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All Journal Biosaintifika: Journal of Biology & Biology Education Biodiversitas Journal of Biological Diversity
RUSDIANTO RUSDIANTO
Research Center for Biosystematics and Evolution, National Research and Innovation Agency. Jl. Raya Jakarta-Bogor Km. 46, Cibinong, Bogor 16911, West Java, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology

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Morphology and COI barcodes reveal local loaches (Nemacheilus spp.) from Pasuruan River, East Java, Indonesia CAHYA AJENG VALENTA TRESNA SULUNG; NISZAMUDDIN EL CHAIR; DWI ANGGOROWATI RAHAYU; ENDIK DENI NUGROHO; RUSDIANTO RUSDIANTO
Biodiversitas Journal of Biological Diversity Vol. 25 No. 7 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d250702

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Abstract. Sulung CAVT, Chair NE, Rahayu DA, Nugroho ED, Rusdianto. 2024. Morphology and COI barcodes reveal local loaches (Nemacheilus spp.) from Pasuruan River, East Java, Indonesia. Biodiversitas 25: 2806-2819. The family Nemacheilidae is one of the most diverse and widespread family of freshwater fishes. The nemacheilid loach in the Pasuruan river is relatively abundant; however, there is limited information available about this species. Therefore, further research is necessary to identify loaches from the Pasuruan area. This research aimed to identify the local loach species from Pasuruan District. The pectoral fins were stored in pure-grade ethanol and subjected to DNA extraction, polymerase chain reaction (PCR), and sequence analysis using bioinformatics tool, BOLD systems, and Automatic Barcode Gap Discovery (ABGD) web. The morphological identification revealed two local loaches, Nemacheilus chrysolaimos Valenciennes 1846 and Nemacheilus fasciatus Valenciennes 1846. The high haplotype diversity (Hd) of 0.9 and nucleotide diversity (?) of 0.1 indicate a wide range of genetic variations. The frequency of parsimony informative sites at 25.6% and 16 polymorphic sites and the overall ts/tv ratio of 2.3. The phylogenetic trees demonstrated a clear and unambiguous branching pattern for N. fasciatus and N. chrysolaimos forming their own monophyletic branches. Kimura's 2-parameter genetic distance of the COI gene sequences between these two species was 0.11. This finding was strengthened by morphological and molecular identification results, which indicated that there are two local loach species in Pasuruan District.
Genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java, Indonesia based on DNA barcode COI DWI ANGGOROWATI RAHAYU; RENI AMBARWATI; ULFI FAIZAH; ENDIK DENI NUGROHO; RUSDIANTO RUSDIANTO; PURITY SABILA AJININGRUM; NOORHIDAYAH BINTI MAMAT
Biodiversitas Journal of Biological Diversity Vol. 25 No. 10 (2024)
Publisher : Society for Indonesian Biodiversity

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13057/biodiv/d251041

Abstract

Abstract. Rahayu DA, Amarwati R, Faizah U, Nugroho ED, Rusdianto, Ajiningrum PS, Mamat NB. 2024. Genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java, Indonesia based on DNA barcode COI. Biodiversitas 25: 3789-3802. Horseshoe crabs or mimi mintuna (Indonesian) are an ancient arthropod with 4 species, but there are limited studies on the species from East Java. This indicates the need for the collection of more accurate genetic resources as an important step for its conservation. Therefore, this study aims to examine genetic diversity and phylogenetic reconstruction of horseshoe crabs from East Java using DNA barcode COI. A total of 20 samples were obtained from Beejay Bakau Resort, Probolinggo, Kenjeran Beach, Surabaya, Batah Timur Beach, Madura, and Lekok Beach, Pasuruan. The 621 bp CO1 gene sequence was used for genetic diversity analysis and phylogenetic tree reconstruction. Subsequently, muscle samples were preserved in pure-grade ethanol and subjected to DNA extraction, polymerase chain reaction (PCR), sequencing, and sequence analysis. The sequence data were analyzed using bioinformatics tools, Barcode of Life Data Systems (BOLD) Systems, the Automatic Barcode Gap Discovery (ABGD) web application, and haplotype network. Phenetic taxonomy was further applied using Ntysc to enhance the robustness of the genetic analysis. The results showed that the high haplotype diversity (Hd) of 0.957, 16 haplotypes, and nucleotide diversity (?) of 0.00097 indicated a wide range of genetic variations. The frequency of parsimony informative sites was 26.48%, with 19 polymorphic sites and an overall ts/tv ratio of 2.32. In addition, the phylogenetic trees showed a clear and unambiguous branching pattern for cluster Carcinoscorpius rotundicauda Latreille 1802 and Tachypleus gigas O.F.Müller 1785. This finding is a matter of concern for managing and conserving horseshoe crab species in East Java waters.
Morphological and Molecular Characterization of Pufferfish from Lekok Coastal Area, Pasuruan Indonesia Viona Angelina Erlan Panjaitan; Adam Dwi Rangga; Cahya Ajeng Valenta Tresna Sulung; Dwi Anggorowati Rahayu; Firas Khaleyla; Endik Deni Nugroho; Rusdianto Rusdianto; Noorhidayah Binti Mamat
Biosaintifika: Journal of Biology & Biology Education Vol. 17 No. 3 (2025): November 2025
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v17i3.26663

Abstract

Pufferfish belong to the Tetraodontidae family, which consists of 28 genera and 184 species; however, there are limited studies on the species from East Java, especially Pasuruan. This indicates the need for the collection of more accurate morphological and genetic resources as an important step for its conservation. Therefore, this study was conducted to identify pufferfish species found in the Lekok Coastal Waters, Pasuruan District, through morphological characterization and molecular analysis using DNA barcoding of the COI gene. A total of 12 samples were collected from the Lekok Coastal Waters, Pasuruan Regency. Fin samples were stored in 96% absolute ethanol. DNA extraction, polymerase chain reaction (PCR), and sequence analysis were performed using bioinformatics tools, the BOLD system, and the Automatic Barcode Gap Discovery (ABGD) web platform. Phenetic taxonomy was further applied using Ntysc to enhance the robustness of genetic analysis. The results showed that there were identified five pufferfish species were identified: Lagocephalus spadiceus, Chelonodontops patoca, Cyclichthys orbicularis, Arothron stellatus, and Arothron reticularis. High haplotype diversity (Hd) of 1 and nucleotide diversity (π) of 0.1 indicate significant genetic variation. The frequency of parsimonious informative sites was 22.6%, with 13 polymorphic sites and an overall ts/tv ratio of 2.2. The phylogenetic tree showed unambiguous branching patterns among species. These findings are supported by morphological and molecular identification results, which indicate the presence of five species of pufferfish along the Lekok Coast, Pasuruan Regency.
Co-Authors Adam Dwi Rangga CAHYA AJENG VALENTA TRESNA SULUNG Cahya Ajeng Valenta Tresna Sulung DWI ANGGOROWATI RAHAYU DWI ANGGOROWATI RAHAYU Dwi Anggorowati Rahayu ENDIK DENI NUGROHO ENDIK DENI NUGROHO Endik Deni Nugroho Firas Khaleyla NISZAMUDDIN EL CHAIR NOORHIDAYAH BINTI MAMAT Noorhidayah Binti Mamat PURITY SABILA AJININGRUM RENI AMBARWATI ULFI FAIZAH Viona Angelina Erlan Panjaitan