable than commercial kits for extracting DNA from ambergris samples. This finding contributes to the development of various scientific fields based on molecular data by providing evidence that each biological sample requires an appropriate method to obtain high-quality DNA.
Co-Authors Ali Suman Anastasia Endang Pulungsari Aswi Andriasari Rofiqoh Dian Bhagawati Dwi Nugroho Wibowo Elly Tuti Winarni Fabian Rizky Fathurahman Hanan Hassan Alsheikh Mahmoud Mohammed Abdalla Mohammed