Local population subdivision in the lichenCladonia subcervicornisas revealed by mitochondrial cytochrome oxidase subunit 1 intron sequences

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.

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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

Jurnal Perlindungan Tanaman Indonesia ◽

10.22146/jpti.38285 ◽

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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