scholarly journals KAJIAN VARIASI SEKUNES INTRASPESIES DAN FILOGENETIK MONYET HITAM SULAWESI (Macaca nigra) DENGAN MENGGUNAKAN GEN COI

2017 ◽  
Vol 17 (1) ◽  
pp. 59
Author(s):  
Fitri Elisabeth Br. Hasibuan ◽  
Feky R Mantiri ◽  
Rooije R.H Rumende
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Intraspecific Variation ◽  
Dna Sequences ◽  
Sequence Variation ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Forest Conversion ◽  
Macaca Nigra

KAJIAN VARIASI SEKUNES INTRASPESIES DAN FILOGENETIK MONYET HITAM SULAWESI (Macaca nigra) DENGAN MENGGUNAKAN GEN COI ABSTRAKMacaca nigra merupakan salah satu spesies yang endemik dan terancam punah di Sulawesi Utara. Eksploitasi yang berlebihan serta alih fungsi hutan menjadi ancaman bagi spesies ini di alam. Penelitian ini dilakukan untuk mengetahui variasi sekuens intraspesies M. nigra yang berada di Pusat Penyelamatan Satwa Tasikoki Bitung. Analisis sekuens menunjukkan terdapat perbedaan sepuluh pasang basa nukleotida pada urutan sekuens sampel dilokasi yang berbeda. Jarak genetik antara kedua sampel yaitu 0.016. Hasil perhitungan jarak genetik menunjukkan variasi genetik masih berada dalam kisaran variasi intraspesies dengan ambang batas untuk variasi intraspesies yaitu 0.015-0.025. Selain itu, variasi juga ditunjukkan pada sampel dengan kerabat dekatnya yang terdata di GenBank disebabkan karena adanya mutasi sinonim dan mutasi nonsinonim. Analisis filogenetik berdasarkan gen COI (Cytochrome Oxidase-I) menunjukkan bahwa sampel M. nigra yang digunakan dalam penelitian ini berada satu klaster dengan M. nigra yang ada di database dan termasuk ke dalam kelompok Silenus.Kata kunci: Variasi sekuens intraspesies, Gen COI, Macaca nigra, analisis filogenetik. THE STUDY INTRASPECIFIC VARIATION SEQUENCES AND PHYLOGENETIC CELEBES BLACK MACAQUE (Macaca nigra) USING COI GENE ABSTRACTMacaca nigra is listed as one of the endemic species and endangered in North Sulawesi. Exploitation and forest conversion have become threats to this species in the wild. This study was conducted to determine the intraspecific sequence variation of M. nigra located in Tasikoki Wildlife Rescue Center, Bitung. Sequence analysis revealed ten nucleotides differences between these two specimens. Genetic distance for both of specimens is 0.016. The result of genetic distance, the genetic variation between the specimens of M. nigra was still within the range of intraspecific variation. Distance analysis was also conducted by comparing with the close relatives of M. nigra based on BLAST search, which showed range from 0.015-0.025. These differences resulted in both synonymous and nonsynonymous mutation. Phylogenetic analysis using DNA sequences of COI (Cytochrome Oxidase-I) gene revealed that the two specimens of M. nigra claster together with M. nigra sequences that have been deposited in GeneBank. Moreover M. nigra is claster in the silenus group which is in accordance with previous reports.Keywords: Intraspecific Sequence Variation, COI Gene, Macaca nigra, Phylogenetic analysis.

scholarly journals Phylogenetic analysis of the grouper family (Serranidae) from various local markets in Indonesian waters using COI (cytochrome oxidase I)

2021 ◽  
Vol 6 (01) ◽  
pp. 74-82
Author(s):  
Tomi Apra Santosa ◽  
Winda Ayu Fietri ◽  
Abdul Razak ◽  
Ramadhan Sumarmin
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Descriptive Analysis ◽  
Cytochrome Oxidase I ◽  
Species Relationships ◽  
Literature Study ◽  
Similar Morphology ◽  
Qualitative Descriptive ◽  
Family Based

Grouper fish (Serranidae) is a type of fish found in Indonesian waters. However, not many people have conducted further research on phylogenetics based on COI (Cytochrome Oxidase I). This study aims to explain the phylogeny of grouper fish from the Serranidae family based on COI (Cytochrome Oxidase I). This research is a literature study. The research samples were grouper fish from Lombok, Karimunjawa, Lampung, Kendari, Madura, Tanakeke, and Numfor. The research instrument was a grouper-type observation sheet and an observation sheet for the results of the MEGA 7 application test. The data were analyzed using qualitative descriptive analysis. The results showed that the level of kinship between the species tested was very close, including Epinephelus areolatus, E. merra, E. fasciatus, E. longispinis, E. coioides, E. ongus, and E. coeruleopunctatus with all genetic distance averages type. 0.02. The conclusion of this study is that in general the species relationships found are several species found in the same location with similar morphology and diet.

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 Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene

2019 ◽  
Vol 21 (1) ◽  
Author(s):  
DEWI IMELDA ROESMA ◽  
DJONG HON TJONG ◽  
DYTA RABBANI AIDIL
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome Oxidase ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Phylogenetic Study ◽  
Mitochondrial Cytochrome ◽  
Base Pairs ◽  
Low Genetic Diversity ◽  
West Sumatra ◽  
Mitochondrial Cytochrome Oxidase

Abstract. Roesma DI, Tjong DH, Aidil DR. 2020. Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene. Biodiversitas 21: 43-48. The transparent gobies fish found in three lakes in Sumatra island is known as Rinuak fish (in Maninjau Lake and Singkarak Lake, West Sumatra, Indonesia) or Badar fish (in Siais Lake, North Sumatra, Indonesia), and are morphologically very similar to the Gobiopterus brachypterus. The phylogenetic study was carried out by analyzing 619 base pairs of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene in 12 fish individuals from the three lakes. Rinuak and Badar fish in three populations have four haplotypes. The sequence divergences in and between populations are very low (0.0-0.5%). This value indicates that Rinuak and Badar fish are the same species with low genetic diversity. The phylogenetic tree illustrates that this fish belongs to the group of Gobiidae and a sister taxon from G. brachypterus.

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.

scholarly journals A new species of Xylophis Beddome, 1878 (Serpentes: Pareidae) from the southern Western Ghats of India

2021 ◽  
Vol 71 ◽  
pp. 219-230
Author(s):  
Surya Narayanan ◽  
Pratyush P. Mohapatra ◽  
Amirtha Balan ◽  
Sandeep Das ◽  
David J. Gower
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Western Ghats ◽  
White Collar ◽  
The Body ◽  
Western Ghats Of India ◽  
Southern Western Ghats ◽  
A New Species

We reassess the taxonomy of the Indian endemic snake Xylophis captaini and describe a new species of Xylophis based on a type series of three specimens from the southernmost part of mainland India. Xylophis deepakisp. nov. is most similar phenotypically to X. captaini, with which it was previously confused. The new species differs from X. captaini by having a broader, more regular and ventrally extensive off-white collar, more ventral scales (117–125 versus 102–113), and by lack of flounces on the body and proximal lobes of the hemipenis. Phylogenetic analysis of mitochondrial 16S DNA sequences strongly indicates that the new species is most closely related to X. captaini, differing from it by an uncorrected pairwise genetic distance of 4.2%. A revised key to the species of Xylophis is provided.

Current issues in species identification for forensic science and the validity of using the cytochrome oxidase I (COI) gene

2010 ◽  
Vol 6 (3) ◽  
pp. 233-241 ◽  
Author(s):  
Linzi Wilson-Wilde ◽  
Janette Norman ◽  
James Robertson ◽  
Stephen Sarre ◽  
Arthur Georges
Keyword(s):  
Forensic Science ◽  
Cytochrome Oxidase ◽  
Species Identification ◽  
Cytochrome Oxidase I ◽  
Coi Gene

Five new species of Myrsidea Waterston (Phthiraptera: Menoponidae) from tanagers (Passeriformes: Thraupidae) in Panama

Zootaxa ◽  
2009 ◽  
Vol 2200 (1) ◽  
pp. 61-68 ◽  
Author(s):  
ROGER D. PRICE ◽  
KEVIN P. JOHNSON
Keyword(s):  
New Species ◽  
Cytochrome Oxidase ◽  
Species Group ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Avian Family ◽  
Mitochondrial Cytochrome Oxidase

There are 23 species of Myrsidea recognized from passerine thraupid hosts. Five new species parasitic on members of this avian family are described. They and their type hosts are Myrsidea rozsai ex the Thick-billed Euphonia, Euphonia laniirostris d'Orbigny & Lafresnaye, M. cruickshanki ex the Carmiol's Tanager, Chlorothraupis carmioli (Lawrence), M. patersoni ex the Grey-headed Tanager, Eucometis penicillata (Spix), M. pagei ex the Crimson-backed Tanager, Ramphocelus dimidiatus Lafresnaye, and M. valimi ex the Tawny-capped Euphonia, Euphonia anneae Cassin. The first species is placed in the bonariensis species group, while the remaining four are placed in the fusca species group. Sequences of a portion of the mitochondrial cytochrome oxidase I (COI) gene were compared to other species of Myrsidea and were highly divergent.

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.

scholarly journals Molecular Detection and Phylogenetic Analysis of Endosymbiont Wolbachia pipientis (Rickettsiales: Anaplasmataceae) Isolated from Dirofilaria immitis in Northwest of Iran

2019 ◽  
Author(s):  
Majid Khanmohammadi ◽  
Reza Falak ◽  
Ahmad Reza Meamar ◽  
Mehdi Arshadi ◽  
Lame Akhlaghi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Dirofilaria Immitis ◽  
Molecular Detection ◽  
Surface Protein ◽  
Coi Gene ◽  
Molecular Pattern ◽  
Filarial Nematodes ◽  
High Consistency ◽  
Wsp Gene

Background: The purpose of this study was molecular detection and phylogenetic analysis of Wolbachia species of Dirofilaria immitis. Methods: Adult filarial nematodes were collected from the cardiovascular and pulmonary arterial systems of natural­ly infected dogs, which caught in different geographical areas of Meshkin Shahr in Ardabil Province, Iran, during 2017. Dirofilaria immitis genomic DNA were extracted.  Phylogenetic analysis for proofing of D. immitis was car­ried out using cytochrome oxidase I (COI) gene. Afterward, the purified DNA was used to determine the molecular pattern of the Wolbachia surface protein (WSP) gene sequence by PCR. Results: Phylogeny and homology studies showed high consistency of the COI gene with the previously-registered sequences for D. immitis. Comparison of DNA sequences revealed no nucleotide variation between them. PCR showed that all of the collected parasites were infected with W. pipientis. The sequence of the WSP gene in Wolbach­ia species from D. immitis was significantly different from other species of Dirofilaria as well as other filarial spe­cies. The maximum homology was observed with the Wolbachia isolated from D. immitis. The greatest distance be­tween WSP nucleotides of Wolbachia species found between D. immitis and those isolated from Onchocerca lupi. Conclusion: PCR could be a simple but suitable method for detection of Wolbachia species. There is a pattern of host specificity between Wolbachia and Dirofilaria that can be related to ancestral evolutions. The results of this phylogenetic analysis and molecular characterization may help us for better identification of Wolbachia species and understanding of their coevolution.  

scholarly journals Taxonomy confirmation of Puntius cf. binotatus from Gunung Tujuh Lake, Jambi, Indonesia based on Cytochrome Oxidase-I (COI) gene

2018 ◽  
Vol 20 (1) ◽  
pp. 54-60
Author(s):  
DEWI IMELDA ROESMA ◽  
DJONG HON TJONG ◽  
WILA KARLINA ◽  
DYTA RABBANI AIDIL
Keyword(s):  
Cytochrome Oxidase ◽  
Black Spot ◽  
Taxonomic Status ◽  
Molecular Study ◽  
Morphological Characters ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Phenotypic Characters ◽  
Subspecies Level ◽  
West Sumatra

Roesma D. I, Tjong D. H, Karlina W, Aidil D. R. 2019. Taxonomy confirmation of Puntius cf. binotatus from Gunung Tujuh Lake based on Cytochrome Oxidase-I (COI) gene. Biodiversitas 20: 54-60. The population of Puntius cf. binotatus Gunung Tujuh Lake in considered as an isolated population which found in the 20-30 meters depth under the water Gunung Tujuh Lake, Sumatra Island. The species often exhibit different phenotypic characters and may genetic characters may also different due to their response to habitat/ecological conditions. Previous study on P. binotatus from several locations in West Sumatra showed the complexity of the genetic and morphological characters. A molecular study using COI gene of P. cf. binotatus from Gunung Tujuh Lake in Sumatera has been conducted to determine the taxonomic status of the fish. The distinct morphological characters of Puntius cf. binotatus is one black spot in the middle of the caudal and the absent of black spot on the base of the anterior dorsal ray. The analysis on COI gene showed that the range of sequence divergences between P. cf. binotatus Gunung Tujuh Lake and other Sumatra P. cf. binotatus is 3.1-7.6% and 4.1% to Barbodes banksi. This value represents the differences at the subspecies level of Barbodes banksi. Therefore Barbodes banksi gunungtujuh is proposed as an appropriate name to P. cf. binotatus Gunung Tujuh Lake.

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