scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

scholarly journals Identifikasi ikan gabus, Channa spp. (Scopoli 1777) stok liar dan generasi I hasil domestikasi berdasarkan gen Cytochrome C Oxidase Subunit I (COI)

2018 ◽  
Vol 17 (2) ◽  
pp. 165 ◽  
Author(s):  
Irmawati Irmawati ◽  
Joeharnani Tresnati ◽  
Liestiaty Fachruddin ◽  
Nur Rahmawaty Arma ◽  
Andi Haerul
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Native Species ◽  
First Generation ◽  
Coi Gene ◽  
Oxidase Subunit ◽  
South Sulawesi ◽  
Phylogenetic Resolution ◽  
Channa Striata

The snakehead fish (Channidae) is widely distributed in inland water of Indonesia. This fish is native species in Suma-tera, Java and Kalimantan, but non-native species in Sulawesi and Papua. Study on molecular identification and phylo-geny of this fish using cytochrome c oxidase subunit I (COI) gene has only been conducted on snakehead fish origin from Tasikmalaya, Ambarawa, Bali, Aceh, Pontianak, and Banjarmasin waters, but none is available in South Sulawesi waters. The objectives of this research are to identify species of snakehead fish from Towuti Lake Sorowako and the first generation (F1) of domesticated snakehead fish from Bantaeng waters of South Sulawesi using COI gene for DNA barcoding, and to analyze the phylogenetic resolution of the fish. Partial sequences of the COI gene of the snakehead fish were aligned with sequences of snakehead fish deposited in GenBank. The phylogenetic tree was constructed using MEGA 7.0.20 program. The result indicated that COI gene nucleotides of snakehead fish from Towuti Lake Sorowako showed 99% homology with Channa striata acc no. KU692418 and KU692421, and showed 98% homology with those of acc no. KU852443. Therefore it can be conclude that Channa striata exist in Towuti Lake Sorowako. Nucleotide sequences of the first generation (F1) of domesticated snakehead fish from Bantaeng waters showed 65% homology with Channa pleurophthalma (acc no. KJ937390) origins from Banjarmasin waters and Channa gachua (acc no. KX389277). Based on this result, it assumed that snakehead fish from Towuti Lake Sorowako are distantly in gene to those from Bantaeng waters, and further analyses are required to identify the population of snakehead fish from Bantaeng waters. Abstrak Populasi ikan gabus (famili Channidae) tersebar luas di wilayah perairan tawar Indonesia. Ikan gabus merupakan ikan asli di Sumatera, Jawa, dan Kalimantan) tetapi merupakan ikan introduksi di Sulawesi dan Papua. Identifikasi berdasar-kan gen cytochrome c oxidase subunit I (COI) telah dilakukan terhadap ikan gabus dari perairan di Tasikmalaya, Amba-rawa, Bali, Aceh, Pontianak dan Banjarmasin, tetapi ikan gabus dari perairan Sulawesi Selatan belum dilakukan. Tuju-an penelitian adalah untuk mengidentifikasi species ikan gabus dari Danau Towuti Sorowako dan ikan gabus generasi I (F1) hasil domestikasi dari induk yang berasal dari perairan tawar Kabupaten Bantaeng Sulawesi Selatan menggunakan gen COI untuk DNA barcoding, dan untuk menganalisis filogeni ikan gabus tersebut. Sekuen gen COI ikan gabus terse-but disejajarkan dengan sekuen nukleotida ikan gabus yang terdeposit di GenBank. Pohon filogenetik dikonstruksi de-ngan menggunakan program MEGA 7.0.20. Hasil penelitian menunjukkan bahwa nukleotida gen COI sampel ikan gabus dari Danau Towuti Sorowako memiliki kemiripan 99% dengan Channa striata nomor aksesi KU692418 dan KU692421 dan 98% dengan Channa striata nomor aksesi KU852443 sehingga dapat disimpulkan bahwa di Danau To-wuti terdapat ikan gabus jenis Channa striata. Tingkat kemiripan sekuen nukleotida ikan gabus F1dari perairan Kabu-paten Bantaeng adalah 65% dengan ikan gabus Channa pleurophthalma (KJ937390) asal perairan Banjarmasin dan ikan gabus Channa gachua (KX389277). Berdasarkan hasil tersebut maka diduga bahwa ikan gabus dari Danau Towu-ti Sorowako berkerabat jauh dengan ikan gabus dari perairan Bantaeng, dan diperlukan analisis yang lebih lanjut untuk menentukan jenis populasi ikan gabus F1 asal perairan tawar Kabupaten Bantaeng tersebut.

scholarly journals DNA barcoding of Crustacean larvae in the eastern areas of Segara Anakan Cilacap, Central Java Indonesia

2020 ◽  
Vol 21 (10) ◽  
Author(s):  
KUSBIYANTO KUSBIYANTO ◽  
DIAN BHAGAWATI ◽  
Agus Nuryanto
Keyword(s):  
Cytochrome C ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Species Level ◽  
Coi Gene ◽  
Reference Species ◽  
Oxidase Gene ◽  
Oxidase Subunit ◽  
Central Java

Abstract. Kusbiyanto, Bhagawati D, Nuryanto A. 2020. DNA barcoding of crustacean larvae in Segara Anakan, Cilacap, Central Java, Indonesia using cytochrome c oxidase gene. Biodiversitas 21: 4878-4887. Species-level identification of crustacean larvae is challenging due to morphological constraints. DNA barcoding offers a precise method to solve the problems. That method has never been applied to crustacean larvae from the eastern of Segara Anakan, Cilacap, Central Java, Indonesia. This study aims to identify crustacean larvae in the eastern of Segara Anakan using the cytochrome c oxidase subunit I (COI) gene as a barcode marker. Larvae morphotypes were identified under a binocular microscope. The COI gene was sequenced from one individual of each morphotype. Microscopic observation placed the samples into 15 morphotypes. DNA barcoding placed twelve morphotypes as Crustacea with sequence homologies from 72.21% to 99.21%. Intra-species genetic divergences between samples and reference species ranged between 0.9% and 31.9%, while genetic distance ranged from 0.0% to 17.80%. Intra-species genetic divergences ranged between 0.00% and 3.9%, while genetic distance ranged from 0.00% to 3.8%. The phylogenetic tree proved the monophyly between samples and reference species and showed clear separation among species. All parameters proved that nine morphotypes were identified into species level and were counted for five species. Three morphotypes were identified into the genus level and were counted for three genera. Eight species of crustacean larvae were successfully identified using the cytochrome c oxidase subunit 1 gene.

scholarly journals DNA barcode of the Lanzones scale insect, Unaspis mabilis Lit & Barbecho (Hemiptera: Diaspididae)

2020 ◽  
Vol 14 (3) ◽  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Scale Insect ◽  
Coi Gene ◽  
Species Identity ◽  
Management Options ◽  
Nucleotide Sequence Alignment ◽  
Coi Sequences

The mitochondrial cytochrome c oxidase subunit 1 (COI) nucleotide sequences of Unaspis mabilis Lit & Barbecho (Hemiptera: Diaspididae), are provided for the first time. The total genomic DNA of each scale insect was extracted from individuals infesting lanzones leaves from three selected sites in Los Baños, Laguna. A partial COI gene amplicon with approximately 750 bp was obtained using the primer pair PcoF1 and LepR1. Nucleotide sequence alignment showed no variation among the COI sequences from all the samples. BLASTn search yielded no significant match with any of the available sequences for Unaspis species. The closest hit was Aulacaspis tubercularis Newstead (GenBank Accession No. HM474091) with 87.4% nucleotide similarity. Nonetheless, phylogenetic analyses revealed that generated COI sequences from U. mabilis form a monophyletic clade with U. yanonensis and U. euonymi, with closer proximity to the former. These findings also strengthen the species status of U. mabilis under the genus Unaspis. The DNA barcodes generated from this study (GenBank Acc. Nos. MN114099, MN14101, and MN114102), could, therefore, be used to verify the species identity of other lanzones scale accessions, as well as monitor the distribution and spread of U. mabilis, which would greatly influence possible pest management options. KEYWORDS: cytochrome C oxidase I, COI, Lansium domesticum Correa, lanzones

scholarly journals Molecular identification and phylogenetic relationships of seven Satyrinae butterflies in Bangladesh using Cytochrome c oxidase subunit I gene

2019 ◽  
Vol 8 (1) ◽  
pp. 67-74
Author(s):  
Ananna Ghosh ◽  
Muhammad Sohel Abedin ◽  
Abdul Jabber Howlader ◽  
Md Monwar Hossain
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Molecular Identification ◽  
Phylogenetic Trees ◽  
Coi Gene ◽  
Neighbor Joining ◽  
Oxidase Subunit ◽  
Traditional Classification ◽  
Nymphalid Butterfly ◽  
Coi Sequences

The Satyrinae is a subfamily of Nymphalid butterfly, which is morphologically and ecologically the most diverse group, occurring in all habitats. In the present study, Cytochrome c oxidase subunit I (COI) gene of seven species of Satyrinae was sequenced, aligned, and used to construct phylogenetic trees. The molecular identification of these Satyrinae species was confirmed by comparing the related sequences in the National Center for Biotechnology Information (NCBI) GenBank. The base compositions of the COI sequences were 39.07% T, 16.44% C, 29.83% A, and 14.64% G, revealing a strong AT bias (68.9%). The sequence distance among Satyrinae species ranged from 0.09% to 0.18%. Phylogenetic trees were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods, using Orthetrum sabina as an outgroup. Both trees had almost identical topologies. The sampled species in Satyrinae exhibited the following relationships: Melanitis leda + [(Mycalesis mineus+(Mycalesis gotama+Mycalesis anaxias)) + (Ypthima baldus + (Lethe chandica+Elymnias hypermnestra))], suggesting that M. leda might be distantly related with the rest of the Satyrinae species. This clustering result is almost identical to current traditional classification. This study confirms that the COI based DNA barcoding is an efficient method for the identification of butterflies including Satyrinae species and, as such, may further contribute effectively to biodiversity and evolutionary research. Jahangirnagar University J. Biol. Sci. 8(1): 67-74, 2019 (June)

scholarly journals Taxonomy and the DNA Barcoding Enterprise

Zootaxa ◽  
2011 ◽  
Vol 2742 (1) ◽  
pp. 67 ◽  
Author(s):  
MALTE C. EBACH
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Type Specimen ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Oxidase Subunit ◽  
Mitochondrial Cytochrome C

DNA Barcoding is elusive to many taxonomists. Like the numbers in a barcode, barcoding attempts to link a type specimen with a part of its DNA, most commonly from the mitochondrial Cytochrome c Oxidase subunit I (COI) gene.

scholarly journals Taxonomic separateness of the subspecies of Noctua interjecta Hübner (Lepidoptera: Noctuidae) inhabiting central Europe

2019 ◽  
Vol 30 (1) ◽  
pp. 33-42
Author(s):  
Janusz Nowacki ◽  
Hanna Panagiotopoulou-Stawnicka ◽  
Robert Rutkowski ◽  
Roman Wąsala
Keyword(s):  
Cytochrome C Oxidase ◽  
Central Europe ◽  
Divergence Time ◽  
Coi Gene ◽  
Before Present ◽  
Cytochrome C Oxidase I ◽  
Central European ◽  
Morphological Differences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

This study focuses on morphological and genetic differences between two central European subspecies of the noctuid moth Noctua interjecta Hübner: N. interjecta interjecta Hübner, 1803 from Transcarpathia in Ukraine and N. interjecta caliginosa (Schawerda, 1919) from Poland. While the morphological differences between these taxa are fairly obvious, individuals from these two populations were found to differ also genetically, as indicated by the cytochrome c oxidase I (COI) gene sequences. The Transcarpathian population exhibits solely the NImizH3 haplotype, but the Polish one the relatively distant NImizH1 and NImizH2 haplotypes. A Neighbour-Joining tree and a network of haplotypes separated the two haplotypes found in Poland (N. i. caliginosa) from those derived from NImizH3 (N. i. interjecta). The divergence time for these two groups was estimated as 400–600 thousand years before present, coinciding with the maximum extent of the Pleistocene ice-sheet covering Europe.

scholarly journals Identification and Confirmation of Chironomus circumdatus Kieffer, 1916 (Diptera: Chironomidae) Using DNA Barcoding

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Rawal Deepak ◽  
Verma Himani ◽  
Prajapat Gyata
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Bioinformatics Analysis ◽  
Molecular Taxonomy ◽  
Species Level ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Dideoxy Sequencing ◽  
Chironomid Species

Present study was performed to identify and confirm collected larval Chironomid up to species level. To assess molecular taxonomy and phylogeny, DNA barcoding was done using Sanger dideoxy sequencing of mitochondrial cytochrome c oxidase subunit I (COI) gene of larval sample. Bioinformatics analysis was done by using NCBI’s BLAST software. By evidence of DNA barcoding, it was confirmed that present larval chironomid species was Chironomus circumdatus Kieffer, 1916.

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