scholarly journals Molecular Species Identification of Six Forensically Important Iranian Flesh Flies (Diptera)

2021 ◽  
Author(s):  
Fahimeh Talebzadeh ◽  
Mohammad Ali Oshaghi ◽  
Kamran Akbarzadeh ◽  
Somayeh PanahiMoghadam
Keyword(s):  
Species Identification ◽  
Restriction Enzymes ◽  
Coi Gene ◽  
Rflp Markers ◽  
Sarcophaga Crassipalpis ◽  
Larval Stages ◽  
Pcr Products ◽  
Coi Sequences ◽  
Species Specific ◽  
Flesh Flies

Background: Flesh flies (Diptera: Sarcophagidae) are considered as myiasis agents and important evidences in forensic investigations. However, their use has been restricted because, at all larval stages and female adults, morphological species identification is difficult or very challenging. This study investigated to test utility of mitochondrial cytochrome oxidase subunit I (mt-COI) sequences for differentiation of six forensically important Iranian flesh flies namely, Sarcophaga crassipalpis, S. flagellifera, S. hirtipes, S. aegyptica, S. africa and S. argyrostoma. Methods: Male specimens were morphologically identified to species level and then the genomic DNA of the flies were extracted and subjected to polymerase chain reaction (PCR) against mt-COI gene. The PCR products were sequenced and the obtained sequences were analyzed for the species specific restriction fragment length polymorphisms (RFLPs). Results: Rate of genetic variation between species was 6–10% which was enough to find restriction enzymes (RE) that were able to produce species-specific RFLP profiles. Combinations of three REs: BsrFI, RsaI and HinfI, provided diagnostic bands for identification of the six Sarcophaga species. Conclusions: The results of this study showed that molecular markers such as RFLPs enhancing the use of evidence from flesh flies in forensic investigation. However, lack proper restriction sites in the COI region inhibited introduction of a single restriction enzyme for easy species identification. It is recommended to apply larger part of DNA such as combination of COI and COII genes to provide better RFLP markers for species identification of flesh flies.

scholarly journals Genetic Homogenity of Commerson’s Anchovy (Stolephorus commersonnii) in Segara Anakan Cilacap Central Java Inferred from PCR-RFLP Markers

2019 ◽  
Vol 7 (1) ◽  
pp. 14
Author(s):  
Agus Nuryanto ◽  
Rani Eva Dewi ◽  
Hendro Pramono
Keyword(s):  
Genetic Diversity ◽  
Restriction Enzymes ◽  
Coi Gene ◽  
Survey Method ◽  
Rflp Markers ◽  
Small Pelagic Fish ◽  
Central Java ◽  
Low Genetic Diversity ◽  
Pcr Rflp ◽  
Pcr Products

Commerson’s anchovy (Stolephorus commersonnii) is a small pelagic fish that live in a group and its existence is very abundant in Segara Anakan Cilacap. This anchovy is widely consumed by communities live around Segara Anakan. This leads to a high exploitation rate. Exploited populations generally have low genetic diversity. This study aims to evaluate genetic diversity of commerson’s anchovy population in Segara Anakan Cilacap inferred from PCR-RFLP of the cytochrome c oxidase 1 (CO1) gene. This study was conducted from January to April 2018 and used survey method by applying random sampling. As many as 30 samples of anchovy were taken. Genomic mtDNA was isolated using modified Chelex method. Partial sequences of the COI gene were amplified using a pair forward commercially available primer. The lengths of 650 base pair of the PCR products were digested with four restriction enzymes. The HindIII enzyme produces PCR-RFLP fragment with the size of 416 bp and 234 bp lengths, VspI produces 435 bp and 214 bp, CO1-TaqI produces 556 bp and 94 bp and RsaI produces 319 bp, 183 bp, and 148 bp fragments, respectively. The PCR-RFLP fragments were obtained from all samples but they produced uniform band pattern for all 30 anchovy individuals. These results indicated that the anchovy population in Segara Anakan Cilacap has monomorphic allele for all PCR-RFLP markers. Hence, it can be concluded that genetic homogenity was observed on anchovy population in Segara Anakan Cilacap as inferred from PCR-RFLP COI gene.

Simultaneous detection ofAureliaandChrysaorascyphozoan jellyfish on a DNA microarray

2009 ◽  
Vol 90 (6) ◽  
pp. 1111-1117 ◽  
Author(s):  
Jang-Seu Ki ◽  
Dae-Sik Hwang ◽  
Jae-Seong Lee
Keyword(s):  
Dna Microarray ◽  
Simultaneous Detection ◽  
Dna Chip ◽  
Coi Gene ◽  
Low Density ◽  
Sequence Comparisons ◽  
Mitochondrial Coi ◽  
Pcr Products ◽  
Jellyfish Species ◽  
Species Specific

To demonstrate the effectiveness of microarrays for the detection of jellyfish, we developed a low density DNA chip based on the mitochondrial COI gene sequences of scyphozoans (jellyfish). We designed species-specific oligonucleotide probes by sequence comparisons between scyphozoans and other cnidarians such as hydrozoans and anthozoans. Each amine-labelled capture probe was arrayed onto a silylated slide. PCR products of the COI gene were hybridized to the DNA microarray that contained COI consensus sequences. We tested the ability of the DNA chip to discriminate between species from the generaAureliaandChrysaorabased on samples of both species from the polyp and ephyra stages. The array produced unique hybridization patterns for each of the two tested jellyfish species. Furthermore, we were able to simultaneously detect individual jellyfish species from mixtures of these two different species in the laboratory and from environmental samples. These results show that the low density DNA chip that we designed can be used as a technical platform for parallel molecular detection of various jellyfish species.

scholarly journals Cytochrome Oxidase I (COI) Divergence Assessment of Family Nemipteridae from Malaysian Waters

2019 ◽  
Vol 1 (1) ◽  
pp. 41-48
Author(s):  
Liew You En ◽  
Salwani Abdullah ◽  
Tan Min Pau ◽  
Mazlan Abd Ghaffar ◽  
Alias Man ◽  
...  
Keyword(s):  
Species Identification ◽  
East Coast ◽  
Peninsular Malaysia ◽  
Coi Gene ◽  
Species Discrimination ◽  
Trawl Survey ◽  
Putative Species ◽  
Commercially Important ◽  
Nucleotide Divergence ◽  
Coi Sequences

DNA Barcoding, primarily focusing on cytochrome c oxidase subunit I (COI) gene has been appraised as an effective tool for species identification. Nonetheless, species identification based on molecular approach is essential for discrimination of look-alike species. In this study, we focused on the marine fishes Family Nemipteridae, one of the commercially important group distributed within the surrounding seas of Malaysia. Some of the samples were collected during the National Demersal Trawl Survey in the Exclusive Economic Zone of East Coast Peninsular Malaysia by the Department of Fishery Malaysia. A 652bp region of COI was sequenced for 74 individuals from nine putative species. Additional 34 COI sequences from GenBank were also included in this study making the total number of samples analysed to 108 individuals. The average Kimura 2-parameter (K2P) nucleotide divergence was 0.34% among individuals within species and 6.97% within genera. All putative species formed monophyletic clades in both Neighbour-joining (NJ) and Maximum-likelihood (ML) trees. However, there was a potential misidentification in specimen identified as Nemipterus tambuloides, as the specimen did not group with their own taxa. It was genetically grouped in Nemipterus thosaporni clade. This study supports the effectiveness of COI gene in species discrimination of Family Nemipteridae.

Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)

Zootaxa ◽  
2007 ◽  
Vol 1522 (1) ◽  
pp. 1-68 ◽  
Author(s):  
THOMAS KNEBELSBERGER ◽  
MICHAEL A. MILLER
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Coi Gene ◽  
Parthenogenetic Species ◽  
Mediterranean Countries ◽  
Coi Sequences

Until recently the subaptera-group of Phyllodromica contained only one species. The revision of the subaptera-group  herein consists of the two newly described bisexual species, P. iberica and P. quadracantha, endemic to the Iberian Peninsula and a parthenogenetic species, P. subaptera (Rambur, 1838), which is widely distributed over most of the Mediterranean countries and islands. Within P. iberica three conspecific morphotypes are distinguished. The morphological characteristics of the subaptera-group are described. The species and their distributions are described and depicted. A key for the morphological determination of P. quadracantha and the morphotypes of P. iberica is given. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene are included in the species descriptions. The sequence data are suitable for species identification (DNA barcodes). A cladistic analysis of the morphological data and a phylogenetic analysis of the DNA sequences were performed to infer the phylogenetic relationships between the species of the subaptera-group.

scholarly journals Phylogeography of cliff racer (Platyceps rhodorachis Jan, 1865) from Punjab, Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
S. Malik ◽  
A. Javid ◽  
Hamidullah ◽  
M. A. Iqbal ◽  
A. Hussain ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Species Identification ◽  
Dna Sequences ◽  
Large Scale ◽  
Coi Gene ◽  
Gene Sequences ◽  
Field Surveys ◽  
Coi Sequences

Abstract The present study reports the existence of cliff racer, Platyceps rhodorachis from the plains of Punjab, Pakistan. A total of 10 specimens were captured during the field surveys from June to September, 2018 from different sites of Punjab. Platyceps rhodorachis was identify on the basis of morphology and confirmed through COI gene sequences. The obtained DNA sequences have shown reliable and exact species identification. Newly produced DNA sequences of Platyceps rhodorachis were submitted to GenBank and accession numbers were obtained (MK936174.1, MK941839.1 and MT790210.1). N-J tree based on COI sequences of Platyceps rhodorachis clearly separated as out-group with other members of family Colubridae based on p-distance. The intra-specific genetic variation ranges from 12% to 18%. The DNA sequences of Platyceps rhodorachis kashmirensis, Platyceps rhodorachis ladacensis, Platyceps ventromaculatus, Platyceps ventromaculatus bengalensis and Platyceps ventromaculatus indusai are not available at NCBI to validate their taxonomic positions. In our recommendations, a large scale molecular based identification of Pakistan’s herpetofauna is required to report more new or subspecies from country.

scholarly journals Molecular Detection of Chevon and Mutton Adulteration by Species-specific PCR Assay Targeting Mitochondrial COI Gene

2017 ◽  
Vol 5 (2) ◽  
pp. 99
Author(s):  
Lan-ping Wang ◽  
Rong-qing Geng
Keyword(s):  
Meat Product ◽  
Meat Products ◽  
Coi Gene ◽  
Processed Meat ◽  
Mitochondrial Coi ◽  
Specific Pcr ◽  
Mitochondrial Coi Gene ◽  
Pcr Products ◽  
Specific Pcr Assay ◽  
Species Specific

A highly species-specific polymerase chain reaction (PCR) was developed for authentic identification of raw and processed meat products of chevon and mutton. To achieve this, four species-specific primers for mitochondrial cytochrome oxidase I (COI) gene were selected from previous reports. The assay generated PCR products of 157, 157, 268, 251, and 177 bp for chevon, mutton, pork, chicken and duck, respectively. The sensitivity for the detection of adulteration was established to be 0.1% (w/w), while the DNA limit for detection was as low as 0.001 ng. The adulteration was found in all meat product types including raw frozen meat, cold cuts, ground meats and cooked foods. These findings showed that species-specific PCR are potentially reliable method in detection of meat products of chevon and mutton authentication.

scholarly journals Development of species-specific marker and molecular diversity of Conogethes punctiferalis and Conogethes sahyadriensis (Lepidoptera: Crambidae)

2021 ◽  
Vol 42 (2) ◽  
pp. 271-279
Author(s):  
V. Kammar ◽  
◽  
D. Sagar ◽  
R.K. Chandel ◽  
P.R. Shashank ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Fragment Size ◽  
Bioinformatic Analysis ◽  
Coi Gene ◽  
Specific Marker ◽  
Mitochondrial Cytochrome ◽  
Coi Sequences ◽  
Species Specific ◽  
Mitochondrial Cytochrome Oxidase

Aim: The aim of this study was to develop species specific marker for quick identification of two Conogethes species and to study their molecular diversity. Methodology: Species-specific markers were developed using mitochondrial cytochrome oxidase 1 (COI) partial gene sequences of Conogethes punctiferalis and C. sahyadriensis and they were validated. Phylogenetic tree was constructed using MEGA X program, tree robustness was evaluated by bootstrapping with 1000 replicates with all sequences of C. punctiferalis and C. sahyadriensis. Results: Bioinformatic analysis of C. punctiferalis and C. sahyadriensis COI sequences revealed that they have sufficient genetic variability to develop species specific marker. The COI based species-specific markers amplified an expected fragment size of 333 bp for C. punctiferalis and 522 bp for C. sahyadriensis, which clearly differentiate these two species. Interpretation: The species specific marker developed in this study will be useful in quick identification of C. punctiferalis and C. sahyadriensis. The use of COI gene as a marker can provide a better estimate of genetic diversity, as it is maternally inherited and can be helpful to understand evolutionary processes. Key words: Conogethes punctiferalis, C. sahyadriensis, MtCOI, Molecular diversity, Species-specific marker

scholarly journals Identification and differentiation among chicken’s, duck’s, quail’s, rabbit’s and turkey's meat using PCR-RFLP technique

2015 ◽  
Vol 31 (1) ◽  
pp. 101-108 ◽  
Author(s):  
S.M. Abdel-Rahman ◽  
A.M. Elmaghraby ◽  
A.S. Haggag
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome B ◽  
Fragment Length ◽  
Restriction Analysis ◽  
Restriction Enzymes ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Species Specific ◽  
Rflp Assay

PCR-RFLP technique was developed for identification and differentiation among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat. DNA from small amount of muscles (0.05 g) was extracted and a region of mitochondrial DNA (cytochrome-b gene) in chicken, duck, quail, rabbit and turkey was amplified by PCR. Fragment length of the PCR product was 371 bp in chicken, 374 bp in duck and rabbit and 377 bp in both quail and turkey. Six nucleotides different makes it difficult to differentiate among these five species-specific meat. For differentiation, three different restriction enzymes (DdeI, MspI and TaqI) were used to digest the PCR products. Restriction analysis showed difference among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat. Where, DdeI yielded two fragments (291 and 83 bp) only in rabbit?s meat. MspI yielded three fragments (221, 85 and 65 bp) in chicken?s meat and two fragments (290 and 87 bp) in both quail?s and turkey's meat. TaqI yielded three fragments (146, 134 and 94 bp) in duck?s meat and two fragments (226 and 151 bp) in quail?s meat. The use of Cytb- PCR-RFLP assay allowed a direct and fast authentication and differentiation among chicken?s, duck?s, quail?s, rabbit?s and turkey's meat.

scholarly journals Initiating DNA barcoding of Eastern Mediterranean deep-sea biota

2018 ◽  
Author(s):  
GUY PAZ ◽  
YANA YUDKOVSKY ◽  
LEE SHAISH ◽  
NIR STERN ◽  
HADAS LUBINEVSKI ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Deep Sea ◽  
Eastern Mediterranean ◽  
Abundant Species ◽  
Coi Gene ◽  
Pcr Products ◽  
The Common ◽  
Coi Sequences ◽  
First Time ◽  
Deep Sea Fauna

Preliminary results of DNA barcoding survey of deep-sea mega-faunal biota are presented, collected by trawl and gillnet off the Israeli coast (SE Mediterranean, depths 700 to 1500 meters) during 2012-2013. 846 organisms were identified to 37 species, mainly fish and decapod crustaceans. The most abundant species were the blackmouth catshark Galeus melastomus, the cosmopolitan decapod Polycheles typhlops and the bivalve Abra longicallus. Two species were sampled for the first time from the southern Levant- the long armed chiroteuthid squid Chiroteuthis veranyi and the common mora, Mora moro. Four of the 18 fish species and two of the 10 crustacean species were abundant, representing 78% and 61%, respectively, of the organisms collected. Most other species are represented by fewer than 10 individuals. PCR products for the cytochrome c oxidase sub unit I (COI) gene for the 37 species were successfully sequenced. The identified and vouchered individuals are stored at the Steinhardt Museum of Natural History (Tel Aviv University, Israel) and their COI sequences were uploaded into the BoLD universal data center as part of the national marine barcoding project. The COI sequences of Acanthephyra eximia, Gryphus vitreus, Galeodea echinophora, Mesothuria intestinalis and Astropecten irregularis, constitute first records of these species in BoLD. When compared to the COI sequences in BoLD, the present results reveal some inconsistency in species identification, an outcome that should be taken into consideration primarily once the taxonomical verifications of collected taxa are elusive. This study is the first step in DNA barcoding of the Levant’s little-known benthic deep-sea fauna.

A molecular framework for the identification of planthopper vectors (Hemiptera: Delphacidae) of central Argentina

2015 ◽  
Vol 105 (6) ◽  
pp. 754-762
Author(s):  
E.B. Argüello Caro ◽  
A.D. Dumón ◽  
M.F Mattio ◽  
V. Alemandri ◽  
G. Truol
Keyword(s):  
Species Identification ◽  
Regional Scale ◽  
Dna Barcode ◽  
Restriction Enzymes ◽  
Common Species ◽  
Molecular Techniques ◽  
Coi Gene ◽  
Morphological Identification ◽  
Accurate Identification ◽  
Central Argentina

AbstractPlanthoppers are important worldwide crop pests as well as vectors of numerous diseases. Different species transmit Mal de Río Cuarto virus, which causes the most economically important corn disease in central Argentina. Epidemiological studies rely on the accurate identification of the species present in the field. Presently, morphological identification of planthoppers requires taxonomic expertise and there are no taxonomic keys for females and nymphs. Nevertheless, no molecular protocols are available for accurate species identification of most frequent delphacid species from central Argentina. In this context, the aim of this study was to evaluate the utility of the cytochrome oxidase I gene (COI) as a DNA barcode and its digestion with restriction enzymes (Restriction Fragment Length Polymorphism, RFLP) for the identification of the most common species of planthoppers in central Argentina. We amplified and sequenced a 843 bp fragment of the COI gene of taxonomically identified specimens and evaluated its use as a DNA barcode. Restriction enzymes were also selected for digesting the COI fragment via RFLP. The high interspecific variability (20.79%; ± 2.32%) and low intraspecific divergence (0.12%; ± 0.17%) observed in the studied species, demonstrate the effectiveness of the COI gene for species identification of major vector delphacids affecting corn crops in Argentina. Moreover, the digestion of this COI gene fragment with Bfa I and Apo I enzymes allows a fast and cost-effective species identification method when numerous specimens need to be processed. Both molecular techniques developed here, allow the accurate identification of planthopper species at regional scale. These new tools would assist traditional identification of these insects, especially for aiding non-experts in morphological taxonomy.

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