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Neighbor-Joining tree showing relationships among selected Anuraphis species estimated using 648 bp at the 3’ end of the COI mitochondrial gene. Distance were estimated using the p-distance model of sequence evolution.
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The discrimination of species in the genus Anuraphis is particularly difficult due to the overlap of morphological characters. In this study, we used the 5’ (barcode) and 3’ regions of cytochrome oxidase I
(COI) to test their utility in the identification of species in this genus as well as closely related species. Both regions were useful to discr...
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Citations
... Furthermore, it is observed that the amino acid sequence changes are relatively slow (Hebert et al., 2003). It has been reported that the COI region is useful for the accurate identification of aphid species, especially in cases where morphological characters are insufficient (Cocuzza et al., 2015). ...
Aphids are one of the most important groups of insects that cause damage to agricultural crops, ornamental plants, as well as herbaceous and woody plants in their natural habitats. Aphids that feed on plant sap can cause significant crop losses worldwide, ranging from 70% to 80%, due to stunted growth, deformation, wilting, and other detrimental effects on plants. Despite the chemical, biological, and integrated pest management methods applied against these damages, aphids have rapidly expanded their distribution areas and their damages have been increasing in recent times. Hyalopterus Koch (Hemiptera: Aphididae), a genus of aphids, are known worldwide as pests that infest Prunus trees, which are stone fruit trees. They cause damage by feeding on the trees and also by transmitting plant viruses. Subsequently, improper and indiscriminate use of chemical control methods negatively impacts both human and environmental health. Accurate identification of aphids, especially in terms of invasive species, is crucial for early detection of their damages in the initial stages. The mitochondrial cytochrome c oxidase subunit I (COI) gene is an effective gene region used in the identification of many economically important plant pests worldwide. In this study, a total of 50 individuals of Hyalopterus pruni (Geoffroy) were collected from three localities Şarköy (Ulaman, Bulgurlu, Gölcük, Cumhuriyet, Mürefte, Hoşköy, Gaziköy, Tepeköy, Palamut), Süleymanpaşa (Yüzüncüyıl, Altınova, Banarlı, Barboros, Bıyıkali, Çınarlı, Değirmenaltı, Ferhadanlı, Hürriyet, Karacakılavuz, Karaevli, Naip, Namık Kemal and Marmaraereğlisi (Bahçelievler, Cedit Ali Paşa, Dereağzı, Mustafa Kemal Paşa, Sultanköy, Türkmenli, Yakuplu and Yeniçiftlik) in Tekirdağ province. The species H11, H41, and H61, which were selected to represent three counties, were sequenced, and the molecular sequence results revealed that H. pruni, as morphologically described, showed 99% consistency at the molecular level.
... All PCRs were performed in 10 µL, with 4.25 µL buffer premix 2 × F (FailSafe tm PCR Premix Selection Kit, Epicentre Technologies, Thane, India), 0.5 µL of each primer (10 pmol, 0.25 µL Taq polymerase (Life Technologies, Carlsbad, CA, USA) and 2 µL DNA template. Thermal PCR cycle and electrophoresis conditions see [25]. PCR products were sent for sequencing to BMR Genomics (Padua, Italy) using ABI PRISM 3730XL DNA sequencer. ...
The genus Myzocallis Passerini (Hemiptera, Aphididae, Calaphidinae, Myzocallidini) is a rather primitive group of aphids currently comprising 45 species and 3 subspecies, subdivided into ten subgenera, three of them having a West Palaearctic distribution. The majority of the species inhabit Fagales plants and some of them are considered pests. Despite their ecological interest and the presence of some taxonomic controversies, there are only a few molecular studies on the group. Here, the main aims were to develop a DNA barcodes library for the molecular identification of West Palaearctic Myzocallis species, to evaluate the congruence among their morphological, ecological and DNA-based delimitation, and verify the congruence of the subgeneric subdivision presently adopted by comparing the results with those obtained for other Panaphidini species. These study findings indicate that Myzocallis (Agrioaphis) leclanti, originally described as a subspecies of M. (A.) castanicola and M. (M.) schreiberi, considered as a subspecies of M. (M.) boerneri, should be regarded at a rank of full species, and the subgenera Agrioaphis, Lineomyzocallis, Neomyzocallis, Pasekia were elevated to the rank of genus, while Myzocallis remain as such.
... All PCRs were performed in 10 µL, with 4.25 µL buffer premix 2 × F (FailSafe tm PCR Premix Selection Kit, Epicentre Technologies, Thane, India), 0.5 µL of each primer (10 pmol, 0.25 µL Taq polymerase (Life Technologies, Carlsbad, CA, USA) and 2 µL DNA template. Thermal PCR cycle and electrophoresis conditions see [25]. PCR products were sent for sequencing to BMR Genomics (Padua, Italy) using ABI PRISM 3730XL DNA sequencer. ...
The aphid Myzocallis macrolepidis sp. n. is described from the Apulia region, Italy, where it was collected on Quercus macrolepis. The new taxon has a pale-yellow colour in life as alate viviparous females and paler nymphs. Its life cycle remains unknown at present, as sexual morphs were not yet collected; nevertheless, being the aphid host plant a deciduous oak species, very probably the insect performs a monoecious holocycle. Morphologically most similar aphids are M. occidentalis and M. schreiberi from which the new species can be mainly distinguished by the different ratio of last rostral joint to second hind tarsomer and a few other morphological and ecological features. The molecular analysis also confirms the genetic difference of the new taxon from the other allied congeneric species, and molecular differences are briefly discussed.
... There is a widespread deployment of the 5'-prime region of COI gene (the Folmer region = barcoding), but, in the case of aphids, it has also been used the 3'-end of COI together with tRNA and partial COII genes (for example: Stern, 1994;1998;Massimino Cocuzza et al., 2015). Therefore, there is not a common marker o consistent use of a gene region for all samples or species of interest. ...
... Finally, molecular data, though a powerful tool, should not be regarded as a substitute either to morphological/morphometric studies or to the trained expert; in that sense, molecular data should be one piece of an integrated approach (Song et al., 2008;Massimino Cocuzza et al., 2015). ...
The aphid genus Cerataphis Lichtenstein is native to Southeast Asia although several species have been distributed to other tropical regions of the world. Cerataphis brasiliensis (Hempel) and Cerataphis lataniae (Boisduval) are of interest due to their potential as pests on palms. Those species and Cerataphis orchidearum (Westwood) may be morphologically confused with each other. In Costa Rica, two species have been reported, C. brasiliensis and C. orchidearum. This work aimed to contribute molecular data and ecological observations for species of Cerataphis present in Costa Rica. Few colonies (low frequency of occurrence) of C. brasiliensis and C. orchidearum were recorded during a survey conducted during 2014. Ten ant species were found associated to these aphid colonies. Partial sequences for the genes COI and EF-1α were obtained and compared to the few sequences available for this genus in public databases. Species identification by COI (barcoding) was not conclusive. Phylogenetic analyses and similarity pairwise comparisons showed a close relationship with the genus Tuberaphis Takahashi, including the clustering of mixed species from both genera. Yeast-like symbionts were detected by PCR in individuals of both Cerataphis species found in Costa Rica. Overall, the results suggest there is a need of curated sequence data representing the different Cerataphis species worldwide.
... Additional examinations of C. vexillum male genitalia compared to the recently collected Chlidonoptera genitalia led to the submission of DNA sequencing samples at Canadian Center for DNA Barcoding (CCDB) in Guelph. Many studies have used the 5' region of the cytochrome oxidase I gene (COI), more commonly referred to as the DNA barcode region, as a useful tool to discriminate various groups of insects (Cocuzza et al. 2015). The results from the DNA sequencing revealed that the specimens from southwestern CAR are different from known C. vexillum Karsch, 1892 specimens from Cameroon and Gabon. ...
Between 1998 and 2012, several scientific expeditions in Dzanga-Sangha Special Reserve and Dzanga-Ndoki National Park led to the collection of many Mantodea specimens from Central African Republic (CAR). Among these specimens, several males of an undescribed species were discovered. Morphologically, this species most closely resembles to Chlidonoptera vexillum Karsch, 1892 and Chlidonoptera lestoni Roy, 1975. A new lineage was revealed by DNA barcoding. Therefore, a new species is described, Chlidonoptera roxanae sp. nov. Habitus images, genitalia illustrations and descriptions, measurement data, a key to species, natural history information, and locality data are provided. These results add to the evidence that cryptic species can be found in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.
Nicolas Moulin.
... In recent years, the usability of DNA barcoding in aphid species identification has been tested in several studies [12,[41][42][43][44][45]. In aphid species, researchers used DNA barcoding for exploring species diversity [45], identification of species with morphological ambiguity and detection of cryptic species [41,43,[46][47][48], and even phylogenetic relationships [49,50]. Most of the DNA barcode sequences from previous studies or barcoding projects of aphids have been submitted to publicly available databases such as GenBank and the Barcode of Life Data Systems [51]. ...
DNA barcoding has proven its worth in species identification, discovering cryptic diversity, and inferring genetic divergence. However, reliable DNA barcode reference libraries that these applications depend on are not available for many taxonomic groups and geographical regions. Aphids are a group of plant sap sucking insects, including many notorious pests in agriculture and forestry. The aphid fauna of the subtropical region has been understudied. In this study, based on extensive sampling effort across main subtropical areas, we sequenced 1581 aphid specimens of 143 morphospecies, representing 75 genera, and 13 subfamilies, to build the first comprehensive DNA barcode library for subtropical aphids. We examined the utility of DNA barcodes in identifying aphid species and population differentiation and evaluated the ability of different species delimitation methods (automatic barcode gap discovery (ABGD), generalized mixed Yule-coalescent (GMYC), and Bayesian Poisson tree processes (bPTP)). We found that most aphid species demonstrated barcode gaps and that a threshold value of 2% genetic distance is suitable for distinguishing most species. Our results indicated that ten morphospecies may have species divergence related to factors such as host plant or geography. By using two pest species Aphis spiraecola and A. gossypii as examples, we also discussed the effect of the sampling scale of host plants on the results and reliability of DNA barcoding of phytophagous insects. This DNA barcode library will be valuable for future studies and applications.
... Our analysis included the 3' region of COI region. It is not the typical DNA barcoding region, but COCUZZA et al. (2015) demonstrated that not only the 5' barcoding regions but also 3' regions were useful for species delimitation in Anuraphis Del Guercio,1907 (Hemiptera: Sternorrhyncha: Aphididae). The sequence data provide additional information to support species delimitation. ...
A subterranean myrmicine ant Crematogaster monocula sp. nov. is described based on two worker specimens from Cambodia. This species belongs to the C. biroi group of the subgenus Orthocrema Santschi, 1918, which is characterized by developed subpetiolar process , developed subpostpetiolar process and sculptured mesosoma. The new species is easily distinguished from other species of Crematogaster Lund, 1831 by having only one omma-tidium. DNA sequences comprising a 761 bp fragment of the 3' region of the mitochondrial COI gene were amplifi ed and analyzed for C. monocula sp. nov. and other closely related species from the same group. The interspecifi c COI divergence is 17.8% for C. monocula sp. nov. and C. reticulata Hosoishi, 2009. This species is unique in having the smallest eye in the genus Crematogaster.
... The lack of relations between the genetic diversity and host crop and environmental variation as shown in the phylogenetic tree suggests that such factors cannot infer the cause of a speciation event; rather they play an important role in the survival of the aphids. This agrees with previous reports showing near genetic homogeneity irrespective of the host crop or differences in geographical distribution of the aphids (Raboudi et al. 2011;Nibouche et al. 2014;Cocuzza et al. 2015). ...
Aphids are major pests of African indigenous vegetables. Information on the genetic diversity and the role of host crop and environmental differentiation in their diversity in East Africa is scanty. The knowledge on genetic diversity is a critical component in the development of sound and sustainable integrated pest management strategy, from detection to control. A portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene was used to characterise the species of aphids on amaranth and nightshades at different agro-ecological zones of Kenya and Tanzania. Aphid samples were collected in localities growing the vegetables in low, mid and high altitude agro-ecological zones. Total DNA was isolated and amplified using universal barcoding primers targeting the 5′ end of the COI barcode region. Nucleotide sequences of the COI barcode, using the Basic Local Alignment Search Tool model, found high homology to four species of aphids: Myzus persicae, Aphis fabae, Aphis craccivora and Macrosiphum euphorbiae. Three subspecies of the A. fabae were also detected. Intraspecific diversity depicted M. euphorbiae having the lowest value, while A. fabae showed the highest diversity. Interspecific diversity between A. fabae and A. craccivora was the lowest while between A. craccivora and M. persicae it was the highest. The phylogenetic tree showed each species clustering together irrespective of the host crop or site where collected. Principal component analysis and haplotype network analyses confirmed these results. Low genetic diversity revealed by COI suggests that the environment or host crop contribute less to the genetic diversity of aphids in both countries.
The aphid genus Eulachnus in Europe is revised to include 12 species, using an integrative taxonomy approach, based on morphometric, molecular and biological traits. Fundatrix, apterous and alate viviparous female of a new species–Eulachnus stekolshchikovi Kanturski sp. nov. are described. Neotypes are designated for E. agilis, E. brevipilosus and E. nigricola. Lectotypes are designated for E. alticola, E. cembrae, E. rileyi and E. tuberculostemmatus. New synonyms are proposed: E. abameleki syn. nov. (= Cinara pini), E. cretaceus syn. nov. (= E. agilis), E. tauricus syn. nov. (= E. rileyi), E. pallidus syn. nov. (= E. tuberculostemmatus). Eulachnus mingazzinii (near Cinara piniphila) and E. nigrofasciatus (near C. brauni) are regarded as incertae sedis. Full species status is given for E. garganicus stat. nov. and E. ibericus stat. nov. Apterous viviparous female of E. cembrae; apterous and alate viviparous females of remaining species are redescribed. Sexual morphs of E. agilis, E. alticola, E. cembrae, E. intermedius, E. nigricola, E. rileyi and oviparous female of E. tuberculostemmatus are fully redescribed and figured for the first time. Fundatrices of E. agilis, E. brevipilosus, E. cembrae, E. rileyi and E. tuberculostemmatus, sexuales of E. brevipilosus and the alate male of E. tuberculostemmatus are described and figured. A new host plant–Pinus cembra for E. brevipilosus is reported, and this species is recorded for the first time from Czech Republic. Eulachnus tuberculostemmatus is reported for the first time from Croatia. Phylogenetic studies, based on the COI and ITS2 molecular markers, are provided to visualize and discuss the relationships within the European species. COI barcodes are provided for seven species.
Efficient methods for the species identification of seafood are important for ensuring food safety and detecting fraud. DNA barcoding, a technique based on PCR amplification and capillary sequencing of a short, standardized segment of a gene, is a reliable method for species identification of processed and packaged seafood when the species cannot be determined visually. Here we report the optimization and evaluation of a DNA barcoding method for identifying representative commercial decapod crustacean species, including select shrimp, crab, crayfish, and lobster. Two different segments of the mitochondrial cytochrome _c_ oxidase 1 (COI) gene were evaluated —a 655 base pair fragment beginning near the 5′ end, representing the “standard” DNA barcode fragment, and a non-overlapping 475 base pair fragment beginning near the 3′ end, representing an alternative DNA barcode marker for shrimp. The standard 5′ fragment was successfully amplified and sufficient to identify most crustacean species tested, but amplification of both the 5′ and 3′ barcodes were often required to efficiently identify shrimp.
