scholarly journals KERAGAMAN GENETIK IKAN TIGER FISH (Datnioides sp.) ASAL KALIMANTAN DAN SUMATERA

2018 ◽  
Vol 13 (3) ◽  
pp. 191
Author(s):  
Melta Rini Fahmi ◽  
Erma Primanita Hayuningtyas ◽  
Mochammad Zamroni ◽  
Bastiar Nur ◽  
Shofihar Sinansari
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Cytochrome B ◽  
Molecular Identification ◽  
Coi Gene ◽  
Cyt B ◽  
Cytochrome Oxidase 1 ◽  
Rag2 Gene

Ikan tiger fish (Datnioides sp.) merupakan ikan hias air tawar yang memiliki nilai ekonomis penting. Distribusi populasi ikan ini meliputi Papua, Kalimantan, dan Sumatera, dengan tingkat eksploitasi yang cukup tinggi di dua lokasi terakhir. Penelitian ini dilakukan untuk mendapatkan informasi keragaman genetik ikan tiger fish yang mendiami perairan Kalimantan dan Sumatera. Sebanyak 24 sampel ikan uji dikoleksi dari Sungai Kapuas, Kalimantan Barat dan Sungai Musi, Sumatera Selatan. Penelitian dilakukan dalam dua tahap, tahap pertama yaitu identifikasi molekuler dengan menggunakan DNA barcoding gen cytochrome oxidase 1 (COI), tahap kedua adalah analisis keragaman genetik dengan menggunakan marka DNA mitokondria gen cytochrome b (Cyt b), dan DNA inti gen recombination activating gene (RAG2). Hasil identifikasi secara molekuler menunjukkan bahwa ikan hasil koleksi memiliki kesamaan genetik sebesar 100% dengan spesies D. undecimradiatus. Keragaman genetik ikan tiger fish antar populasi berkisar pada nilai 0,023 (standar deviasi 0,001) sedangkan keragaman intra populasi adalah sebesar 0,002 dan 0,003 masing-masing untuk populasi Kalimantan dan Sumatera. Jarak genetik sampel baik yang berasal dari Sumatera maupun Kalimantan dengan spesies D. undeciumradiatus masing-masing 0,003 dan 0,006; sedangkan dengan spesies D. microlepis yaitu 0,142. Analisis menggunakan gen RAG2 menunjukkan sampel yang diuji memiliki struktur populasi yang terpisah ditandai dengan terjadinya mutasi pada enam nukleotida dan tiga asam amino.The Tiger fish (Datnioides sp.) is a freshwater ornamental fish that has important economic value. The distribution of this fish included Papua, Kalimantan, and Sumatra, but intensive exploitation occurs in the last two population. This research was conducted to obtain the genetic diversity of tiger fish that inhabited in Kalimantan and Sumatra. A total of 24 fish were collected from Kapuas River, West Kalimantan and Musi River, at Sumatra. The study was conducted in two stages, the first stage is molecular identification of sample by using DNA barcoding cytochrome oxidase 1 (COI) gene, the second stage is analyses of genetic diversity of tiger fish within and between population by using the mitochondrial DNA cytochrome b (Cyt b) gene, and nucleus DNA recombination (RAG2) gene. The molecular identification has shown that the collected fish has a genetic similarity of 100% with D. undecimradiatus. The genetic diversity of tiger fish between populations is 0.023 (standard deviation of 0.001) whereas intra-population is 0.002 and 0.003 for Kalimantan and Sumatra, respectively. The genetic distance of samples with species D. undeciumradiatus were 0.003 and 0.006 for Kalimantan and Sumatera, respectively, whereas the genetic distance with D. microlepis was 0.142. The analysis of mutation on RAG2 gene shows there are six nucleotides and three amino acids have mutation.

scholarly journals Illuminating species diversity of nudibranch in Indonesian coral reef ecosystem using molecular identification

2021 ◽  
Vol 944 (1) ◽  
pp. 012033
Author(s):  
I G W D Dharmawan ◽  
D G Bengen ◽  
I Setyobudiandi ◽  
B Subhan ◽  
I Verawati ◽  
...  
Keyword(s):  
Species Diversity ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Morphological Characters ◽  
Species Level ◽  
Coi Gene ◽  
Interspecific Genetic Distance ◽  
The Difference ◽  
Source Of Information

Abstract Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to identify nudibranch up to species level, which will be a source of information in knowing the distribution and the genetic distance.

scholarly journals Karakteristik Molekuler Kelelawar (Microchiroptera), berdasarkan DNA Mitokondria (Gen COI) di Gua Sukabumi dan Sentul Jawa Barat

2021 ◽  
Vol 14 (1) ◽  
pp. 20-28
Author(s):  
Ismayati Afifah ◽  
Dedy Duryadi Solihin ◽  
Arzyana Sunkar
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Cytochrome Oxidase I ◽  
Genetic Identity ◽  
Genetic Identification ◽  
Coi Gene ◽  
Genetic Characteristics ◽  
Spin Column

AbstrakCytochrome Oxidase I (COI) merupakan salah satu gen mitokondria untuk membantu konstruksi dari pohon filogeni yang dapat bertindak sebagai gen marker. Gen COI memiliki keakuratan dalam mengidentifikasi spesies dan umumnya digunakan sebagai “DNA Barcoding”. Informasi mengenai karakteristik genetik berdasarkan DNA mitokondria pada kelelawar di Sukabumi dan Sentul belum banyak dilaporkan. Tujuan dari penelitian ini untuk mengetahui keragaman genetik kelelawar berdasarkan DNA mitokondria dengan penanda Cytochrome Oxidase I (COI) sebagai DNA barcoding. Isolasi DNA total dilakukan menggunakan Kit Dneasy® Blood and Tissue Kit cat no 69504 (50) berdasarkan prosedur Spin-Column Protocol dengan modifikasi. Hasil penelitian ini menunjukkan bahwa gen COI telah berhasil mengidentifikasi karakteristik spesies. Dua haplotipe didapatkan dari masing-masing populasi. Berdasarkan barcode DNA menunjukkan populasi Sukabumi merupakan spesies Chaerephon plicatus dengan nilai identitas genetik sebesar 97,08%, sedangkan populasi Sentul menunjukkan perbedaan secara genetik dengan spesies Hipposideros larvatus dengan nilai identitas genetik sebesar 94,85%. Identifikasi secara genetik dengan menggunakan gen COI menunjukkan bahwa kelelawar yang berasal Sukabumi adalah spesies Chaerephon plicatus dengan jarak genetik sebesar 3,1%. Kelelawar yang berasal dari Sentul memiliki kedekatan dengan spesies Hipposideros larvatus namun memiliki jarak genetik sebesar 5,2%. AbstractCytochrome Oxidase I (COI) is one of the mitochondrial genes to help the construction of phylogeny trees that can act as marker genes. The COI gene has accuracy in identifying species and is commonly used as "DNA Barcoding". Information about genetic characteristics based on mitochondrial DNA in bats in Sukabumi and Sentul has not been widely reported. The purpose of this study was to determine the genetic diversity of bats based on Mitochondrial DNA with Cytochrome Oxidase I (COI) markers as DNA barcoding. Total DNA isolation was carried out using the Dneasy® Blood and Tissue Kit paint no. 69504 (50) based on the Spin-Column Protocol procedure with modifications. The results of this study indicate that the COI gene has successfully identified species characteristics. Two haplotypes were obtained from each population. Based on DNA barcodes, the population of Sukabumi is a species of Chaerephon plicatus with a genetic identity value of 97.08%, while the Sentul population shows genetic differences with the Hipposideros larvatus species with a genetic identity value of 94.85%. Genetic identification using the COI gene shows that the bats originating from Sukabumi is a spesies Chaerephon plicatus with a genetic distance of 3.1%. The bats originating from Sentul are closely related to the species Hipposideros larvatus but have a genetic distance of 5.2%.

scholarly journals DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY

2020 ◽  
Vol 26 (2) ◽  
pp. 97
Author(s):  
Melta R. Fahmi ◽  
Eni Kusrini ◽  
Erma P. Hayuningtiyas ◽  
Shofihar Sinansari ◽  
Rudhy Gustiano
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Gene Sequence ◽  
Ornamental Fish ◽  
Coi Gene ◽  
Tree Construction ◽  
In The Wild ◽  
Blast Program

The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.

Genetic diversity within Scorpio maurus (Scorpiones: Scorpionidae) from morocco: Preliminary evidence based on CO1 mitochondrial DNA sequences

Biologia ◽  
2008 ◽  
Vol 63 (6) ◽  
Author(s):  
Elsa Froufe ◽  
Pedro Sousa ◽  
Paulo Alves ◽  
David Harris
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Preliminary Analysis ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Preliminary Evidence ◽  
Evidence Based ◽  
Cytochrome Oxidase 1

AbstractThe large-clawed scorpion, Scorpio maurus, is a medically important scorpion and yet nothing is known regarding genetic diversity within this species. As a preliminary analysis we determined variation within the cytochrome oxidase 1 (CO1) mitochondrial gene from specimens from Morocco. High levels of genetic diversity were found that presented some geographical coherence. Of the two identified subspecies from Morocco, S. maurus birulai and S. maurus fuliginosus, the latter included genetically distinct lineages (8.0% uncorrected sequence divergence), indicating a detailed morphological and molecular revision is needed for this species.

scholarly journals Morphometrics and genetic diversity of Tegal, Magelang and their crossbred ducks based on Cytochrome b gene

2018 ◽  
Vol 43 (1) ◽  
pp. 9
Author(s):  
H. Henrik ◽  
D. Purwantini ◽  
I. Ismoyowati
Keyword(s):  
Genetic Diversity ◽  
Body Weight ◽  
Genetic Distance ◽  
Cytochrome B ◽  
Body Length ◽  
The Body ◽  
Chest Circumference ◽  
Neck Length ◽  
Significant Difference ◽  
Cyt B Gene

This experiment was conducted to study the morphometric and genetic diversity of Tegal, Magelang, and their crossbred ducks. Each ten female about twenty weeks old ducks from Tegal, Magelang, Gallang, and Maggal ducks, respectively, were used as the group materialss. The body weight, chest circumference, body length, shank length, neck length, and pubis width were recorded and tested by analysis of variance of one way classification as the morphometric characteristics. Polymorphism of cytochrome b (cyt b) gene on mitochondrial DNA (mtDNA) was analyzed by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). Genetic distance was analyzed based on value of heterozygosity, whereas the phylogeny tree was reconstructed using MEGA6 software. The results showed there were highly significant difference (P<0.01) on body weight, chest circumference, body length, and neck length between population, while shank and pubis width were not significant different. The genetic distance between Gallang and Maggal ducks (0.206) was higher than Tegal and Magelang ducks (0.169). It is concluded that the reciprocal crosses increased the morphometric and genetic diversity of Indonesian local duck population.

scholarly journals Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh

2019 ◽  
Vol 5 (1) ◽  
pp. 25-30
Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam
Keyword(s):  
Genetic Diversity ◽  
Cytochrome B ◽  
Tissue Sample ◽  
Sequence Similarity ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Multiple Sequence ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30

scholarly journals Pengujian Dua Pasang Primer Universal Untuk Amplifikasi Gen Cytochrome Oxidase I Copepoda

Jurnal MIPA ◽  
2015 ◽  
Vol 4 (1) ◽  
pp. 93
Author(s):  
Thalita C. P. Sumampow
Keyword(s):  
Cytochrome Oxidase ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Universal Primer ◽  
Cytochrome Oxidase I Gene ◽  
I Gene

Copepoda merupakan zooplankton kaya manfaat dengan diversitas yang sangat tinggi dan terdiri dari banyak spesies kriptik. Identifikasi cepat, akurat, dan hemat dapat dilakukan dengan menggunakan teknik DNA Barcoding. Kesuksesan teknik tersebut sangat dipengaruhi oleh penggunaan primer yang tepat. Tujuan penelitian ini adalah untuk menguji kemampuan dua pasang primer universal, yakni LCO1490-HCO2198 dan FF2d-FR1d, mengamplifikasi gen COI Copepoda. Dalam penelitian ini, pasangan primer LCO1490-HCO2198 tidak berhasil mengamplifikasi gen target. Sekuens-sekuens hasil amplifikasi menggunakan pasangan primer FF2d-FR1d diidentifikasi melalui BLAST. Hasil yang diperoleh menunjukan bahwa sekuens-sekuens tersebut memiliki persentase kemiripan sebesar 92% dengan bakteri Pandoraea pnomenusa. Melalui hasil yang didapatkan disimpulkan bahwa kedua pasangan primer universal LCO1490-HCO2198 dan FF2d-FR1d tidak cukup spesifik untuk amplifikasi gen cytochrome oxidase I Copepoda.Copepoda is a very beneficial and highly diverse zooplankton with many cryptic species. A fast, reliable, and affordable identification can be done through DNA Barcoding. The success of this technique is affected by the usage of correct primers. The aim of this research was to test the ability of two universal primer pairs, which were LCO1490-HCO2198 and FF2d-FR1d, amplifying COI gene of Copepoda. In this research, LCO1490-HCO2198 primer pairs weren’t able to amplify COI gene of Copepoda. Sequences which were successfully amplified using FF2d-FR1d primer pairs were identified through BLAST. The result shows that the sequences are 92% similar to bacteria named Pandoraea pnomenusa. It can be concluded that both primer pairs are not specific enough to amplify cytochrome oxidase I gene of Copepoda.

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