scholarly journals Testing the utility of mitochondrial cytochrome oxidase subunit 1 sequences for phylogenetic estimates of relationships between crane (Grus) species

2011 ◽  
Vol 10 (4) ◽  
pp. 4048-4062 ◽  
Author(s):  
D.B. Yu ◽  
R. Chen ◽  
H.A. Kaleri ◽  
B.C. Jiang ◽  
H.X. Xu ◽  
...  
Keyword(s):  
Cytochrome Oxidase ◽  
Mitochondrial Cytochrome ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Cytochrome Oxidase Subunit 1 ◽  
Mitochondrial Cytochrome Oxidase

scholarly journals Genetic diversity of indigenous catfish from Indonesia based on mitochondrial Cytochrome Oxidase Subunit II gene

2021 ◽  
Vol 22 (2) ◽  
Author(s):  
Vista Budiariati ◽  
Trini Susmiati ◽  
Siti Munawaroh ◽  
Rachmawati Cahyaningtyas Arie Putri ◽  
Rini Widayanti Widayanti
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Cytochrome Oxidase ◽  
Mitochondrial Cytochrome ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Coii Gene ◽  
Mitochondrial Cytochrome Oxidase ◽  
Cytochrome Oxidase Subunit Ii

Abstract. Budiariati V, Susmiati T, Waroh S, Putri RCA, Widayanti R. 2021. Genetic diversity of indigenous catfish from Indonesia based on mitochondrial Cytochrome Oxidase Subunit II gene. Biodiversitas 22: 593-600. Catfish is one of the most demanding fish in Indonesia and served in a variety of traditional culinary. Due to their identical morphology and close relation between species in the order of Siluriformes, it is quite tricky to distinguish the species. This can be a threat to develop catfish production in Indonesia since there is a wide variety of catfish species in this mega biodiversity country. The study aimed to analyze the genetic diversity of Indonesian indigenous catfish especially those known as Baung fish by local people based on COII gene. The study also aimed to determine the phylogenetic relationship between the samples and compare them with the GenBank data. A total of 24 samples used in this study from 8 different rivers from 3 different islands and two samples were collected from coastal areas. The study results showed that there is genetic diversity of the Indonesian indigenous catfish based on COII gene. The sequences among 24 samples showed that from 691 nucleotides of COII gene, there were very subtle nucleotides differences of samples that originated from Bojonegoro, Magelang, and samples collected from Baru Beach, Yogyakarta. Based on COII amino acid sequences, 6 polymorphic amino acid sites were on-site number 64, 115, 123, 129, 144, and 165. The samples encoded LLB1 and LPB1 from Baru Beach, Yogyakarta, showed highest different amino acids in the six sites. Samples from the river of Central Java, Sumatra, and Kalimantan belonged to Bagridae family and consist of two different species Hemibagrus sp. and Mystus sp while samples from East Java belonged to Pangasiidae family. The Samples from coastal belonged to Ariidae family.

scholarly journals Genetic variation and phylogenetic analysis of Indonesian indigenous catfish based on mitochondrial cytochrome oxidase subunit III gene

2019 ◽  
Vol 12 (6) ◽  
pp. 896-900 ◽  
Author(s):  
Rini Widayanti ◽  
Aris Haryanto ◽  
Wayan Tunas Artama ◽  
Suhendra Pakpahan
Keyword(s):  
Amino Acids ◽  
Genetic Variation ◽  
Cytochrome Oxidase ◽  
Phylogenetic Reconstruction ◽  
Mitochondrial Cytochrome ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Subunit Iii ◽  
Mitochondrial Cytochrome Oxidase

Aim: This study aimed to analyze the genetic variation and phylogenetic reconstruction of Indonesian indigenous catfish using mitochondrial cytochrome oxidase subunit III sequences. Materials and Methods: A total of 19 samples of catfish were collected from seven rivers (Elo [EM], Progo [PM], Kampar [KR], Musi [MP], Mahakam [MS], Kapuas [KS], and Bengawan Solo [BSBJ]) in five different geographical locations in Indonesia. The genome was isolated from the tissue. Mitochondrial DNA cytochrome oxidase subunit III was amplified using polymerase chain reaction (PCR) with CO3F and CO3R primers. The PCR products were sequenced and continued to analyze genetic variation and phylogenetic relationship using MEGA version 7.0 software. Results: Cytochrome c oxidase (COX)-III gene sequencing obtained 784 nucleotides encoding 261 amino acids. Sequenced COX-III gene fragments were aligned along with other catfish from Genbank using ClustalW program and genetic diversity among species was analyzed using the MEGA Version 7.0 software. Among all samples, there were substitution mutations at 78 nucleotide sites, and there were 14 variations in amino acids. Catfish from PM, KR, MP, and KS had the same amino acids as Hemibagrus nemurus (KJ573466.1), while EM catfish had eight different amino acids and catfish BSBJhad 12 different amino acids. Conclusion: Indonesian catfish divided into four clades. BBSJ Catfish were grouped with Pangasianodon gigas, EM catfish were grouped with Mystus rhegma, and KS catfish were grouped with Hemibagrus spilopterus, while catfish MS, KR, PM, and MP were grouped with H. nemurus.

scholarly journals Selecting Primers for RAPD, Microsatellite and Mitochondrial Cytochrome Oxidase Subunit 1 for Genetic Variation Analysis of Asian Corn Borer (Ostrinia furnacalis Guenée) Population in Java, Indonesia

2019 ◽  
Vol 23 (2) ◽  
pp. 234
Author(s):  
Ahmad Taufiq Arminudin ◽  
Y. Andi Trisyono ◽  
Arman Wijonarko ◽  
Suputa Suputa
Keyword(s):  
Genetic Diversity ◽  
Cytochrome Oxidase ◽  
Mitochondrial Cytochrome ◽  
Ostrinia Furnacalis ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Corn Borer ◽  
Asian Corn Borer ◽  
Cytochrome Oxidase Subunit 1 ◽  
Mitochondrial Cytochrome Oxidase

Primer plays an important role in studying genetic diversity of an insect species. This research was aimed to select the suitable primers to visualize the genetic diversity of Asian corn borer (Ostrinia furnacalis) using Random Amplified Polymorphic DNA (RAPD), microsatellite, and mitochondrial cytochrome oxidase subunit 1 gene (mtCO1). Twenty four RAPD primers (OPA1, OPA4, OPA7,OPA8, OPA10, OPA11, OPA12, OPA13, OPB7, OPB10, OPB11, OPB12, OPB15, OPC4, OPC5, OPC14, OPC16, OPC18, OPC20, OPD3, OPD8, OPD10, OPD13, OPD14) and five microsatellite primers (T3, T4, T5, T81, D25) resulted high polymorphic informations of the genetics of O. furnacalis in Java Indonesia. Universal primers, Lep and Heb were appropriateto do molecular identification of O. furnacalis based on BLAST system on GenBank and BOLD systems.

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