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.

scholarly journals The efficiency of universal mitochondrial DNA barcodes for species discrimination of Pomacea canaliculata and Pomacea maculata

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8755
Author(s):  
Adrian Kannan ◽  
Suganiya Rama Rao ◽  
Shyamala Ratnayeke ◽  
Yoon-Yen Yow
Keyword(s):  
16S Rdna ◽  
Dna Barcoding ◽  
Peninsular Malaysia ◽  
Coi Gene ◽  
Diagnostic Tools ◽  
Species Discrimination ◽  
Pomacea Canaliculata ◽  
Agricultural Wetlands ◽  
Barcoding Gap ◽  
Species Specific

Invasive apple snails, Pomacea canaliculata and P. maculata, have a widespread distribution globally and are regarded as devastating pests of agricultural wetlands. The two species are morphologically similar, which hinders species identification via morphological approaches and species-specific management efforts. Advances in molecular genetics may contribute effective diagnostic tools to potentially resolve morphological ambiguity. DNA barcoding has revolutionized the field of taxonomy by providing an alternative, simple approach for species discrimination, where short sections of DNA, the cytochrome c oxidase subunit I (COI) gene in particular, are used as ‘barcodes’ to delineate species boundaries. In our study, we aimed to assess the effectiveness of two mitochondrial markers, the COI and 16S ribosomal deoxyribonucleic acid (16S rDNA) markers for DNA barcoding of P. canaliculata and P. maculata. The COI and 16S rDNA sequences of 40 Pomacea specimens collected from six localities in Peninsular Malaysia were analyzed to assess their barcoding performance using phylogenetic methods and distance-based assessments. The results confirmed both markers were suitable for barcoding P. canaliculata and P. maculata. The phylogenies of the COI and 16S rDNA markers demonstrated species-specific monophyly and were largely congruent with the exception of one individual. The COI marker exhibited a larger barcoding gap (6.06–6.58%) than the 16S rDNA marker (1.54%); however, the magnitude of barcoding gap generated within the barcoding region of the 16S rDNA marker (12-fold) was bigger than the COI counterpart (approximately 9-fold). Both markers were generally successful in identifying P. canaliculata and P. maculata in the similarity-based DNA identifications. The COI + 16S rDNA concatenated dataset successfully recovered monophylies of P. canaliculata and P. maculata but concatenation did not improve individual datasets in distance-based analyses. Overall, although both markers were successful for the identification of apple snails, the COI molecular marker is a better barcoding marker and could be utilized in various population genetic studies of P. canaliculata and P. maculata.

scholarly journals First Record of Traumatic Myiasis Obtained From Forest Musk Deer (Moschus Berezovskii) Using DNA Barcoding

2020 ◽  
Author(s):  
Yunyun Gao ◽  
Yajun Fu ◽  
Liping Yan ◽  
Defu Hu ◽  
Benmo Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Animal Husbandry ◽  
First Record ◽  
Coi Gene ◽  
Common Disease ◽  
Human Society ◽  
Musk Deer ◽  
Two Samples ◽  
Nucleotide Divergence ◽  
Coi Sequences

Abstract Background: Myiasis is a common disease occurring in humans and livestock all over the world. It is closely related to human society and of great significance to animal husbandry, forensic science, and medicine. Myiasis is known to occur in wild animals, while no information is reported in forest musk deer. On July 6, 2019, we found severe traumatic myiasis of an injured forest musk deer (Moschus berezovskii) (Flerov, 1929), infected by lots of maggots and clusters of eggs. However, the precise identification of the larvae that we collected was difficult with few specific morphology characteristics.Methods: DNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from one larva and one egg respectively. The cytochrome oxidase I (COI) gene barcoding region was amplified by polymerase chain reaction (PCR) and bidirectionally sequenced by Sanger sequencing. The sequences were searched for similarity using BLAST and the best hits were Lucilia. To identify these blowflies accurately, these newly generated sequences were subsequently analyzed with COI sequences of Lucilia and Calliphora downloaded from GenBank, to calculate nucleotide divergence, and to construct a neighbor-joining tree.Results: Our results suggest that nucleotide divergence between the two samples is 0.0033cM, between two samples and Lucilia caesar (Diptera: Calliphoridae) (Linnaeus, 1758) is 0.0016–0.0050cM. Furthermore, the NJ tree construction indicates that the flies collected from the musk deer are Lucilia caesar.Conclusions: Our results indicate that DNA barcoding can successfully identify pathogenic species. As far as the authors know, this is the first time that myiasis is detected in forest musk deer caused by a traumatic infection in China. The affected individual was clinically treated immediately and apparently recovered.

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.

Barcoding deep-water chondrichthyans from mainland Portugal

2015 ◽  
Vol 66 (6) ◽  
pp. 508 ◽  
Author(s):  
T. Moura ◽  
M. C. Silva ◽  
I. Figueiredo
Keyword(s):  
Species Identification ◽  
Deep Water ◽  
Current Knowledge ◽  
Species Discrimination ◽  
Identification Problems ◽  
Closely Related Species ◽  
Mainland Portugal ◽  
Putative Species ◽  
Molecular Databases ◽  
Almost All

Most deep-water chondrichthyans occurring off mainland Portugal are distributed worldwide. There are many closely related species with similar morphology, and the lack of diagnostic characters that unambiguously allow species discrimination has led to extensive identification problems. Here, DNA barcodes were used to evaluate the suitability of cytochrome c oxidase I (COI) to identify deep-water chondrichthyans and to further contribute to the worldwide molecular databases currently in use. The sample was composed of 40 individuals from the families Chimaeridae, Centrophoridae, Somniosidae, Etmopteridae, Oxynotidae, Dalatiidae, Scyliorhinidae, Mitsukurinidae, Chlamydoselachidae and Hexanchidae. COI proved to be adequate for species identification, with almost all putative species recovered as well supported monophyletic clades, with low intraspecific variation. Sequence matches against the BOLD database provided evidence for the existence of identification problems particularly within the genera Hydrolagus, Galeus and Centrophorus. Present results suggest that three different Centrophorus species occur off the Portuguese mainland, C. squamosus, C. granulosus and C. uyato. The sample also included an albino Deania calcea and a C. squamosus specimen without dermal denticles. This study updates the current knowledge on diversity and distribution of deep-water chondrichthyans occurring along the Portuguese coast, and provides an essential tool for species identification and consistency of taxonomic designations worldwide.

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 Mitochondrial DNA analyses reveal widespread tardigrade diversity in Antarctica

2015 ◽  
Vol 29 (6) ◽  
pp. 578 ◽  
Author(s):  
Alejandro Velasco-Castrillón ◽  
Sandra J. McInnes ◽  
Mark B. Schultz ◽  
María Arróniz-Crespo ◽  
Cyrille A. D'Haese ◽  
...  
Keyword(s):  
Geographic Region ◽  
Tierra Del Fuego ◽  
Coi Gene ◽  
Operational Taxonomic Units ◽  
Putative Species ◽  
Extensive Region ◽  
Continental Antarctica ◽  
Terrestrial Habitats ◽  
Coi Sequences ◽  
The Antarctic

Antarctica contains some of the most challenging environmental conditions on the planet due to freezing temperatures, prolonged winters and lack of liquid water. Whereas 99.7% of Antarctica is permanently covered by ice and snow, some coastal areas and mountain ridges have remained ice-free and are able to sustain populations of microinvertebrates. Tardigrades are one of the more dominant groups of microfauna in soil and limno-terrestrial habitats, but little is known of their diversity and distribution across Antarctica. Here, we examine tardigrades sampled from across an extensive region of continental Antarctica, and analyse and compare their partial mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences with those from the Antarctic Peninsula, maritime and sub-Antarctica, Tierra del Fuego and other worldwide locations in order to recognise operational taxonomic units (OTUs). From 439 new tardigrade COI sequences, we identified 98 unique haplotypes (85 from Antarctica) belonging to Acutuncus, Diphascon, Echiniscus, Macrobiotus, Milnesium and unidentified Parachela. Operational taxonomic units were delimited by Poisson tree processes and general mixed Yule coalescent methods, resulting in 58 and 55 putative species, respectively. Most tardigrades appear to be locally endemic (i.e. restricted to a single geographic region), but some (e.g. Acutuncus antarcticus (Richters, 1904)) are widespread across continental Antarctica. Our molecular results reveal: (i) greater diversity than has previously been appreciated with distinct OTUs that potentially represent undescribed species, and (ii) a lack of connectivity between most OTUs from continental Antarctica and those from other Antarctic geographical zones.

scholarly journals Characterization of Some Commercially Important Octopus (Mollusca: Cephalopoda) from Indonesian Waters using Mitochondrial DNA Cytochrome Oxidase Sub-Unit I (Mt-DNA COI)

2021 ◽  
Vol 26 (1) ◽  
pp. 17-26
Author(s):  
Nenik Kholilah ◽  
Norma Afiati ◽  
Subagiyo Subagiyo
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Species Level ◽  
The Other ◽  
Mt Dna ◽  
Commercially Important ◽  
The Difference ◽  
Coi Sequences

As per the FAO data, octopus identification is very limited in the species level at world fishery and also they are cryptic nature. On the other hand, Indonesia is one of the top ten highest octopus exporters. This study therefore aimed to determine the species of octopus based on phylogenetic analysis of mt-DNA COI. Octopuses were collected from nine different locations throughout Indonesia, i.e., Anambas, Bangka-Belitung, Cirebon, Karimunjawa, Tuban, Lombok, Buton, Wakatobi and Jayapura. Samples were mostly in the form of tentacles that were directly collected from fishermen. After being preserved in 96% ethanol, the sample was extracted in 10% chelexÒ, PCR amplification using Folmer’s primer then was further analysed by sequencing in Sanger methods. Of the 24 samples sequenced, the results recognized four species Octopodidae belongs to the three genera, named Amphioctopus aegina, Hapalochlaena fasciata, Octopus laqueus and Octopus cyanea. Mean pair-wise distances of within-species were ranged from 0 to 5.5 % and between-species was ranged from 12.9 to 15.8 %. This study distinctly confirmed the difference between genus Amphioctopus and Hapalochlaena (15.5 %), as also between O. laqueus and O. cyanea (12.9%) which was previously not completely distinguished. Although performing species identification using DNA sequences for shallow-water benthic octopus species is perhaps considered premature, this study indicated the possible application of COI sequences for species identification, thereby providing a preliminary dataset for future DNA barcoding of octopus, in particular for Indonesia waters.

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.

Genetic diversity of marine oligochaetous clitellates in selected areas of the South Atlantic as revealed by DNA barcoding

2018 ◽  
Vol 32 (3) ◽  
pp. 524 ◽  
Author(s):  
Alessandro L. Prantoni ◽  
Ricardo Belmonte-Lopes ◽  
Paulo C. Lana ◽  
Christer Erséus
Keyword(s):  
Genetic Diversity ◽  
Atlantic Ocean ◽  
East Coast ◽  
South Atlantic ◽  
South Atlantic Ocean ◽  
The South ◽  
Closely Related Species ◽  
Putative Species ◽  
Coi Barcoding ◽  
Coi Sequences

Marine oligochaetous clitellates are poorly investigated in the South Atlantic Ocean, especially along the east coast of South America. Closely related species are often difficult to distinguish based on morphology. The lack of specialists and modern identification guides have been pointed out as the main reasons for the scarcity of studies in the South Atlantic Ocean as a whole. To increase the knowledge of this group in the South Atlantic, the genetic diversity of a sample of marine oligochaetous clitellates from Brazil, South Africa and Antarctica was assessed by the Automatic Barcode Gap Discovery (ABGD) and the generalised mixed Yule coalescent (GMYC) approaches. In total, 80 cytochrome c oxidase subunit I (COI) sequences were obtained, each with ~658bp, estimated to represent 32 distinct putative species. ABGD established a barcoding gap between 3% and 14% divergence for uncorrected p-distances and the estimates of GMYC were largely concordant. All the clusters or putative species were genetically associated with previously known species or genera. This study thus confirms the adequacy of the COI barcoding approach combined with a genetic divergence threshold at the order of 10% for marine oligochaetous clitellates.

COI barcoding of Hydroides: a road from impossible to difficult

2012 ◽  
Vol 26 (6) ◽  
pp. 539 ◽  
Author(s):  
Y. Sun ◽  
E. K. Kupriyanova ◽  
J. W. Qiu
Keyword(s):  
Species Identification ◽  
Evolutionary Ecology ◽  
Cytochromec Oxidase ◽  
Coi Gene ◽  
Universal Primers ◽  
Marine Animals ◽  
Modern Species ◽  
Wide Range ◽  
Coi Barcoding ◽  
Coi Sequences

A fragment of the cytochromec oxidase subunitI (COI) gene has been used increasingly for species identification and discovery in eukaryotes. However, amplifying COI has proven difficult, or even impossible, in some taxa due to non-homology between the universal primers and the target DNA region. Among the most problematic animal groups is Serpulidae (Annelida). These sedentary marine animals live in self-secreted calcareous tubes and many of them, especially of the genus Hydroides, are economically important reef-builders, foulers, and biological invaders. We developed novel taxon-specific primers for amplifying COI from Hydroides, and for the first time generated 460-bp COI sequences from 11 of 14 species attempted. Average Kimura-2-parameter interspecific sequence distance (26.2%) was >60 times greater than the average intraspecific distance (0.43%), indicating that the COI gene is effective for species delimitation in Hydroides. Although applicability of the new primers for a wide range of serpulids needs to be tested, barcoding of Hydroides is now on its way from impossible to difficult. We anticipate that COI barcoding will provide a modern species identification tool and, combined with other molecular markers, yield important insights in phylogeny and evolutionary ecology of this large and important genus.

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