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 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.

scholarly journals The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool

2018 ◽  
Vol 19 (3) ◽  
pp. 997-1003
Author(s):  
R. SUSANTI ◽  
RETNO SRI ISWARI ◽  
FIDIA FIBRIANA ◽  
INDRIAWATI INDRIAWATI
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Gene Sequence ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Central Java ◽  
Synonym Substitution ◽  
Haplotype A

Susanti R, Iswari RS, Fibriana F, Indriawati. 2018. The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool. Biodiversitas 19: 997-1003. The local duck DNA barcoding is still rarely conducted in Indonesia while DNA barcoding is extensively used as a tool of species identification and delineation tool. This study aimed to analyze the sequence and patterns of Central Javanese ducks mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Feather samples of seven breeds of native duck were collected from traditional husbandries in Central Java. The samples were employed for DNA extraction and COI gene amplification. Five haplotypes were obtained from 35 samples, i.e., haplotype A, B, C, D, and E. Also, 9 variable sites with synonym substitution was detected in four nucleotides number 55, 61, 100, and 109; whereas five synonym substitutions were identified in the nucleotides number 36, 48, 51, 66, and 756. In conclusion, this study annotates that COI mtDNA gene is essential for local ducks barcoding system.

scholarly journals MOLECULAR IDENTIFICATION OF EXOTIC FRUIT FLY Bactrocera occipitalis (DIPTERA: TEPHRITIDAE) USING MITOCHONDRIAL CYTOCHROME OXIDASE I (COI) GENE

2018 ◽  
Vol 6 (1) ◽  
pp. 34
Author(s):  
I Putu Sudiarta ◽  
Dwi Martiningsia ◽  
I Nyoman Wijaya
Keyword(s):  
Cytochrome Oxidase ◽  
Molecular Identification ◽  
Fruit Fly ◽  
Fruit Flies ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Morphological Identification ◽  
Mitochondrial Cytochrome ◽  
Accurate Identification ◽  
Mitochondrial Cytochrome Oxidase

Some of fruit flies have been reported as the important pest on fruits and vegetables in the world. Agricultural Quarantine Agency Denpasar reported that there was new coming species (exotic) of fruit flies in Bali in 2014 based on the morphological identification, namely Bactrocera occipitalis. However Bactrocera dorsalis complex have similar morphological characters and have a less distinctive character for taxonomic identification, therefore it is difficult to identify fruit flies accurately. Based on that phenomena, the accurate identification is needed. One of the more accurate identification techniques is based on molecular identification using DNA-based barcode. To identify fruit flies, DNA-based barcode using mitochondrial cytochrome oxidase I (COI) gene has been conducted. PCR analysis using Fruit Fly MT-CO1-F (FFMT-CO1-F) 5’-GGAGCATTAATYGGRGAYG-3’ as forward primer and HCO 5’-TAAACTTCAGGGTGACCAAAAATCA-3’ as reverse primer was successfully amplified around 600 bp of COI gene of fruit flies. Based on similarity of sequence product, the species was identifiedas Bactrocera occipitalis and same result was revealed using morphological identification. Phylogenetic analysis of B. occipitalis based on COI genes showed that B. occipitalis from Bali were in the same groups with Bactrocera species from Tarakan and Philippines. In addition, Bactrocera occipitalis as exotic fruit fly is a new report in Bali, Indonesia.

Evolutionary analyses of phylum Chaetognatha based on mitochondrial cytochrome oxidase I gene

2020 ◽  
Vol 44 (6) ◽  
pp. 508-518
Author(s):  
Sam PETER ◽  
Manoj Kumar BHASKARAN NAIR ◽  
Devika PILLAI
Keyword(s):  
Cytochrome Oxidase ◽  
Ribonucleic Acid ◽  
Cytochrome Oxidase I ◽  
Rrna Genes ◽  
Coi Gene ◽  
Phylogenetic Study ◽  
Mitochondrial Cytochrome ◽  
Ribosomal Ribonucleic Acid ◽  
Developmental Features ◽  
Mitochondrial Cytochrome Oxidase

Chaetognaths (arrow worms) are an enigmatic group of transparent planktonic invertebrates and play an important role in the marine food web. Their morphological and developmental features have raised extensive debates since the discovery of the phylum in the 18th century. Uncertainty in the phylogenetic placement of certain chaetognath species still exists and is puzzling many scientists who have tried to clarify this task. Studies using a portion of both small subunit ribosomal ribonucleic acid (SSU rRNA) and large subunit ribosomal ribonucleic acid (LSU rRNA) genes when integrated with conventional taxonomy were contributed to resolve taxonomical issues in this group. Here we present the first phylogenetic study of Chaetognatha based on a portion of mitochondrial cytochrome oxidase I (COI) gene and compare our results with the earlier morphological and molecular evolutionary hypotheses. This study includes 16 extant species, representing 8 genera and 6 of which are among the 9 extant families. We recommend the following clade structure for the phylum: Aphragmophora comprising Sagittidae with Pterosagittidae and Krohnittidae included in the Sagittidae and Phragmophora comprising Eukrohniidae, Spadellidae, and Heterokrohniidae. Phylogenetic analyses also supported the division of Phragmophora into two monophyletic groups: the Monophragmophora and Biphragmophora. Moreover, Ctenodontina/Flabellodontina and Syngonata/Chorismogonata suborders were not validated. Precise phylogenetic investigations using various molecular markers and specimens from diverse regions are definitely needed to provide an exact evolutionary concept on this phylum.

New host records and descriptions of five new species of Myrsidea Waterston, 1915 (Phthiraptera: Menoponidae) from passerine birds (Aves: Passeriformes)

Zootaxa ◽  
2011 ◽  
Vol 3097 (1) ◽  
pp. 1 ◽  
Author(s):  
MICHEL P. VALIM ◽  
ROGER D. PRICE ◽  
KEVIN P. JOHNSON
Keyword(s):  
New Species ◽  
Cytochrome Oxidase ◽  
Cytochrome Oxidase I ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Passerine Birds ◽  
New Host ◽  
Mitochondrial Cytochrome Oxidase ◽  
New Host Records

Three species of previously described Myrsidea from the birds Lochmias nematura obscurata Cabanis, Automolus ochrolaemus (Tschudi, 1844) (both Furnariidae) and Pachyramphus cinnamomeus Lawrence, 1861 (Cotingidae) are redescribed, including new host and geographical records. Five new species of Myrsidea from the Neotropics are described and illustrated. These species and their type hosts are: M. waterstoni n. sp. from Anabacerthia variegaticeps (Sclater), M. meyi n. sp. from Syndactyla subalaris (Sclater) (Furnariidae), M. dalgleishi n. sp. from Glyphorynchus spirurus (Vieillot) (Dendrocolaptidae), M. cicchinoi n. sp. from Rhynchocyclus olivaceus (Temminck) (Tyrannidae), and M. castroae n. sp. from Atlapetes albinucha gutturalis (Lafresnaye) (Emberizidae). Sequences of a portion of the mitochondrial cytochrome oxidase I (COI) gene for four of these new species were highly divergent from those of other species of Myrsidea.

scholarly journals Molecular identification of two gobi fishes of Bangladesh using cytochrome oxidase subunit I (CoI) gene sequences

2017 ◽  
Vol 44 (2) ◽  
pp. 175-184
Author(s):  
Mehnus Tabassum ◽  
Hawa Jahan ◽  
Gulshan Ara Latifa
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Coi Gene ◽  
Cytochrome Oxidase Subunit ◽  
Molecular Systematic ◽  
Cytochrome Oxidase Subunit I ◽  
Multiple Sequence ◽  
Oxidase Subunit

DNA barcoding has been proposed as a means of quick species identification using a short standardized segment of DNA. Two species (Eleotris fusca and Glossogobius giuris) from the family Gobiidae and Eleotridae were selected for DNA barcoding using samples collected from different regions of Bangladesh. Cytochrome Oxidase Subunit I (COI) gene was sequenced from two different gobi fishes and compared with two previously published similar sequences from the genera Eleotris and Glossogobius. Multiple sequence alignment and the molecular systematic study were performed. The DNA barcode technique identified the two species. The study provides a good example of how DNA barcoding can build upon its primary mission of species identification and use available data to integrate genetic variation investigated at the local scale into a global framework.Bangladesh J. Zool. 44(2): 175-184, 2016

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.

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