scholarly journals Parasitic wasps as natural enemies of aphid populations in the Mashhad region of Iran: New data from DNA barcodes and SEM

2011 ◽  
Vol 63 (4) ◽  
pp. 1225-1234 ◽  
Author(s):  
Reyhaneh Darsouei ◽  
Javad Karimi ◽  
Mehdi Modarres-Awal
Keyword(s):  
Dna Barcoding ◽  
Modern Method ◽  
Diaeretiella Rapae ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Parasitic Wasps ◽  
Pome Fruit ◽  
Initial Attempt ◽  
Morphometric Characters ◽  
Preliminary Identification

DNA barcoding is a modern method for the identification of different species, including insects. Among animals, the major emphasis of DNA barcoding is on insects. Due to this global trend we addressed this approach for surveying a group of insects. The parasitic wasps (including primary and hyperparasitoids) of pome fruit orchard aphids were collected from Iran-Mashhad during 2009-2010. Preliminary identification of this group was performed by using morphological and morphometric characters and SEM. The COI gene in the specimens was amplified and sequenced. In this survey, Aphidius matricariae, Binodoxys angelicae, Diaeretiella rapae, Ephedrus persicae, Lysiphlebus fabarum and Praon volucre parasitoids and Alloxysta sp., Asaphes suspensus, Dendrocerus carpenteri, Pachyneuron aphidis, Syrphophagus aphidivorus hyperparasitoids were studied. Based on intra-interspecies distances and phylogenetic analysis using NJ, all species possess diagnostic barcode sequences. The results of this study show that the COI sequence could be useful in identification study of this group of insects. Here we have provided the first GenBank data for the COI gene of the above-mentioned hyperparasitoids as well as an initial attempt toward preparing DNA barcodes for Iranian parasitoid and hyperparasitoid aphids.

scholarly journals Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

2018 ◽  
Author(s):  
Kam-Cheng Yeong ◽  
Haruo Takizawa ◽  
Thor-Seng Liew
Keyword(s):  
Dna Barcoding ◽  
West Coast ◽  
Leaf Beetle ◽  
Coi Gene ◽  
Beetle Species ◽  
Dna Barcodes ◽  
The West ◽  
Leaf Beetles ◽  
Baseline Knowledge ◽  
Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Lauren M. Overdyk ◽  
Heather E. Braid ◽  
Stephen S. Crawford ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcoding ◽  
Lake Huron ◽  
Coi Gene ◽  
Sampling Effort ◽  
Coregonus Clupeaformis ◽  
Dna Barcodes ◽  
Lake Whitefish ◽  
Life Data ◽  
New Perspective ◽  
St Lawrence River

AbstractDNA barcoding is a useful tool for both species identification and discovery, but the latter requires denser sampling than typically used in barcode studies. Lake Whitefish (Coregonus clupeaformis) is a valuable species, fished traditionally, commercially, and recreationally in Lake Huron. Based on the natural geographic and bathymetric separation of the three major basins in Lake Huron, the potential separation of Lake Whitefish within these basins, and the variation among life history (early and late spawning), we predicted that Lake Huron might harbour cryptic lineages of Lake Whitefish at the basin level. To test this prediction, DNA barcodes of the mitochondrial 5’ cytochrome c oxidase subunit I (COI) gene sequences were recovered from spawning phase Lake Whitefish (n = 5 per site), which were collected from sites (n = 28) around Lake Huron during Fall 2012. These sequences, combined with other publically available DNA barcodes from the Barcode of Life Data System (BOLD), revealed twelve unique haplotypes across North America, with seven unique to Lake Huron. The dominant haplotype was found throughout Lake Huron and east to the St. Lawrence River. No deep divergences were revealed. This comprehensive lake-wide sampling effort offers a new perspective on C. clupeaformis, and can provide insight for environmental assessments and fisheries management.

DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries

Zootaxa ◽  
2008 ◽  
Vol 1839 (1) ◽  
pp. 1 ◽  
Author(s):  
MANUEL ELÍAS-GUTIÉRREZ ◽  
FERNANDO MARTÍNEZ JERÓNIMO ◽  
NATALIA V. IVANOVA ◽  
MARTHA VALDEZ-MORENO ◽  
PAUL D. N. HEBERT
Keyword(s):  
Dna Barcoding ◽  
Classification Systems ◽  
Coi Gene ◽  
Aquatic Environments ◽  
Dna Barcodes ◽  
Chydorus Sphaericus ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Current Classification ◽  
Excellent Tool

DNA barcoding, based on sequence diversity in the mitochondrial COI gene, has proven an excellent tool for identifying species in many animal groups. Here, we report the first barcode studies for freshwater zooplankton from Mexico and Guatemala and discuss the taxonomic and biological implications of this work. Our studies examined 61 species of Cladocera and 21 of Copepoda, about 40% of the known fauna in this region. Sequence divergences among conspecific individuals of cladocerans and copepods averaged 0.82% and 0.79%, respectively, while sequence divergences among congeneric taxa were on average 15-20 times as high. Barcodes were successful in discriminating all species in our study, but sequences for Mexican Daphnia exilis overlapped with those of D. spinulata from Argentina. Our barcode data revealed evidence of many species overlooked by current classification systems —for example, based on COI genotypes the Diapahanosoma birgei group appears to include 5 species, while Ceriodaphnia cf. rigaudi, Moina cf. micrura, Mastigodiaptomus albuquerquensis and Mastigodiaptomus reidae all include 2–3 taxa. The barcode results support recent taxonomic revisions, such as recognition of the genus Leberis, and the presence of several species in the D. birgei and Chydorus sphaericus complexes. The present results indicate that DNA barcoding will provide powerful new insights into both the incidence of cryptic species and a better understanding of zooplankton distributions, aiding evaluation of the factors influencing competitive outcomes, and the colonization of aquatic environments.

scholarly journals Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

2018 ◽  
Author(s):  
Kam-Cheng Yeong ◽  
Haruo Takizawa ◽  
Thor-Seng Liew
Keyword(s):  
Dna Barcoding ◽  
West Coast ◽  
Leaf Beetle ◽  
Coi Gene ◽  
Beetle Species ◽  
Dna Barcodes ◽  
The West ◽  
Leaf Beetles ◽  
Baseline Knowledge ◽  
Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

scholarly journals DNA barcoding for identification of some fish species (Carangidae) in Vietnam coastal area

2020 ◽  
Vol 19 (4) ◽  
pp. 527-536
Author(s):  
Pham The Thu ◽  
Nguyen Manh Linh ◽  
Nguyen Van Quan ◽  
Pham Van Chien ◽  
Dao Huong Ly ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Yellow Card ◽  
Mtdna Coi ◽  
Seriola Quinqueradiata ◽  
Mitochondrial Cytochrome Oxidase ◽  
The Eu

Carangidae family has got about 148 species belonging to 32 genera. In Vietnam, Carangidae is of high commercial value and playing an important role in the ecosystem. In the context Vietnam has received yellow card for seafood since Nov. 2017 by the EU, in which one of the main reasons was related to the restriction of traceability. In this study, DNA barcoding technique of mitochondrial cytochrome oxidase I (COI) gene was used to classify 56 specimens of Carangidae from three coastal areas (Northern, Central and Southern) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 21 species belonging to 16 genera were determined by the COI barcode while 18 species (16 genera) were determined when using morphological method. Seriola quinqueradiata and Trachinotus anak were newly recorded in Vietnam. From 56 sequences with 660 bp of mtDNA (COI), total 27 haplotypes were detected; haplotype diversity (h) and nucleotide diversity (π) were 0.903 ± 0.00060 and 0.14%, respectively. The DNA barcodes of COI gene of 21 species in Carangidae which were developed in this study could be used as a basis for comparison and traceability of their products. In addition, the results showed the high potentiality in using COI barcode to identify Carangidae fish in Vietnam.

scholarly journals Identifikasi Caesio cuning berdasarkan Karakterisasi Morfometrik dan DNA Barcoding yang didaratkan di Pasar Ikan Muara Baru, Jakarta

2020 ◽  
Vol 23 (2) ◽  
pp. 199-206
Author(s):  
Muhammad Fahmi Zuhdi ◽  
Hawis Madduppa
Keyword(s):  
Dna Barcoding ◽  
Morphological Analysis ◽  
Morphological Character ◽  
Coi Gene ◽  
Fish Sample ◽  
Morphometric Characters ◽  
Precise Information ◽  
Fish Market ◽  
Pcr Method ◽  
Species Authentication

Yellow-tailed fish (Caesio cuning) have morphologically similarities with Lutjanidae families, it causes ambiguity on species authentication process. The process of species identification using morphological characteristic does not provide a precise information related to the species.This study was aimed to identify the morphometric and molecular of Yellow-tailed fish (Caesio cuning) which landed on Muara Baru Fish Market, Jakarta using COI gene. A total 30 fishes were observed their nineteen morphometric characters, and 1 fish sample was taken from the fins for DNA extraction, amplification using PCR method, electrphoresis visualization, and sequensing. Sample was analyzed by MEGA 6 software. Based on morphological analysis showed that sampel are Yellow-tailed fish which part of Caesio genus and Caesionidae family. While, genetic analysis using COI gene showed has similarities with database of Genbank NCBI. It can be concluded that identification using morphological character and DNA barcoding methode showed the species belong to Yellow-tailed fish (Caesio cunning).  Ikan Ekor Kuning (Caesio cuning) memiliki kemiripan morfologi dengan anggota famili Lutjanidae lainnya, hal tersebut menyebabkan kesulitan dalam proses autentikasinya.  Proses identifikasi pada suatu spesies menggunakan karakteristik morfologinya belum mampu memberikan informasi yang akurat terkait spesies tersebut. Penelitian ini bertujuan untuk mengidentifikasi ikan ekor kuning (Caesio cuning) yang didaratkan di Pasar Muara Baru, Jakarta melalui kajian karakteristikmorfometrik dan DNA barcoding menggunakan marka gen COI. Total 30 ikan diamati karakter morfometriknya, dan 1 sampel ikan diambil bagian siripnya untuk dilakukan ekstraksi DNA, amplfikasi PCR, elektroforesis, sekuensing dan dianalisis menggunakan aplikasi MEGA 6. Hasil analisis morfologi menunjukkan sampel ikan berasal dari genus Caesio dan termasuk famili Caesionidae. Sedangkan berdasarkan analisis secara molekuler menggunakan marka gen COI, didapatkan hasil bahwa spesies yang diamati (Caesio cuning) memiliki kemiripan dengan database GenBank NCBI. Dapat simpulkan bahwa identifikasi secara morfologi dan DNA menunjukkan bahwa spesies yang di peroleh yaitu Ikan ekor kuning (Caesio cuning).

DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 348-357 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Fernanda Montes De Oca ◽  
Sean W.J. Prosser ◽  
Paul D.N. Hebert ◽  
T. Ryan Gregory ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Black Flies ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
Species Groups

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

scholarly journals DNA barcoding of Zygaenidae (Lepidoptera): results and perspectives

2019 ◽  
Vol 42 (2) ◽  
pp. 137-150
Author(s):  
Konstantin A. Efetov ◽  
Anna V. Kirsanova ◽  
Zoya S. Lazareva ◽  
Ekaterina V. Parshkova ◽  
Gerhard M. Tarmann ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Coi Gene ◽  
Dna Barcodes ◽  
The Family ◽  
The World ◽  
Biological Characters

The present study provides a DNA barcode library for the world Zygaenidae (Lepidoptera). This study reports 1031 sequence data of the COI gene DNA barcodes for more than 240 species in four of the five subfamilies of the family Zygaenidae. This is about 20% of the world Zygaenidae species. Our results demonstrate the specificity of the COI gene sequences at the species level in most of the studied Zygaenidae and agree with already established taxonomic opinions. The study confirms the effectiveness of DNA barcoding as a tool for determination of most Zygaenidae species. However, some of the results are contradictory. Some cases of shared barcodes have been found, as well as cases of deep intraspecific sequence divergence in species that are well separated by morphological and biological characters. These cases are discussed in detail. Overall, when combined with morphological and biochemical data, as well as biological and ecological observations, DNA barcoding results can be a useful support for taxonomic decisions.

scholarly journals Italian Odonates in the Pandora’s Box: A Comprehensive DNA Barcoding Inventory Shows Taxonomic Warnings at the Holarctic Scale

2020 ◽  
Author(s):  
Andrea Galimberti ◽  
Giacomo Assandri ◽  
Davide Maggioni ◽  
Fausto Ramazzotti ◽  
Daniele Baroni ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Genetic Divergence ◽  
Species Delimitation ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Mitochondrial Coi ◽  
Haplotype Networks ◽  
Mitochondrial Coi Gene

AbstractThe Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference datasets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658 bp 5’ end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the dataset to 1294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC, bGMYC) methods were used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct Molecular Operational Units, whereas the remaining ones were classified as ‘warnings’ (i.e., showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped in three categories depending on if they showed low, high, or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic, and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

scholarly journals DNA Barcoding of Endangered Paphiopedilum species (Orchidaceae) of Peninsular Malaysia

Phytotaxa ◽  
2019 ◽  
Vol 387 (2) ◽  
pp. 94-104 ◽  
Author(s):  
MICHEAL C. RAJARAM ◽  
CHRISTINA S.Y. YONG ◽  
JUALANG A. GANSAU ◽  
RUSEA GO
Keyword(s):  
Phylogenetic Tree ◽  
Dna Barcoding ◽  
Dna Markers ◽  
High Accuracy ◽  
Peninsular Malaysia ◽  
Dna Barcodes ◽  
Accurate Identification ◽  
Barcoding Gap ◽  
Preliminary Identification ◽  
Sequence Quality

In this study, the efficacy of four DNA markers and their combinations (rbcL, matK, ITS, trnH-psbA) as barcode markers were tested across the endangered Paphiopedilum species from Peninsular Malaysia. Four species of Paphiopedilum were sampled and barcoded. The DNA barcodes reliabilities were evaluated using NCBI BLASTn program, phylogenetic tree via Neighbour-Joining method with 1000 bootstrap replicates in MEGA 6 and barcoding gap assessment. matK is the most promising barcode with high sequence quality (100%), high accuracy in BLASTn (100%), clear resolution of species in Neighbour-Joining phylogenetic tree (100%) and a distinct barcoding gap followed by ITS, trnH-psbA and rbcL. The combination of barcode regions revealed the lack of variation in rbcL and trnH-psbA but they are still useful for preliminary identification followed up by matK for accurate identification.

Sign in / Sign up

Export Citation Format

Share Document