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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Jurnal Kelautan Tropis Jurnal Abdi Insani Jurnal Aplikasi dan Inovasi Iptek (JASINTEK) Journal of Fisheries & Marine
Kholilah, Nenik
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Characterization of Some Commercially Important Octopus (Mollusca: Cephalopoda) from Indonesian Waters using Mitochondrial DNA Cytochrome Oxidase Sub-Unit I (Mt-DNA COI) Nenik Kholilah; Norma Afiati; Subagiyo Subagiyo
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 26, No 1 (2021): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.26.1.17-26

Abstract

As per the FAO data, octopus identification is very limited in the species level at world fishery and also they are cryptic nature. On the other hand, Indonesia is one of the top ten highest octopus exporters. This study therefore aimed to determine the species of octopus based on phylogenetic analysis of mt-DNA COI. Octopuses were collected from nine different locations throughout Indonesia, i.e., Anambas, Bangka-Belitung, Cirebon, Karimunjawa, Tuban, Lombok, Buton, Wakatobi and Jayapura. Samples were mostly in the form of tentacles that were directly collected from fishermen. After being preserved in 96% ethanol, the sample was extracted in 10% chelexÒ, PCR amplification using Folmer’s primer then was further analysed by sequencing in Sanger methods. Of the 24 samples sequenced, the results recognized four species Octopodidae belongs to the three genera, named Amphioctopus aegina, Hapalochlaena fasciata, Octopus laqueus and Octopus cyanea. Mean pair-wise distances of within-species were ranged from 0 to 5.5 % and between-species was ranged from 12.9 to 15.8 %. This study distinctly confirmed the difference between genus Amphioctopus and Hapalochlaena (15.5 %), as also between O. laqueus and O. cyanea (12.9%) which was previously not completely distinguished. Although performing species identification using DNA sequences for shallow-water benthic octopus species is perhaps considered premature, this study indicated the possible application of COI sequences for species identification, thereby providing a preliminary dataset for future DNA barcoding of octopus, in particular for Indonesia waters.
Meta-analysis of Indonesian Octopus laqueus Kaneko & Kubodera 2005 (Cephalopoda: Octopodidae) using Mt-DNA COI as Genetic Marker Nenik Kholilah; Norma Afiati; Subagiyo Subagiyo; Retno Hartati
Jurnal Kelautan Tropis Vol 24, No 1 (2021): JURNAL KELAUTAN TROPIS
Publisher : Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jkt.v24i1.10190

Abstract

O. laqueus was first discovered not long ago in 2005 in the Ryuku Islands, Japan. Its geographical distribution and molecular identification are therefore still rarely. Nucleotide sequences based on mt-DNA COI for O. laqueus that have been uploaded in the GenBank until before this study was carried out were only six sequences. Since DNA barcoding of mt-DNA COI has some advantageous characteristics, this study aimed to analyse the genetic difference of Indonesian O. laqueus to the data available in the GenBank. Samples were collected in 2019 - 2020 from Karimunjawa (n=16) and Bangka-Belitung (n=2). The mt-DNA COI was extracted using 10% chelex methods, PCR amplified using Folmer’s primer and sequenced in Sanger methods. Pairwise alignment and genetic distance were carried out in MEGA-X, whereas the phylogenetic tree was reconstructed using Bayesian methods. BLAST identification resulted in 685 bp with a range of 92,07-99,24  percentages of identity. The genetic mean pair-wise distances within-clade were 0,002 and 0,006, whilst the distance between the clade was 0.0883. Combining the suggestion with the ITF current, it is concluded that O. laqueus taken from Karimunjawa raised from the same species as those in Malaysia (MN711655) and Japan (AB302176). Specimens from Bangka-Belitung were suggested came from different species, as they were separated into the second clade by 8.83%. One single sample from Japan (AB430543) which laid outside the two clades by 11.63%-11.38% was also suggested to represent a different species. Overall, this study opens to various further studies on O. laqueus using other loci of genetic markers.
Genetic and Morphological Variation of the Redbelly Yellow Tail Fusilier, Caesio cuning (Bloch, 1971) from the Nyamuk Waters, Karimunjawa Archipelago Nining Nursalim; Agus Trianto; Ni Kadek Dita Cahyani; Nenik Kholilah; Galank Fad'qul Janarkho; Eko Hardianto; Subagiyo Subagiyo
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 27, No 4 (2022): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.27.4.341-348

Abstract

Yellowtail fusilier, Caesio cuning (Bloch, 1971) is the main catch of fishermen on the Nyamuk Island, Karimunjawa. C. cuning also has a unique character in the form of different eye color, white, red, and white-red. These differences were raise question whether the eye colors will be differentiated the morphology, and the genetic diversity of C. cuning. This research aims to study the biodiversity of C. cuning caught by fishermen on Nyamuk Island, Karimunjawa, based on their morphology, and molecular using mtDNA control region gene marker.  This study also wanted to test, if different eye colors observed on the sample also reflected at the genetic level. A unique thing was found in morphological observations in the form of eye colors in C. cuning (white, red and white-red). Measurements of 19 morphometric characters were conducted on 44 samples directly in the field. Twenty four  (24) samples with three different eye colors were selected for molecular assay of locus control region mtDNA in the laboratory. Morphological analysis showed the total length of 44 samples of C. cuning ranged from 15-29.4 cm. The total length of white eye color ranged from 15-29.4 cm from 20 samples, red-eye color 17-26 cm from 20 samples and white-red eye color 22-24.6 from 4 samples. Molecular test showed that the fish observed was indeed C. cuning with a similarity of 97.07%-99.27% of NCBI data. The genetic distance C. cuning between individuals was 0-3%.  Genetic distance in the same eye color and different have the same value of 2%. Twenty haplotypes were obtained from 24 samples with high haplotypes diversity, values ranging from 0.978-1,000. The nucleotide diversity ranges from 0.019-0.021. There is no molecular difference between C. cuning with different eye colors.
DNA Barcoding on Indian Ocean Squid, Uroteuthis duvaucelii (D'Orbigny, 1835) (Cephalopoda: Loliginidae) from the Java Sea, Indonesia Norma Afiati; Subagiyo Subagiyo; Christina Retna Handayani; Retno Hartati; Nenik Kholilah
Jurnal Ilmiah Perikanan dan Kelautan Vol. 14 No. 2 (2022): JURNAL ILMIAH PERIKANAN DAN KELAUTAN
Publisher : Faculty of Fisheries and Marine Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jipk.v14i2.33448

Abstract

Highlight ResearchThe possibility of U. duvauceli be a polymorph cryptic species is further reinforced by the results of the present study.Phylogenetic analysis showed two separate clusters though did not perfectly segregate north to the south waters.Individuals in cluster II from the south coast showed the highest polymorphism levels by 40 segregating sites (S), compared to only 2-4 sites in that of cluster IFrequencies of A, C, G, and T in mitochondrial DNA of all specimens skewed toward A and T, with T being the most preferred and G being the least preferred nucleotideAll specimens showed no amino acid frequency for glutamic acid. Further, all four individuals in cluster II (south coast) were also have no amino acid frequencies for aspartic acid and valine as well.AbstractUroteuthis duvauceli (D' Orbigny, 1835) also known as the Indian Ocean Squid is a highly important commercial marine organism along the Java coast, Indonesia. Based on genetic variation this species-complex are polymorphic and cryptic. In the present study, the genetic diversity and stock structure of loliginid squid U. duvauceli is investigated using a mitochondrial gene cytochrome oxidase subunit I (COI). Samples were collected by hand-jigging onboard of an 8hp small fisher-boat equipped with a few lamps during May to August 2015, May 2016 and August to November 2018. Sample collection started at dusk until midnight. The attractor was a weighed-quill attached to nylon string, manually immersed into the water and pulled quickly and continuously for about 3-5 minutes at each effort. The determination was conducted with BLAST. Phylogenetic analysis showed two separate clusters with 100% bootstrap value, in which cluster II from Palabuhanratu has divergences of 5.9 - 7.0%, compared to cluster I.  Genetic variations exist within and among individuals over the locations. Palabuhanratu individuals have the highest polymorphism levels compared to other locations as shown by 40 segregating sites (S). Frequencies of A, C, G, and T in mtDNA of the 20 specimens U. duvauceli are biased toward A and T, with T being the most favoured and G being the least favoured nucleotide. All specimen showed no amino acid frequency for glutamic acid and all four individuals in cluster II (south coast) also have no amino acid frequencies for aspartic acid and valine as well.
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.
Unveiling the DNA Barcoding of Threadfin Breams (Nemipteridae) at Oeba Fish Landing Site and Oesapa Fish Market in Kupang, East Nusa Tenggara Wora, Umbu Domu; Wijayanti, Diah Permata; Widowati, Ita; Ginzel, Fanny Iriany; Nursalim, Nining; Kholilah, Nenik; Bachtiar, Muggi
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 2 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.2.170-180

Abstract

Threadfin breams (Nemipteridae) are demersal fish species that constitute a significant catch for East Nusa Tenggara fishermen at the Oeba Fish Landing Site and Oesapa Fish Market, where they are landed year-round. Over the years, there has been a noticeable increase in the capture of threadfin breams, raising concerns about the potential impact on their genetic diversity. The ongoing trend could affect the region’s overall population structure of threadfin breams. This study addresses the need to identify threadfin breams in the landing above sites of threadfin breams through molecular analysis of mtDNA COI. The research involved the examination of 24 samples obtained from the Oeba Fish Landing Site and Oesapa Fish Market. The analysis revealed the presence of five distinct threadfin bream species: Nemipterus hexodon, N. japonicus, N. zysron, N. aurora, and Pristipomoides typus. The genetic distance between individual threadfin breams ranged from 0-0.8%, indicating a relatively close genetic relationship within the population. Also, phylogenetic tree reconstruction further delineated five distinct clades based on the species obtained from the samples. Given these findings, the study emphasizes the importance of sustainable threadfin bream capture to preserve genetic diversity. The results underscore the need for ongoing monitoring and management strategies to ensure the threadfin bream population’s long-term health and stability. Additionally, the study suggests that a more in-depth analysis of genetic diversity and the environmental factors influencing this species is warranted for a comprehensive understanding and effective conservation measures.
Pelatihan Pengolahan Pangan Berbahan Dasar Rumput Laut Cokrowati, Nunik; Lumbessy, Salnida Yuniarti; Diniarti, Nanda; Fitriani, Syawalina; Waspodo, Saptono; Hilyana, Sitti; Buhari, Nurliah; Rahman, Ibadur; Wahyudi, Rhojim; Larasati, Chandrika Eka; Kholilah, Nenik; Nuryadin, Rusmin; Mujib, Abdul Saddam; Yasir; Basmal, Jamal; Suwarti
Jurnal Aplikasi dan Inovasi Iptek Vol 6 No Risdamas (2024): Jurnal Aplikasi dan Inovasi Iptek No. 6 Vol. Risdamas Desember, 2024
Publisher : Denpasar Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52232/jasintek.v6iRisdamas.199

Abstract

Pemanfaatan rumput laut saat ini sudah beragam, baik untuk produk pangan maupun non pangan. Produk turunan rumput laut dapat dikelompokkan menjadi 5P, yaitu Pangan, Pakan, Pupuk, Produk Kosmetik, dan Produk Farmasi. Untuk itu kegiatan ini bertujuan untuk transfer ilmu, teknologi dan inovasi pengolahan pangan berbahan dasar rumput laut sebagai camilan sehat. Kegiatan dilaksanakan pada tanggal 20 November 2024 di Desa Paremas Kecamatan Jerowaru Kabupaten Lombok Timur. Metode kegiatan ini adalah ceramah dan praktek langsung pembuatan produk olahan berbahan rumput laut. Masyarakat sasaran kegiatan ini sejumlah 30 orang yang terdiri dari ibu-ibu rumah tangga dan remaja putri. Masyarakat sasaran berasal dari Desa Paremas, Seriweh, Keruak, Lungkak, Jerowaru dan Ketapang Raya Kabupaten Lombok Timur. Hasil kegiatan ini adalah cara membuat pilus rumput laut dan keripik dari Ulva telah diajarkan oleh tim kegiatan kepada masyarakat sasaran. Kripik Ulva memiliki cita rasa gurih, renyah dan ringan dan tetap nampak berwarna hijau. Pilus rumput laut memiliki cita rasa gurih dan masih terasa taste rumput laut. Kesimpulan kegiatan ini adalah keterampilan pembuatan kripik Ulva dan pilus rumput laut telah diajarkan oleh tim kegiatan dan masyarakat sasaran memahami keterampilan tersebut
PENDAMPINGAN PEMENUHAN PERSYARATAN PENGAJUAN SERTIFIKAT HALAL UNTUK PRODUK OLAHAN IKAN YANG DIHASILKAN OLEH POKLAHSAR PUTRI BAHARI DI KAWASAN KONSERVASI GILI MATRA Gigentika, Soraya; Hilyana, Sitti; Waspodo, Saptono; Amir, Sadikin; Paryono, Paryono; Rahman, Ibadur; Larasati, Chandrika Eka; Sakina, Sholihati Lathifa; Nuryadin, Rusmin; Kholilah, Nenik; Ashari, Rowi; Murdin, Lalu Ferdi Alfarisi; Martanina, Martanina
Jurnal Abdi Insani Vol 12 No 5 (2025): Jurnal Abdi Insani
Publisher : Universitas Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/abdiinsani.v12i5.2471

Abstract

Pada kawasan konservasi Pulau Gili Air, Gili Meno, dan Gili Trawangan (Gili Matra) terdapat tiga kelompok pengolah dan pemasar ikan (Poklahsar), salah satunya adalah Poklahsar Putri Bahari yang mengolah abon ikan. Produk olahan yang dihasilkan oleh poklahsar tersebut telah memiliki Sertifikat Produksi Pangan Industri Rumah Tangga (SPP-IRT), tetapi belum memiliki sertifikat halal. Sementara itu, produk olahan ikan yang dihasilkan oleh poklahsar tersebut perlu melakukan pengembangan dan perluasan pasar, dimana salah satu strateginya adalah melalui kepemilikan sertifikat halal pada produk olahan abon ikan yang dihasilkan. Oleh karena itu, perlu dilakukan pendampingan untuk pemenuhan persyaratan sertifikat halal pada Poklahsar Putri Bahari. Target yang akan dicapai dari kegiatan pengabdian ini adalah poklahsar di kawasan konservasi Gili Matra mendapatkan pengetahuan dan pemahaman mengenai sertifikat halal pada produk perikanan, pendetailan terhadap persyaratan pengajuan sertifikat halal, serta tahapan pengajuan sertifikat halal. Kegiatan pendampingan ini menggunakan metode kaji tindak partisipatif melalui diskusi dan wawancara. Pelaksanaan kegiatan pendampingan yang dilakukan adalah alih pengetahuan teoritis dan implementasi. Kegiatan pengabdian ini dilakukan pada bulan Mei-Agustus tahun 2024. Hasil dari kegiatan pendampingan yang dilakukan adalah Poklahsar Putri Bahari telah memiliki dokumen profil perusahaan, daftar produk dan bahan yang digunakan, sertifikat bahan baku, proses produksi, serta manual SJPH. Melalui kegiatan pendampingan ini, maka Poklahsar Putri Bahari telah dapat mengatasi semua kendala yang umumnya dihadapi oleh usaha mikro dan kecil dalam mempersiapkan dokumen persyaratan pengajuan sertifikasi halal.
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 Abd Saddam Mujib Agus Trianto Ambariyanto , Ashari, Rowi Bachtiar, Muggi Chandrika Eka Larasati, Chandrika Eka Christina Retna Handayani Diah Permata Wijayanti Eka Maya Kurniasih, Eka Maya Eko Hardianto Fitriani, Syawalina Galank Fad'qul Janarkho Gigentika, Soraya Ginzel, Fanny Iriany Ita Widowati Jamal Basmal, Jamal Janarkho, Galank Fad’qul Kurniatami, Gabriella Tarida Lumbessy, Salnida Yuniarti Marita Ika Joesidawati Martanina, Martanina Murdin, Lalu Ferdi Alfarisi Nanda Diniarti Ni Kadek Dita Cahyani Ni Kadek Dita Cahyani, Ni Kadek Dita Nining Nursalim Norma Afiati Norma Afiati Nunik Cokrowati Nurliah Buhari, Nurliah Nursalim, Nining Paryono Rahman, Ibadur Retno Hartati Retno Hartati Rhojim Wahyudi Rusmin Nuryadin Sadikin Amir Sakina, Sholihati Lathifa Sapto P Putro Saptono Waspodo Sitti Hilyana Subagiyo Subagiyo Subagiyo Subagiyo Subagiyo Subagiyo SUWARTI Wora, Umbu Domu Yasir