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Widantara, Handang
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Veterinary

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Characterization of CO1 and 18S rDNA genes from Indonesian native ornamental shrimp Caridina boehmei cultured in Jakarta Romadhona, Ekky Ilham; Megawati, Novi; Widantara, Handang; Sutanti, Sutanti; Rahman Ardiansyah, Arif; Mariya Dewi, Kiki; Fitri Larassagita, Annisa; Firman, Aditia; Risky, Moh; Rahmat, Rahmat; Ayub, Ayub
Jurnal Akuakultur Indonesia Vol. 23 No. 2 (2024): Jurnal Akuakultur Indonesia
Publisher : Indonesian Society of Scientific Aquaculture (ISSA)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.19027/jai.23.2.147-156

Abstract

Caridina boehmei is an ornamental shrimp native to Sulawesi that has been successfully cultured and marketed in Indonesia. However, molecular information about this shrimp is not yet available. This study aimed to characterize cytochrome c oxidase subunit I (CO1) and small subunit ribosomal RNA (18S rDNA) genes. Shrimp samples were extracted, and DNA was amplified using CO1 and 18S rDNA primers. The sequencing results were then analyzed by the neighbor-joining method. The 654 bp partial coding sequence (cds) of the CO1 and 380 bp partial cds of 18S rDNA have been successfully amplified from genomic DNA. The CO1 sequencing produced fragments consisting of 25.84% adenine, 20.95% cytosine, 19.11% guanine, and 34.10% thymine. The 18S rDNA sequencing produced fragments consisting of 24.47% adenine, 26.05% cytosine, 28.16% guanine, and 21.32% thymine. Phylogenetic analysis based on the CO1 gene revealed that C. boehmei was grouped with C. variabilis (MK190014), C. brachydactyla (MK190011), and Caridina sp. (MK190012). Phylogenetic analysis based on the 18S rDNA gene revealed that C. boehmei was identical to Caridina sp. Suphan Buri-1 MF622000, C. serratirostris KP725708, C. multidentata JF346236, C. formosae GQ131924, and Caridina sp. Suphan Buri-2 MF622001. The lowest-highest pairwise distance based on CO1 and 18S rDNA was consecutively 0.0017-0.2247 (0.17-22.47%) and 0.0000-0.1218 (0-12.18%). Keywords: 18S rDNA, Caridina boehmei, CO1, DNA barcoding, ornamental shrimp ABSTRAK Caridina boehmei merupakan udang hias asli Sulawesi yang telah berhasil dibudidayakan dan dipasarkan di Indonesia. Kendati demikian, informasi molekuler mengenai udang ini belum tersedia. Tujuan penelitian ini yaitu melakukan karakterisasi menggunakan gen sitokrom c oksidase subunit I (CO1) dan RNA ribosomal subunit kecil (18S rDNA). Sampel udang diekstraksi kemudian DNA diamplifikasi dengan menggunakan primer CO1 dan 18S rDNA. Hasil sekuensing kemudian dianalisis dengan metode neighbor-joining. Sekuen koding (coding sequence, cds) parsial 654 bp dari CO1 dan cds parsial 380 bp dari gen 18S rDNA) telah berhasil diamplifikasi dari DNA genom. Sekuensing CO1 menghasilkan fragmen yang terdiri dari 25,84% adenin, 20,95% sitosin, 19,11% guanin, dan 34,10% timin, sedangkan 18S rDNA menghasilkan fragmen yang terdiri dari 24,47% adenin, 26,05% sitosin, 28,16% guanin, dan 21,32% timin. Analisis filogenetik berdasarkan gen CO1 menunjukkan bahwa C. boehmei sekelompok dengan C. variabilis (MK190014), C. brachydactyla (MK190011), dan Caridina sp. (MK190012). Analisis filogenetik berdasarkan gen 18S rDNA menunjukkan bahwa C. boehmei identik dengan Caridina sp. Suphan Buri-1 MF622000, C. serratirostris KP725708, C. multidentata JF346236, C. formosae GQ131924, and Caridina sp. Suphan Buri-2 MF622001. Jarak berpasangan terendah hingga tertinggi berdasarkan CO1 dan 18S rDNA berturut-turut adalah 0,0017-0,2247 (0,17-22,47%) dan 0,0000-0,1218 (0-12,18%). Kata kunci: 18S rDNA, Caridina boehmei, CO1, DNA barcode, udang hias
First Record of Anguillid Herpesvirus 1 Linked to a Mass Mortality Event in Shortfin Eel (Anguilla bicolor) in Indonesia Romadhona, Ekky Ilham; Widantara, Handang; Aslia, Aslia; Megawati, Novi; Ardiansyah, Arif Rahmat; Larassagita, Annisa Fitri; Dewi, Kiki Mariya; Farman, Aditia; Chaidir, Iding; Sujatmiko, Wisnu; Yaniharto, Dedy; Budiardi, Tatag; Aliah, Ratu Siti; Sutanti, Sutanti
Jurnal Medik Veteriner Vol. 8 No. 1 (2025): April
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jmv.vol8.iss1.2025.134-143

Abstract

Anguillid herpesvirus 1 (AngHV-1), a member of the Alloherpesviridae family, is known to cause high mortality in both wild and farmed eels. Notably, no cases of AngHV-1 infection in Indonesia until June 2023, when a significant mortality rate exceeding 75% among cultured glass eels was documented in Bogor, Indonesia. This study investigated the outbreak by collecting 30 diseased fish from multiple cultured tanks to examine clinical symptoms, histopathological changes, and viral presence through PCR targeting the viral DNA polymerase gene. Hemorrhagic lesions in the abdomen and anal regions were the primary clinical symptoms. Histopathological examination revealed hyperplasia, fusion, and epithelial lifting of the gill secondary lamellae. PCR, using 394 bp primer specific for AngHV-1, confirmed 100% infection among the collected samples, indicating rapid viral transmission within the rearing environment. Phylogenetic analysis of partial DNA polymerase amino acid sequences showed that Indonesian AngHV-1 isolate is genetically diverse and shares similarities with strains from China, Taiwan, Canada, and several European countries, suggesting the emergence of a novel strain. This study highlights the urgent need for enhanced biosecurity measures to curb AngHV-1 spread in the Indonesian eel aquaculture sector.
Comparative Morphometric Analysis of a Salinity-Tolerant Nile Tilapia (Oreochromis niloticus) Local Strain (Salina) and Its Parental Strains Bawono, Yohanes Pamungkas; Dewi, Kiki Mariya; Romadhona, Ekky Ilham; Widantara, Handang; Sujatmiko, Wisnu; Aliah, Ratu Siti; Sutanti, Sutanti; Larassagita, Annisa Fitri; Firmansyah, Muhamad Kholik; Megawati, Novi; Aslia, Aslia; Ardiansyah, Arif Rahmat; Chaidir, Iding; Yaniharto, Dedy
Jurnal Medik Veteriner Vol. 8 No. 2 (2025): October
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jmv.vol8.iss2.2025.424-444

Abstract

This study focuses on the morphology of the Nile tilapia local strain (Salina), a salinity-tolerant tilapia hybrid strain developed by crossbreeding between female Nile tilapia Red NIFI with male Nile tilapia Sultana. The research aimed to analyse the morphometric characteristics of the Salina strain to understand species adaptation to suboptimal environmental conditions compared with the parental groups. A total of 60 Nile tilapia fish, ten female and ten male samples from each strain (Salina, Sultana, and red NIFI), were measured for their total length (TL), standard length (SL), head length (HL), body width (WID), dorsal fin length (DL), caudal fin length (CL), pectoral fin length (PL), caudal peduncle depth (CPD), eye diameter (ED), snout length (SNL), and body weight (BW). Each measurement parameter was then normalized by comparing it with the standard length (SL). The data were analysed using MS Excel 2019 and R v4.5.1 for all statistical analysis including MANOVA, Canonical Variance Analysis, Principal Component Analysis, and Hierarchical Clustering Analysis. Condition factor (K) and length-weight relationship (LWR) were calculated to investigate growth conditions and allometric growth patterns, respectively. Based on the findings, the six tilapia populations exhibit overlapping morphological traits, except for female Salina with slight differences in morphological variations. This implies its potential unique traits acquired from crossbreeding between two different strains. Meanwhile, male Salina showed morphometric traits closely aligned with its male parent, the Sultana strain. The condition factor across all populations indicates favourable growth conditions, although the negative allometric growth pattern suggests that length increases more rapidly than body weight, implying an adaptive trade-off in suboptimal environments.
Co-Authors Ardiansyah, Arif Rahmat Aslia, Aslia Ayub Ayub, Ayub Bawono, Yohanes Pamungkas Chaidir, Iding dedy yaniharto Dewi, Kiki Mariya Farman, Aditia Firman, Aditia Firmansyah, Muhamad Kholik Fitri Larassagita, Annisa Larassagita, Annisa Fitri Mariya Dewi, Kiki Megawati, Novi Rahman Ardiansyah, Arif Rahmat Rahmat Ratu Siti Aliah Risky, Moh Romadhona, Ekky Ilham Sujatmiko, Wisnu sutanti sutanti Tatag Budiardi