Exploring the Utility of Partial Cytochrome c Oxidase Subunit 1 for DNA Barcoding of Gobies

Estimation of postmortem interval (PMI) is paramount in modern forensic investigation. After the disappearance of the early postmortem phenomena conventionally used to estimate PMI, entomologic evidence provides important indicators for PMI estimation. The age of the oldest fly larvae or pupae can be estimated to pinpoint the time of oviposition, which is considered the minimum PMI (PMImin). The development rate of insects is usually temperature dependent and species specific. Therefore, species identification is mandatory for PMImin estimation using entomological evidence. The classical morphological identification method cannot be applied when specimens are damaged or have not yet matured. To overcome this limitation, some investigators employ molecular identification using mitochondrial cytochrome c oxidase subunit I (COI) nucleotide sequences. The molecular identification method commonly uses Sanger’s nucleotide sequencing and molecular phylogeny, which are complex and time consuming and constitute another obstacle for forensic investigators. In this study, instead of using conventional Sanger’s nucleotide sequencing, single-nucleotide polymorphisms (SNPs) in the COI gene region, which are unique between fly species, were selected and targeted for single-base extension (SBE) technology. These SNPs were genotyped using a SNaPshot® kit. Eleven Calliphoridae and seven Sarcophagidae species were covered. To validate this genotyping, fly DNA samples (103 adults, 84 larvae, and 4 pupae) previously confirmed by DNA barcoding were used. This method worked quickly with minimal DNA, providing a potential alternative to conventional DNA barcoding. Consisting of only a few simple electropherogram peaks, the results were more straightforward compared with those of the conventional DNA barcoding produced by Sanger’s nucleotide sequencing.

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Can DNA barcoding be used to identify closely related Clunio Haliday, 1855 species (Diptera: Chironomidae, Orthocladiinae)?

Zootaxa ◽

10.11646/zootaxa.4927.1.1 ◽

2021 ◽

Vol 4927 (1) ◽

pp. 1-8

Author(s):

PARASKEVA MICHALOVA ◽

VALERIA LENCIONI ◽

MOMCHIL NENOV ◽

SVETOSLAV NIKOLOV

Keyword(s):

Cytochrome C ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Methodological Approach ◽

Dna Barcode ◽

Mitochondrial Cytochrome ◽

Base Pairs ◽

Oxidase Subunit ◽

Gene Coi ◽

Mitochondrial Cytochrome C

DNA barcoding based on a fragment of mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) was applied to the two chironomids Clunio balticus Heimbach (690 base pairs) and C. ponticus Michailova (691 base pairs). The two species differed by one deletion in the nucleotide sequence Adenine. However, the 658-nucleotide long sequences of DNA from the mitochondrial Cytochrome C Oxidase subunit 1 gene (COI) of C. balticus and C. ponticus were identical upon comparison. Further, they compared with homologous sequences for C. marinus Holiday and C. tsushimensis Tokunaga from the Barcode of Life (BOLD) database and the results plotted as a weighted graph, where C. tsushimensis, C. marinus and C. balticus C. ponticus formed three almost equidistant groups. From this, we established that the genetic distance between the respective COI sequences of C. balticus and C. ponticus is minimal, indicating a close relationship between the species indicative of recent common origin. However, the comparative analysis between C. tsushimensis, C. marinus, C. balticus and C. ponticus showed a wider divergence in their respective nucleotide sequences. Overall, our results emphasized that the COI region does not work well as a DNA barcode to identify species within the Clunio genus. Either longer sequences or a multifaceted methodological approach, including morphology, cytogenetic and ecology is needed to distinguish some members of Clunio genus.

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First molecular characterization of the facultative myiasis agent Eristalis tenax in Turkey using mitochondrial cytochrome c oxidase subunit I DNA barcoding sequences

TURKISH JOURNAL OF VETERINARY AND ANIMAL SCIENCES ◽

10.3906/vet-1911-82 ◽

2020 ◽

Vol 44 (2) ◽

pp. 449-455

Author(s):

Mübeccel OKUR ◽

Alparslan YILDIRIM ◽

Abdullah İNCİ

Keyword(s):

Cytochrome C ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Molecular Characterization ◽

Mitochondrial Cytochrome ◽

Oxidase Subunit ◽

Mitochondrial Cytochrome C

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

Jurnal Iktiologi Indonesia ◽

10.32491/jii.v17i2.356 ◽

2018 ◽

Vol 17 (2) ◽

pp. 165 ◽

Cited By ~ 2

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.

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

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d211054 ◽

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.

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