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molecular barcoding

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https://www.readbyqxmd.com/read/28449274/a-dna-barcode-library-for-germany-s-mayflies-stoneflies-and-caddisflies-ephemeroptera-plecoptera-trichoptera
#1
Jérôme Morinière, Lars Hendrich, Michael Balke, Arne J Beermann, Tobias König, Monika Hess, Stefan Koch, Reinhard Müller, Florian Leese, Paul D N Hebert, Axel Hausmann, Christoph F Schubart, Gerhard Haszprunar
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28448639/cryptic-diversity-of-the-subfamily-calaphidinae-hemiptera-aphididae-revealed-by-comprehensive-dna-barcoding
#2
Yerim Lee, Wonhoon Lee, Mariusz Kanturski, Robert G Foottit, Shin-Ichi Akimoto, Seunghwan Lee
Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank)...
2017: PloS One
https://www.readbyqxmd.com/read/28443113/barcode-system-for-genetic-identification-of-soybean-glycine-max-l-merrill-cultivars-using-indel-markers-specific-to-dense-variation-blocks
#3
Hwang-Bae Sohn, Su-Jeong Kim, Tae-Young Hwang, Hyang-Mi Park, Yu-Young Lee, Kesavan Markkandan, Dongwoo Lee, Sunghoon Lee, Su-Young Hong, Yun-Ho Song, Bon-Cheol Koo, Yul-Ho Kim
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439828/interrogation-of-functional-mirna-target-interactions-by-crispr-cas9-genome-engineering
#4
Yale S Michaels, Qianxin Wu, Tudor A Fulga
Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28431212/dna-barcoding-and-traditional-taxonomy-an-integrated-approach-for-biodiversity-conservation
#5
Bhavisha P Sheth, Vrinda S Thaker
Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks...
April 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28420399/distinct-parasite-populations-infect-individuals-identified-through-passive-and-active-case-detection-in-a-region-of-declining-malaria-transmission-in-southern-zambia
#6
Kelly M Searle, Ben Katowa, Tamaki Kobayashi, Mwiche N S Siame, Sungano Mharakurwa, Giovanna Carpi, Douglas E Norris, Jennifer C Stevenson, Philip E Thuma, William J Moss
BACKGROUND: Substantial reductions in the burden of malaria have been documented in parts of sub-Saharan Africa, with elimination strategies and goals being formulated in some regions. Within this context, understanding the epidemiology of low-level malaria transmission is crucial to achieving and sustaining elimination. A 24 single-nucleotide-polymorphism Plasmodium falciparum molecular barcode was used to characterize parasite populations from infected individuals identified through passive and active case detection in an area approaching malaria elimination in southern Zambia...
April 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28419161/unidentifiable-by-morphology-dna-barcoding-of-plant-material-in-local-markets-in-iran
#7
Abdolbaset Ghorbani, Yousef Saeedi, Hugo J de Boer
Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution...
2017: PloS One
https://www.readbyqxmd.com/read/28416672/bisulfite-converted-duplexes-for-the-strand-specific-detection-and-quantification-of-rare-mutations
#8
Austin K Mattox, Yuxuan Wang, Simeon Springer, Joshua D Cohen, Srinivasan Yegnasubramanian, William G Nelson, Kenneth W Kinzler, Bert Vogelstein, Nickolas Papadopoulos
The identification of mutations that are present at low frequencies in clinical samples is an essential component of precision medicine. The development of molecular barcoding for next-generation sequencing has greatly enhanced the sensitivity of detecting such mutations by massively parallel sequencing. However, further improvements in specificity would be useful for a variety of applications. We herein describe a technology (BiSeqS) that can increase the specificity of sequencing by at least two orders of magnitude over and above that achieved with molecular barcoding and can be applied to any massively parallel sequencing instrument...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28414813/dna-barcoding-evaluation-and-implications-for-phylogenetic-relationships-in-lauraceae-from-china
#9
Zhi-Fang Liu, Xiu-Qin Ci, Lang Li, Hsi-Wen Li, John G Conran, Jie Li
Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China...
2017: PloS One
https://www.readbyqxmd.com/read/28407723/dna-barcodes-and-insights-into-the-phylogenetic-relationships-of-corvidae-aves-passeriformes
#10
Zuhao Huang, Rujue Ruan
DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes...
April 13, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28405837/the-nuclear-28s-gene-fragment-d3-as-species-marker-in-oribatid-mites-acari-oribatida-from-german-peatlands
#11
Ricarda Lehmitz, Peter Decker
To make oribatid mites an applicable tool in monitoring programs it is necessary to find a molecular species marker that allows distinct, rapid and easy species identification. In previous studies, the common barcoding sequence COI showed to be too variable to serve as species marker in oribatid mites. The aim of the present study is to evaluate the potential use of the D3 region of the nuclear 28S rDNA gene for species identification. Therefore, we generated a reference DNA library of 28S D3 to identify specimens of the Oribatida from Germany, with focus on species occurring in peatlands being one of the most endangered habitats in Europe...
April 12, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28402794/increased-phylogenetic-resolution-within-the-ecologically-important-rhizopogon-subgenus-amylopogon-using-10-anonymous-nuclear-loci
#12
Nicholas J Dowie, Lisa C Grubisha, Brent A Burton, Matthew R Klooster, Steven L Miller
Rhizopogon species are ecologically significant ectomycorrhizal fungi in conifer ecosystems. The importance of this system merits the development and utilization of a more robust set of molecular markers specifically designed to evaluate their evolutionary ecology. Anonymous nuclear loci (ANL) were developed for R. subgenus Amylopogon. Members of this subgenus occur throughout the United States and are exclusive fungal symbionts associated with Pterospora andromedea, a threatened mycoheterotrophic plant endemic to disjunct eastern and western regions of North America...
2017: Mycologia
https://www.readbyqxmd.com/read/28399227/genetic-diversity-and-identification-of-palearctic-black-flies-in-the-subgenus-wilhelmia-diptera-simuliidae
#13
Abdullah Inci, Alparslan Yildirim, Onder Duzlu, Zuhal Onder, Arif Ciloglu, Gunther Seitz, Peter H Adler
Accurate species identifications are the essential first step in understanding the medical, economic, and ecological importance of black flies. The utility of DNA barcoding based on cytochrome c oxidase subunit 1 (COI) sequences was evaluated for identifying six common species of Palearctic black flies in the subgenus Wilhelmia, including several that are virulent pests. Chromosomally identified larvae from Turkey and Germany and COI sequences in GenBank were analyzed. Intraspecific genetic divergence was 0...
March 8, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28399213/morphological-and-molecular-characteristic-of-megaselia-scalaris-diptera-phoridae-larvae-as-the-cause-of-urinary-myiasis
#14
R Solgi, N Dinparast Djadid, A Eslamifar, A Raz, S Zakeri
We report a case of urinary myiasis occurring in a 60-yr-old Iranian male patient with urinary tract problems and a history of travel to Thailand who was referred to Shafagh Medical Laboratory in Tehran (Iran). Larvae excreted in the patient's urine were confirmed by morphological identification key and DNA barcoding to belong to the species Megaselia scalaris Loew, which is known as the scuttle fly. Based on the patient's history, he was infected with M. scalaris in Thailand. To the best of our knowledge, this is the first report of urinary myiasis caused by M...
February 4, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28395577/developing-an-apicomplexan-dna-barcodoing-system-to-detect-blood-parasites-of-small-coral-reef-fishes
#15
Lance P Renoux, Maureen Dolan, Courtney Cook, Nico Smit, Paul Sikkel
Apicomplexan parasites are obligate parasites of many species of vertebrates. To date, there is very limited understanding of these parasites in the most diverse group of vertebrates, actinopterygian fishes. While DNA barcoding targeting the eukaryotic 18S small subunit (SSU) rRNA gene sequence has been useful in identifying apicomplexans in tetrapods, identification of apicomplexans infecting fishes has relied solely on morphological identification by microscopy. In this study, a DNA barcoding method was developed that targets the 18S rRNA gene primers for identification apicomplexans parasitizing certain actinopterygian fishes...
April 10, 2017: Journal of Parasitology
https://www.readbyqxmd.com/read/28395362/phylogenetic-analysis-and-molecular-characterization-of-xanthium-sibiricum-using-dna-barcoding-pcr-rflp-and-specific-primers
#16
Salvatore Tomasello, Günther Heubl
The fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X...
April 10, 2017: Planta Medica
https://www.readbyqxmd.com/read/28385922/multiplex-digital-colour-coded-barcode-technology-on-rna-extracted-from-routine-cytological-samples-of-patients-with-non-small-cell-lung-cancer-pilot-study
#17
Roberta Sgariglia, Pasquale Pisapia, Mariantonia Nacchio, Caterina De Luca, Francesco Pepe, Maria Russo, Claudio Bellevicine, Giancarlo Troncone, Umberto Malapelle
In the advanced stages of non-small cell lung cancer (NSCLC), molecular testing is often performed on archival cytological smears. The nCounter system (NanoString Technologies) is a new promising multiplex digital colour-coded barcode technology. However, its feasibility to evaluate the RNA expression of clinical relevant biomarkers on routine cytological smears is still uncertain. To this end, RNA was extracted from 12 NSCLC routine stained cytological smears, and nCounter analysis performed by using a 48-gene panel...
April 6, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28382652/a-new-promising-phylogenetic-marker-to-study-the-diversity-of-fungal-communities-the-glycoside-hydrolase-63-gene
#18
L Pérez-Izquierdo, E Morin, J P Maurice, F Martin, A Rincón, M Buée
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for Fungi, but this marker was criticized for idel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in Basidiomycetes...
April 6, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28370147/morphology-and-dna-barcoding-reveal-three-species-in-one-description-of-culicoides-cryptipulicaris-sp-nov-and-culicoides-quasipulicaris-sp-nov-in-the-subgenus-culicoides
#19
S Talavera, F Muñoz-Muñoz, M Verdún, N Pagès
Species of the genus Culicoides (Diptera: Ceratopogonidae) are well known for their importance in the field of medical and veterinary entomology. Culicoides spp. transmit a wide variety of pathogens, primarily viruses that affect animals and humans. In Europe, the most economically important disease transmitted by Culicoides is bluetongue (BT). Culicoides spp. have been recently involved as primary vectors for Schmallenberg disease. The taxonomy within the subgenus Culicoides has been historically difficult and reorganizations have been proposed regularly...
March 28, 2017: Medical and Veterinary Entomology
https://www.readbyqxmd.com/read/28370102/plant-mediated-resource-partitioning-by-coexisting-parasitoids
#20
Xinqiang Xi, Yangheshan Yang, Yonghua Yang, Michal Segoli, Shucun Sun
Although it has been frequently suggested that resource partitioning of species coexisting at the same trophic level can be mediated by interactions with species at non-adjacent trophic levels, empirical evidence supporting this claim is scarce. Here we demonstrate that plants may mediate resource partitioning for two parasitoids that share the same herbivorous host. The tephritid fly Tephritis femoralis is the primary pre-dispersal seed predator of two Asteraceae species, Saussurea nigrescens and Anaphalis flavescens, both of which dominate the plant community in the alpine meadows of the Tibetan Plateau...
March 29, 2017: Ecology
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