scholarly journals AN INTEGRATIVE TAXONOMY OF MOLECULAR AND TRADITIONAL APPROACHES FOR IDENTIFICATION OF A STORAGE MITE, ALEUROGLYPHUS OVATUS (ACARI: ASTIGMATA: ACARIDAE) IN MALAYSIA

2016 ◽  
Vol 6 (2) ◽  
pp. 882-889
Author(s):  
Ernieenor Faraliana Che Lah
Keyword(s):  
Molecular Identification ◽  
Dna Sequences ◽  
Correct Diagnosis ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
Its2 Region ◽  
Morphological Identification ◽  
Taxonomic Identification ◽  
Internal Transcribed Spacer Region ◽  
Accurate Identification

A reliable and rapid taxonomic identification of a mite is the basis for a correct diagnosis of important mite associated allergies as they produce species-specific allergens. A double approach (molecular and morphological) to the taxonomic identification of Aleuroglyphus ovatus was presented. Molecular identification was performed with amplification of the internal transcribed spacer region (ITS2), whilst morphological characters were examined under light microscope. The BLAST results obtained from molecular analysis of A. ovatus was shown to be in concordance with the morphological identification with 97% genetic similarity. Thus, the molecular identification based on the ITS2 region can be applied as a reliable and efficient tool for species identification of Aleuroglyphus and probably any other astigmatid mites. Our findings suggest the need for a broad taxonomic sampling especially from closely related species for an accurate identification of local mites using both DNA sequences and morphology.

scholarly journals Short Communication: Species confirmation of juvenile cloudy grouper, Epinephelus erythrurus (Valenciennes, 1828), based on a morphologic analysis and partial CO1 gene sequencing

2019 ◽  
Vol 20 (3) ◽  
pp. 914-921
Author(s):  
YANTI ARIYANTI ◽  
ACHMAD FARAJALLAH
Keyword(s):  
Dna Sequences ◽  
Molecular Genetic ◽  
Gene Sequencing ◽  
Morphological Characters ◽  
Morphological Description ◽  
Morphological Identification ◽  
Genetic Technique ◽  
Morphologic Analysis ◽  
Identification Techniques ◽  
Molecular Genetic Technique

Abstract. Ariyanti Y, Farajallah A. 2019. Species confirmation of juvenile cloudy grouper, Epinephelus erythrurus (Valenciennes, 1828), based on a morphologic analysis and partial CO1 gene sequencing. Biodiversitas 20: 914-921. The genus Epinephelus is the most species among the genera within the subfamily Epinephelinae. Species identification techniques for groupers, especially in the Epinephelus, are commonly based on color patterns and a suite of morphological characters, including body shape and the size and number of fins, scales and gill rakers. In some species, juveniles are morphologically distinct from adults of the same species, making morphological identification highly problematic. This present work will provide some morphological description or variations of juveniles that have been identified as Epinephelus erythrurus based on CO1 sequences. Further, the present study demonstrates that a molecular genetic technique, based on partial sequencing of the mitochondrial CO1 gene, may be used for the rapid species confirmation of every developmental stage and phase of an organism (juvenile E. erythrurus). Two DNA sequences of E. erythrurus from the Pangandaran District (7o43’8.31”S 108o30’11.59”E) have been submitted to GenBank under accession numbers KP998441 and KP998442.

scholarly journals Genetic Diversity and Molecular Characterization of Mosquitoes (Diptera: Culicidae) In North-Central Nigeria Using Ribosomal DNA ITS2 and Mitochondrial 16S-DNA Sequences

2020 ◽  
Vol 44 (2) ◽  
pp. 78-91
Author(s):  
Oluyinka A. Iyiola
Keyword(s):  
16S Rdna ◽  
Dna Sequences ◽  
Mosquito Species ◽  
Evolutionary Relationship ◽  
Malaria Vector Control ◽  
Phylogenetic Study ◽  
Its2 Region ◽  
Morphological Identification ◽  
North Central ◽  
Mitochondrial 16S Rdna

Mosquitoes are vectors of various life-threatening diseases like malaria, yellow fever, dengue fever etc. Their close proximity to human habitations allows ease for disease transmission. They have been identified by key morphological tools like their wings, legs, bristles etc. but closely related species are difficult to identify based on morphology. Molecular tools have, therefore, been employed to help with the more accurate identification. This study was aimed at identifying and characterizing different mosquito species in five different states in North-Central Nigeria using internal transcribed spacer 2 (ITS2) and mitochondrial 16S rDNA regions. Mosquito larvae were collected from stagnant water in breeding places at each collection site in North-central Nigeria. Morphological identification was carried out using standard keys. DNA extraction was performed using EZNA extraction kit. PCR amplification of ribosomal ITS2 and mitochondrial 16S-rDNA gene regions were carried out. The PCR amplicons were sequenced using primers initially used for the PCR. Sequence data were aligned in MEGA 6.0 using ClustalW multiple alignment feature and then compared with GenBank databases for similarity.  Phylogenetic analysis of DNA sequences from the ITS2 region was able to distinguish two mosquito subfamilies; Anophelinae and Culicinae as well as differentiate between and amongst Culex and Aedes species. However, it was unable to effectively distinguish between the two different species of Anopheles sequenced. Mitochondrial 16S rRNA marker was also able to distinguish the two mosquito subfamilies. It efficiently identified and differentiated Culex, Aedes and Anopheles mosquito species sequenced in this study. This study concludes that heterogeneity among Nigerian populations of Anopheles mosquitoes of may likely impact malaria vector control programs. We recommend the combination of nuclear and mitochondrial markers for effective and reliable phylogenetic study and determination of evolutionary relationship among mosquito species.

Another plea for ‘best practice’ in molecular approaches to trematode systematics: Diplostomum sp. clade Q identified as Diplostomum baeri Dubois, 1937 in Europe

Parasitology ◽  
2022 ◽  
pp. 1-16
Author(s):  
Anna Faltýnková ◽  
Olena Kudlai ◽  
Camila Pantoja ◽  
Galina Yakovleva ◽  
Daria Lebedeva
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Best Practice ◽  
Sequence Data ◽  
Integrative Taxonomy ◽  
Systematic Parasitology ◽  
Intermediate Hosts ◽  
Accurate Identification ◽  
Molecular Approaches ◽  
Radix Auricularia

Abstract DNA sequence data became an integral part of species characterization and identification. Still, specimens associated with a particular DNA sequence must be identified by the use of traditional morphology-based analysis and correct linking of sequence and identification must be ensured. Only a small part of DNA sequences of the genus Diplostomum (Diplostomidae) is based on adult isolates which are essential for accurate identification. In this study, we provide species identification with an aid of morphological and molecular (cox1, ITS-5.8S-ITS2 and 28S) characterization of adults of Diplostomum baeri Dubois, 1937 from naturally infected Larus canus Linnaeus in Karelia, Russia. Furthermore, we reveal that the DNA sequences of our isolates of D. baeri are identical with those of the lineage Diplostomum sp. clade Q , while other sequences labelled as the ‘D. baeri’ complex do not represent lineages of D. baeri. Our new material of cercariae from Radix balthica (Linnaeus) in Ireland is also linked to Diplostomum sp. clade Q. We reveal that D. baeri is widely distributed in Europe; as first intermediate hosts lymnaeid snails (Radix auricularia (Linnaeus), R. balthica) are used; metacercariae occur in eye lens of cyprinid fishes. In light of the convoluted taxonomy of D. baeri and other Diplostomum spp., we extend the recommendations of Blasco-Costa et al. (2016, Systematic Parasitology 93, 295–306) for the ‘best practice’ in molecular approaches to trematode systematics. The current study is another step in elucidating the species spectrum of Diplostomum based on integrative taxonomy with well-described morphology of adults linked to sequences.

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.

scholarly journals Mycosphaerella musicola Identified as the Only Pathogen of the Sigatoka Disease Complex Present in Minas Gerais State, Brazil

Plant Disease ◽  
2013 ◽  
Vol 97 (12) ◽  
pp. 1537-1543 ◽  
Author(s):  
Lahyre Izaete S. Gomes ◽  
Greg W. Douhan ◽  
Líllian B. J. Bibiano ◽  
Luiz A. Maffia ◽  
Eduardo S. G. Mizubuti
Keyword(s):  
Dna Sequences ◽  
Leaf Tissue ◽  
Morphological Characters ◽  
Minas Gerais ◽  
Control Measures ◽  
Leaf Spot Disease ◽  
Black Sigatoka ◽  
Internal Transcribed Spacer Region ◽  
Minas Gerais State ◽  
Mycosphaerella Musicola

A thorough assessment of the distribution of Mycosphaerella spp. associated with banana in Minas Gerais State, Brazil, was conducted after Mycosphaerella fijiensis was first reported to occur in this region in 2005. From 2009 to 2011, 80 fields located in 20 municipalities including the same fields where the disease was first reported were sampled. A total of 800 samples of leaf tissue with symptoms similar to those of yellow or black Sigatoka diseases were examined, and 239 isolates were obtained. The identification of the fungi was based on morphological characters combined with DNA sequences obtained after amplification with species-specific primers and phylogeny inferred from the internal transcribed spacer region of Mycosphaerella strains from banana. All 239 isolates were identified as Mycosphaerella musicola. The absence of M. fijiensis in the samples may have been due to misidentification of M. fijiensis or the displacement of M. fijiensis by M. musicola. It is now apparent that yellow Sigatoka caused by M. musicola is the prevailing leaf spot disease of bananas in Minas Gerais State and that regulatory/legislative control measures need to be revised based on our findings.

scholarly journals Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas

2019 ◽  
Vol 20 (10) ◽  
Author(s):  
ANNA ROOSIANA DEVI ◽  
Ari Susilowati ◽  
RATNA SETYANINGSIH
Keyword(s):  
Molecular Identification ◽  
Dna Sequences ◽  
Pathogenic Bacteria ◽  
Morphological Characters ◽  
Foodborne Disease ◽  
16S Rrna Sequence ◽  
Blood Clam ◽  
Agar Media ◽  
Anadara Granosa ◽  
Vibrio Spp

Abstract. Devi AR, Susilowati A, Setyaningsih R. 2019. Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas. Biodiversitas 20: 2890-2896. Seafood is very popular among Indonesian people, especially in coastal areas. In Bantul Yogyakarta, blood clams have become one of tourist's favorite, either cooked or raw. Blood clams are filter feeders that cause the clams to be vulnerable to contamination of pathogenic bacteria that can cause foodborne disease, including Escherichia, Pseudomonas, and Vibrio. The 10-20% cases of foodborne disease transmitted through seafood caused by Vibrio spp. Three species of Vibrio can cause foodborne disease in humans, i.e., V. cholerae, V. parahaemolyticus, and V. vulnificus. The purpose of this study was to determine the character of Vibrio using morphological and molecular identification and pathogenicity on blood clam (Anadara granosa). Blood clams samples were collected from Depok, Goa Cemara, and Kwaru beaches in Bantul, Yogyakarta, Indonesia. Isolation of Vibrio spp. from blood clams was done using selective differential Thiosulfate Citrate bile salts sucrose (TCBS) culture medium. The morphological characters of the isolate colonies were determined based on the color, shape, texture, and size of the colony. Hemolysis test was also performed to evaluate the pathogenicity by using blood agar media. Molecular identification of Vibrio species was made using 16S rRNA sequence. Phylogenetic analysis was performed using Neighbor-Joining method in Mega X software. Samples for the analysis came from DNA sequences of this study and those from the GenBank database. Of the total 15 isolates obtained, four isolates showed positive β-hemolysis, namely, isolate P2S2 -1bH, P3S1-1aH, P2S1-1aK and P2S2-1aK, and one isolate had positive α-hemolysis (P3S2-1aK). Seven species of Vibrio were identified as V. algynolyticus, V. parahaemolyticus, V. diabolicus, V neocaledonicus, V. azureus, V. natrigens, and V. cholerae.

scholarly journals Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

ZooKeys ◽  
2018 ◽  
Vol 763 ◽  
pp. 1-111 ◽  
Author(s):  
Tricia C. Goulding ◽  
Munawar Khalil ◽  
Shau Hwai Tan ◽  
Benoît Dayrat
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Comparative Anatomy ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
The Philippines ◽  
Coral Triangle ◽  
Yellow Orange

A new genus of onchidiid slugs,WallaconchisGoulding & Dayrat,gen. n., is described, including ten species. Five species were previously described but known only from the type material:Wallaconchisater(Lesson, 1830),W.graniferum(Semper, 1880),W.nangkauriense(Plate, 1893),W.buetschlii(Stantschinsky, 1907), andW.gracile(Stantschinsky, 1907), all of which were originally classified inOnchidiumBuchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new:WallaconchisachleitneriGoulding,sp. n.,W.comendadoriGoulding & Dayrat,sp. n.,W.melanesiensisGoulding & Dayrat,sp. n.,W.sinanuiGoulding & Dayrat,sp. n., andW.uncinusGoulding & Dayrat,sp. n.Nine of the tenWallaconchisspecies are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia).Wallaconchisis distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify allWallaconchisspecies. The copulatory organs ofWallaconchisspecies are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed,nomina dubiaare discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

Identification of Neoceratitis asiatica (Becker) (Diptera: Tephritidae) based on morphological characteristics and DNA barcode

Zootaxa ◽  
2017 ◽  
Vol 4363 (4) ◽  
pp. 553
Author(s):  
SHAOKUN GUO ◽  
JIA HE ◽  
ZIHUA ZHAO ◽  
LIJUN LIU ◽  
LIYUAN GAO ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Gap Analysis ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Coi Gene ◽  
Economic Losses ◽  
Morphological Identification ◽  
Lycium Barbarum ◽  
Accurate Identification

Neoceratitis asiatica (Becker), which especially infests wolfberry (Lycium barbarum L.), could cause serious economic losses every year in China, especially to organic wolfberry production. In some important wolfberry plantings, it is difficult and time-consuming to rear the larvae or pupae to adults for morphological identification. Molecular identification based on DNA barcode is a solution to the problem. In this study, 15 samples were collected from Ningxia, China. Among them, five adults were identified according to their morphological characteristics. The utility of mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) gene sequence as DNA barcode in distinguishing N. asiatica was evaluated by analysing Kimura 2-parameter distances and phylogenetic trees. There were significant differences between intra-specific and inter-specific genetic distances according to the barcoding gap analysis. The uncertain larval and pupal samples were within the same cluster as N. asiatica adults and formed sister cluster to N. cyanescens. A combination of morphological and molecular methods enabled accurate identification of N. asiatica. This is the first study using DNA barcode to identify N. asiatica and the obtained DNA sequences will be added to the DNA barcode database. 

scholarly journals Integrated taxonomy supports the identification of some species of Phytoseiidae (Acari: Mesostigmata) from Georgia

Acarologia ◽  
2021 ◽  
Vol 61 (4) ◽  
pp. 824-844
Author(s):  
Marie-Stephane Tixier ◽  
Philippe Auger ◽  
Alain Migeon ◽  
Martial Douin ◽  
Amandine Fossoud ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Abundant Species ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
12S Rrna ◽  
Amblyseius Andersoni ◽  
Integrated Taxonomy ◽  
Well Differentiated ◽  
Mtdna Markers ◽  
Eleven Species

The present study reports results of a survey carried out mostly on Citrus sp. and Rubus sp. in Georgia. Morphological and molecular (12S rRNA, COI and CytB mtDNA markers) data were analysed in a framework of integrative taxonomy. Eleven species were identified and among them seven are new for the Georgian fauna. Euseius stipulatus and Phytoseius finitimus were the most abundant species during this survey. We assume that Amblyseius eharai, only reported from eastern Asia, was most probably introduced. Neoseiulus californicus, retrieved from uncultivated vegetation, was almost certainly originating from commercial strains. DNA sequences comparisons disclosed phylogenetic closeness between Amblyseius andersoni and Transeius wainsteini, despite these species (i) being morphologically well differentiated and (ii) classified in different genera, thereby questioning the reliability of the genus Transeius. General morphological characters, including measurements, are provided for species for which diagnoses were doubtful.

scholarly journals Molecular identification of Trichogramma species from South and South-East Asia and natural Wolbachia infection

2019 ◽  
Vol 28 (2) ◽  
pp. 57-66 ◽  
Author(s):  
Yu-Di Liu ◽  
Mao-Lin Hou ◽  
Kai Song
Keyword(s):  
East Asia ◽  
Molecular Identification ◽  
Natural Populations ◽  
Wolbachia Strain ◽  
Its2 Region ◽  
Morphological Identification ◽  
South East Asia ◽  
Trichogramma Chilonis ◽  
Wsp Gene ◽  
Multilocus Sequencing

Trichogramma wasps were collected from the parasitized eggs of lepidopteran pests from 21 sampling sites in East Asia and South-East Asia. Six Trichogramma species were identified based on the molecular identificationmethod using the internal transcribed spacer 2 (ITS2) region of the rDNAof Trichogramma chilonis, T. evanescens, T. ostriniae, T. embryophagum, T. dendrolimi and T. japonicum. The results of molecular identification were confirmed by morphological identification. Additionally, natural populations were screened for the prevalence of Wolbachia. Five out of 21 populations were infected by the same Wolbachia strain, which was identified by using Wolbachia wsp gene and multilocus sequencing approach. The phylogenetic analysis of Wolbachia wsp sequences revealed that the Wolbachia strain was classified in the strain wEvaA in the group of EvA of the supergroup A.

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