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All Journal BIOTROPIA - The Southeast Asian Journal of Tropical Biology Biology, Medicine, & Natural Product Chemistry Journal of Tropical Biodiversity and Biotechnology Depik Jurnal Ilmu-Ilmu Perairan, Pesisir dan Perikanan
Abdul Razaq Chasani, Abdul Razaq
Faculty of Biology, Universitas Gadjah Mada, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Education Engineering Environmental Science Immunology & microbiology Medicine & Pharmacology Public Health Veterinary

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Diversity and Phenetic Relationship of Mountain Papaya (Vasconcellea Pubescens) in Dieng Plateau Based on Morphological Marker Rifqi, Muhammad Said; Chasani, Abdul Razaq
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 2 (2024): June
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.88061

Abstract

Vasconcellea pubescens A. DC., commonly referred to as mountain papaya, belongs to the Caricaceae family and is native to the Andean highlands.  In Indonesia, mountain papaya can be found on the Dieng Plateau and has become one of the typical processed products from the Dieng area. The aim of the study is to explore the diversity and phenetic relationship of mountain papaya from the Dieng Plateau based on morphological markers. This study is important to provide information in guiding future conservation efforts. 18 samples were collected from three areas with different altitudes in the Dieng Plateau. In addition, it proved valuable results by elucidating patterns of variation, enabling the identification of distinct groups. A total of 18 samples were collected from three areas with varying altitudes in the Dieng Plateau. Morphological analysis used 22 characters with The Clustering Analysis Method, Principal Component Analysis (PCA), and Diversity Analysis using Multivariate Statistical Package (MVSP) software version 3.1A. The results of cluster analysis showed that mountain papaya accessions were grouped into two main clusters and five sub-clusters. Cluster grouping based on sex distribution characters, flower stalk length, and inflorescence density; there is no grouping based on geographical location or altitude. The Shannon's Index Value (H') for mountain papaya shows moderate phenetic diversity. This suggests that the mountain papaya community remains stable within its substrate and its environmental parameters. 
Molecular insights into the biodiversity of freshwater red macroalgae in Indonesia Aristya, Ganies Riza; Nugroho, Rifat Rizki Adi Nugroho; Chasani, Abdul Razaq
Depik Jurnal Ilmu Ilmu Perairan, Pesisir, dan Perikanan Vol 14, No 2 (2025): JUNE 2025
Publisher : Faculty of Marine and Fisheries, Universitas Syiah Kuala

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13170/depik.14.2.38211

Abstract

Many Asian countries, including Indonesia, have experienced negative effects from pollution brought on by industrialization and modernization, which have harmed freshwater ecosystems as well as natural habitats. Red macroalgaeand other creatures that depend on these ecosystems for their survival may suffer as a result, which could increase the strain on freshwater ecosystems and resources. Due to freshwater red macroalgaeare primary producers in their own ecosystems, they are essential to the cycling of nutrients and the preservation of water quality. The objective of this study is to evaluate freshwater red macroalgae in Indonesia utilizing various approaches particularly emphasis on DNA barcoding. As a result, molecular methods like DNA barcoding are employed to uncover hidden species and elucidate the evolutionary connections between different taxa, thereby exposing the diversity of red macroalgae. It is anticipated that the outcomes will yield data for further research.Keywords:DNA barcodeFreshwaterHidden speciesMolecularRed macroalgae
Optimization of Genomic DNA Extraction Method on Nutmeg (Myristica fragrans Houtt.) Agustina, Tanti; Chasani, Abdul Razaq
Biology, Medicine, & Natural Product Chemistry Vol 14, No 2 (2025)
Publisher : Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14421/biomedich.2025.142.783-786

Abstract

Nutmeg (Myristica fragrans) is one of the commodities in the Myristicaceae family that has numerous benefits and has high phenolic compounds. Elevated amounts of secondary metabolites in the Myristica genus pose significant challenges for obtaining high-quality DNA. This complexity often results in reduced DNA recovery and suboptimal absorbance ratios, attributed to contamination by RNA and proteins in DNA extraction yields.. The results of DNA extraction that have been obtained through several variations of optimized methods are compared. The DNA extraction method using a modified Geneaid Genomic DNA Mini Kit was determined to produce the highest quality and quantity of DNA. Compared to other protocols such as Doyle and Doyle, modified Doyle and Doyle, and the basic protocol of the Geneaid kit without improvement, the modified Geneaid Genomic DNA Mini Kit had a high mean range purity of 1.83, and bands appeared.
MICROSATELLITE-BASED GENETIC VARIATION IN Rhizophora apiculata AND Rhizophora mucronata FROM EAST KALIMANTAN Widyasari, Adristi Shafa; Chasani, Abdul Razaq; Prihatini, Istiana; Atmoko, Tri; Mukhlisi; Adman, Burhanuddin; Sitepu, Bina Swasta
BIOTROPIA Vol. 33 No. 2 (2026): BIOTROPIA Vol. 33 No. 2 May 2026
Publisher : SEAMEO BIOTROP

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11598/btb.2026.33.2.2715

Abstract

ARTICLE HIGHLIGHTS- Microsatellite markers were used to study population genetic variation in Rhizophora- Molecular systematic analysis showed moderate genetic diversity with low heterozygosity- Population genetic structure was dominated by within-population variation (AMOVA)- Phenetic analyses revealed weak clustering among Rhizophora populations- Genetic patterns supported connectivity within Rhizoporaceae populations in East KalimantanABSTRACTMangroves of the family Rhizophoraceae are pantropical, with the genus Rhizophora forming a major component of tropical mangrove ecosystems. Rhizophora apiculata and Rhizophora mucronata are widely distributed in the Paser region, Balikpapan Bay, and the Mahakam Delta of East Kalimantan, Indonesia. This study examined genetic diversity and population structure of both Rhizophora species using simple sequence repeat (SSR) markers. The results showed moderate genetic diversity but relatively low heterozygosity in both species. Most genetic variation occurred within populations, as indicated by AMOVA, while R. apiculata exhibited lower genetic differentiation among populations and lacked private alleles, and R. mucronata showed higher population differentiation and possessed private alleles, suggesting localized genetic variation. Cluster and principal coordinate analyses revealed extensive overlap among populations for both species, indicating weak population structure and ongoing gene flow across the study area. Overall, the findings suggest that populations of R. apiculata and R. mucronata in East Kalimantan function as genetically connected units rather than as strongly differentiated populations. These results highlight the importance of maintaining habitat connectivity and protecting genetically unique populations to support the long-term resilience and sustainable management of mangrove genetic resources in East Kalimantan.
Co-Authors Agustina, Tanti Burhanuddin Adman Ganies Riza Aristya Istiana Prihatini, Istiana Mukhlisi Nugroho, Rifat Rizki Adi Nugroho Rifqi, Muhammad Said Sitepu, Bina Swasta Tri Atmoko Widyasari, Adristi Shafa