Article Per Year (5 Year)
p-Index From 2020 - 2025
0.817
P-Index
This Author published in this journals
All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Jurnal Kelautan Tropis
Ni Kadek Dita Cahyani, Ni Kadek Dita
Indonesian Biodiversity Research Center, Jl. Raya Sesetan Gg. Markisa No. 6. Denpasar, Bali, 80223 Indonesia
Earth & Planetary Sciences

Published : 4 Documents Claim Missing Document
Claim Missing Document
Check
Articles

Found 4 Documents
Search

 1 
DNA Barcoding of Anchovy in Tuban Regency as Database of Indonesian Marine Genetic Diversity Joesidawati, Marita Ika; Nursalim, Nining; Kholilah, Nenik; Kurniasih, Eka Maya; Cahyani, Ni Kadek Dita; Ambariyanto, Ambariyanto
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 28, No 4 (2023): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.28.4.383-391

Abstract

Anchovy is the main catch and the primary consumption of coastal communities in Indonesia, and its production shows an increase of more than 10% in 2021. Tuban district, in East Java, Indonesia is part of the WPP 712 (Wilayah Pengelolaan Perikanan or Fisheries Management Area) and highly produces anchovies’ fisheries. Anchovy has a small size, making it difficult to identify morphologically. This study aimed to genetically identify anchovy samples obtained from North Java (Tuban) waters. Molecular identification was conducted by utilizing Cytochrome Oxidase Subunit I (COI) gene using jg-HCO and jg-LCO primers. This study observed 12 individual samples with 623 base pair sequence length. Five species were obtained, namely four species of anchovies (Encrasicholina heteroloba, Encrasicholina punctifer, Stolephorus waitei, and Stolephorus insularis) and one species of sardines (Dussumieria elopsoides) with 99.84-100% similarity to NCBI sequences data. Anchovies typically have a streamlined body with a slightly compressed shape. Anchovies have cycloid scales, which are smooth-edged and relatively small, ranging from a few centimeters to around 20 centimeters in length. Some of the genus from the Anchovy group are Encrasicholina and Stolephorus. The phylogenetic tree reconstruction leads into four clades with a genetic distance between clades of 17,9-24,5 %. This research provides methods and data on the genetic diversity of anchovies taxa caught in Tuban, East Java. The findings are expected to support promoting new standards for healthier and more sustainable anchovy stocks in the country. Overall, this study contributes to providing valuable insights for fisheries management and conservation efforts in Indonesia.
Utilizing Environmental DNA to Identify Eukaryotic Diversity in Mangrove Sediments at Demak, Central Java, Indonesia Cahyani, Ni Kadek Dita; Jumari, Jumari; Hariyati, Riche; Rahadian, Rully; Rahim, Aulia; Zega, Enita Setiawati; Kholifah, Rizqi Widya Nur; Barber, Paul Hendry; Putro, Sapto Purnomo; Soeprobowati, Tri Retnaningsih
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 4 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.4.543-556

Abstract

The mangrove ecosystem, found along tropical and subtropical coasts, adapts to extreme conditions like rapid tidal changes, high salinity, anthropogenic influences, and anoxic environments. Mangrove sediments host diverse organisms, particularly invertebrates and bacteria, which significantly influence sediment structure and biochemical processes by enhancing permeability and water flow. Modern molecular approaches, notably Next-Generation Sequencing (NGS), are increasingly used to identify macro and microorganism communities in sediments. NGS, a powerful tool for DNA and RNA sequencing, allows for parallel sequencing of numerous DNA fragments, providing comprehensive insights into genome structure, genetic variants, gene expression, and epigenetic modifications. Its efficiency and cost-effectiveness make NGS vital for both basic biological research and clinical diagnostics. Recent NGS studies on mangrove sediments have focused on bacterial, archaeal, and fungal diversity. The study examines eukaryotic diversity in mangrove sediments at two locations, targeting the Cytochrome Oxidase Subunit I (COI) gene, a universal marker for eukaryotes. Results indicate distinct taxa at each site with minimal overlap, demonstrating eDNA's potential for assessing both macro and microorganism diversity in mangrove sediments. This preliminary study underscores the utility of molecular techniques in biodiversity research and also dynamic ecosystem changes in the mangrove sediment ecosystem. The high influence of the environment around the mangrove ecosystem will affect the quality of the mangrove itself. eDNA here provides a fast method for recording possible changes to be able to carry out better management in the future.
Challenges in Molecular and Morphological Identification of Sponge Species in Raja Ampat Aisyah, Siti Zanuba; Zamani, Neviaty Putri; Cahyani, Ni Kadek Dita; Elfahmi, Elfahmi; Syafrizayanti, Syafrizayanti; Andriani, Yosie; Arafat, Dondy; Bashari, Muhammad Hasan; Hanif, Novriyandi; Sani, Lalu M. Iqbal; Ayu, Inna Puspa; Akbar, Nebuchadnezzar; Subhan, Beginer
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 30, No 1 (2025): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.30.1.115-125

Abstract

Sponges (Phylum Porifera) are a group of highly diverse, sessile, and filter-feeding basal metazoans, except spongillids. The majority of sponges are marine species that play an important role in benthic habitat by maintaining the stability of marine ecosystems through nutrient cycling, habitat provision, and bioerosion. However, marine sponges are not easily identifiable because of their lack of species-level distinctive morphological features, which limits efforts to monitor actual species biodiversity. Indonesia is home to approximately 850 identified species of marine sponges, and Raja Ampat archipelago of West Papua province is known for its exceptional marine biodiversity. Despite the species abundance, the exact number of sponges in the region is not well-documented due to the lack of specific studies providing comprehensive data on their diversity. Therefore, this study aimed to conduct a DNA barcoding analysis using the mitochondrial cytochrome oxidase I (COI) gene as a marker, combined with morphological analyses of 22 individuals collected in the waters of Waigeo, Mansuar, and Gam Islands in Raja Ampat. The results showed that 3 samples were identified at the species level (Halichondria sp. and Stylissa carteri) with good query cover and percent identity. This showed the possible presence of undescribed or cryptic species, suggesting a severe lack of reference data for both morphology and molecular analyses of marine sponges in the region. Consequently, the analysis showed the presence of a significant gap in the understanding of sponge biodiversity in Raja Ampat's waters.
Genetic Analysis on Horseshoe Crab for Phylogenetic Tree Study from Jambi, Bangka Belitung, Central Java, and East Java Province, Indonesia Kholilah, Nenik; Kurniatami, Gabriella Tarida; Kurniasih, Eka Maya; Nursalim, Nining; Janarkho, Galank Fad’qul; Ambariyanto, Ambariyanto; Wijayanti, Diah Permata; Putro, Sapto Purnomo; Cahyani, Ni Kadek Dita
Jurnal Kelautan Tropis Vol 28, No 2 (2025): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v28i2.25923

Abstract

Order Xiphosura, or horseshoe crabs, are rarely found and classified as macrofossils. In Indonesian waters, there are three species: Tachypleus tridentatus, Tachypleus gigas, and Carcinoscorpius rotundicauda. The genetic analysis of their kinship, however, has been extensively unexplored. This study aims to utilize DNA barcoding, focusing on the cytochrome c oxidase subunit I (COI) locus from mitochondrial DNA and investigating the phylogenetic relationships of horseshoe crabs from the four sites (Tanjung Jabung Timur Regency in Jambi, Bangka Regency in Bangka Belitung, Demak Regency in Central Java, and Tuban Regency in East Java). Additionally, the study provides insights into the biodiversity and ecological roles of horseshoe crabs within their ecosystems and surrounding habitats. Through molecular methods, this research focuses on biodiversity analysis through Sanger sequencing and MEGA 11 software for constructing phylogenetic trees and calculating genetic distances. With a total of 22 horseshoe crabs, the DNA samples from four different sites were amplified via Sanger sequencing, targeting the COI locus and analyzing with MEGA 11. The phylogenetic tree analysis revealed two distinct species, Tachypleus gigas, and Carcinoscorpius rotundicauda, exhibiting significant genetic variation between them. A clear genetic separation between the two species was observed. Otherwise, within the C. rotundicauda species, a minor genetic variation was detected between sampling sites. Notably, the genetic composition displayed greater differences between samples from Java and Sumatra compared to differences within each island. The future research should expand the sampling size and include additional genetic markers to provide a more comprehensive understanding of the genetic diversity and evolutionary history of horseshoe crabs in Indonesian waters. Integrating ecological and environmental data could further elucidate the factors driving genetic differentiation and inform conservation strategies.
Co-Authors Aisyah, Siti Zanuba Ambariyanto , Ayu, Inna Puspa Barber, Paul Hendry Bashari, Muhammad Hasan Beginer Subhan Diah Permata Wijayanti Dondy Arafat Eka Maya Kurniasih, Eka Maya Elfahmi Elfahmi, Elfahmi Janarkho, Galank Fad’qul Jumari Jumari, Jumari Kholifah, Rizqi Widya Nur Kholilah, Nenik Kurniatami, Gabriella Tarida Marita Ika Joesidawati Nebuchadnezzar Akbar NEVIATY PUTRI ZAMANI Novriyandi Hanif Nursalim, Nining Rahim, Aulia Riche Hariyati Rully Rahadian Sani, Lalu M. Iqbal Sapto P Putro Syafrizayanti, Syafrizayanti Tri Retnaningsih Soeprobowati Yosie Andriani Zega, Enita Setiawati