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molecular barcoding

Chen Wang, Shobhit Agrawal, Jürgen Laudien, Vreni Häussermann, Christoph Held
BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers...
December 1, 2016: BMC Evolutionary Biology
Bernd Wemheuer, Franziska Wemheuer
Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes...
2017: Methods in Molecular Biology
Árpád V Patai, Barbara Kinga Barták, Bálint Péterfia, Tamás Micsik, Réka Horváth, Csaba Sumánszki, Zoltán Péter, Árpád Patai, Gábor Valcz, Alexandra Kalmár, Kinga Tóth, Tibor Krenács, Zsolt Tulassay, Béla Molnár
Colorectal sessile serrated adenomas (SSA) are hypothesized to be precursor lesions of an alternative, serrated pathway of colorectal cancer, abundant in genes with aberrant promoter DNA hypermethylation. In our present pilot study, we explored DNA methylation profiles and examined selected gene mutations in SSA. Biopsy samples from patients undergoing screening colonoscopy were obtained during endoscopic examination. After DNA isolation and quality analysis, SSAs (n = 4) and healthy controls (n = 5) were chosen for further analysis...
November 29, 2016: Pathology Oncology Research: POR
Roberto Arrigoni, Benoît Vacherie, Francesca Benzoni, Fabrizio Stefani, Eric Karsenti, Olivier Jaillon, Fabrice Not, Flavia Nunes, Claude Payri, Patrick Wincker, Valérie Barbe
Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly-used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are largely adopted as barcode marker to investigate marine plankton community structure worldwide...
November 27, 2016: Molecular Ecology Resources
Marcus Davidsson, Paula Diaz-Fernandez, Oliver D Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries...
November 22, 2016: Scientific Reports
Julia Baudart, Delphine Guillebault, Erik Mielke, Thomas Meyer, Neeraj Tandon, Sabine Fischer, Wilfried Weigel, Linda K Medlin
Monitoring the quality of drinking water is an important issue for public health. Two of the main objectives of the European Project μAQUA were (i) the development of specific probes to detect and quantify pathogens in drinking water and (ii) the design of standardized sampling programs of water from different sources in Europe in order to obtain sufficient material for downstream analysis. Our phylochip contains barcodes that specifically identify freshwater pathogens for enabling the detection of organisms that can be risks for human health...
November 21, 2016: Applied Microbiology and Biotechnology
Jaffarali H Abdul, Soban Akram, Kaleem M L Arshan
Ascidians (tunicates) are marine benthic organisms possessing various pharmacological activities, including anti-oxidant, anti-tumour, antimicrobial, etc. They also play a key role as model organisms to study various neurobehavioral disorders. Ascidian diversity is reportedly less in India due to lack of taxonomists as well as the limitations in morphology based taxonomy. Molecular taxonomy, comprising the sequencing of cytochrome c oxidase 1 gene (barcode region) otherwise known as DNA barcoding reduces these bottlenecks...
November 22, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Hongtao Wang, Na Hao, Lei Chen, Guisheng Li
BACKGROUND: Salvia miltiorrhiza (Danshen) is one of the most widely used medicinal herbs in traditional Chinese medicine. Locality-level and cultivar identification is of great importance not only for protecting highest therapeutic effectiveness of Daodi Danshen, but also for the genetic conservation and utilization of existing S. miltiorrhiza populations. RESULTS: Intron polymorphisms including SNPs (single nucleotide polymorphisms) and indels were exploited in major latex-like protein (MLP) gene...
2016: SpringerPlus
C Rune Stensvold, C Graham Clark
Several typing methods have been used in studies aiming to unravel the molecular epidemiology of Blastocystis, which is one of the most common intestinal parasites in human and many non-human hosts. Such studies have the potential to add to knowledge on Blastocystis transmission, host specificity, phylogeography, and clinical and public health significance, but rely on robust, standardized methods by which data can be generated and compared directly between studies. One of the most used methods is "barcoding,", which involves single-round PCR amplification and sequencing of partial small subunit ribosomal RNA genes of the parasites...
November 18, 2016: Current Protocols in Microbiology
Sonali Garg, S D Biju
The monotypic anuran family Ranixalidae is endemic to India, with a predominant distribution in the Western Ghats, a region that is home to several unique amphibian lineages. It is also one of the three ancient anuran families that diversified on the Indian landmass long before several larger radiations of extant frogs in this region. In recent years, ranixalids have been subjected to DNA barcoding and systematic studies. Nearly half of the presently recognized species in this family have been described over the last three years, along with recognition of a new genus to accommodate three previously known members...
2016: PloS One
Trevor T Bringloe, Karl Cottenie, Gillian K Martin, Sarah J Adamowicz
Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity...
August 18, 2016: Genome Génome / Conseil National de Recherches Canada
Richard Green, Courtney Wilkins, Sunil Thomas, Aimee Sekine, Renee C Ireton, Martin T Ferris, Duncan M Hendrick, Kathleen Voss, Fernando Pardo-Manuel de Villena, Ralph Baric, Mark Heise, Michael Gale
Flaviviruses are hematophagous arthropod-viruses that pose global challenges to human health. Like Zika virus, West Nile Virus (WNV) is a flavivirus for which no approved vaccine exists [1]. The role host genetics play in early detection and response to WNV still remains largely unexplained. In order to capture the impact of genetic variation on innate immune responses, we studied gene expression following WNV infection using the collaborative cross (CC). The CC is a mouse genetics resource composed of hundreds of independently bred, octo-parental recombinant inbred mouse lines [2]...
December 2016: Genomics Data
Andreas Krueger, Natalia Ziętara, Marcin Łyszkiewicz
T cells are continually generated in the thymus in a highly dynamic process comprising discrete steps of lineage commitment, T cell receptor (TCR) gene rearrangement, and selection. These steps are linked to distinct rates of proliferation, survival, and cell death, but a quantitative picture of T cell development is only beginning to emerge. Here we summarize recent technical advances, including genetic fate mapping, barcoding, and molecular timers, that have allowed the implementation of computational models to quantify developmental dynamics in the thymus...
November 11, 2016: Trends in Immunology
Renan Gabriel Gomes Júnior, Carlos Henrique Schneider, Thatianna de Lira, Natália Dayane Moura Carvalho, Eliana Feldberg, Maria Nazareth Ferreira da Silva, Maria Claudia Gross
Oecomys Thomas, 1906 is one of the most diverse and widely distributed genera within the tribe Oryzomyini. At least sixteen species in this genus have been described to date, but it is believed this genus contains undescribed species. Morphological, molecular and cytogenetic study has revealed an uncertain taxonomic status for several Oecomys species, suggesting the presence of a complex of species. The present work had the goal of contributing to the genetic characterization of the genus Oecomys in the Brazilian Amazon...
2016: Comparative Cytogenetics
Christoph von Beeren, Munetoshi Maruyama, Daniel J C Kronauer
Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae)...
2016: PloS One
Xinli Wei, Bruce McCune, H Thorsten Lumbsch, Hui Li, Steven Leavitt, Yoshikazu Yamamoto, Svetlana Tchabanenko, Jiangchun Wei
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H...
2016: PloS One
Ana S Barreira, Darío A Lijtmaer, Pablo L Tubaro
DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit...
October 6, 2016: Genome Génome / Conseil National de Recherches Canada
Stuart Cantsilieris, Holly A Stessman, Jay Shendure, Evan E Eichler
Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform...
2017: Methods in Molecular Biology
Vasily V Zlatogursky, Vladimir I Klimov
The first application of DNA-barcoding for the centrohelids is reported. The character-rich genus Acanthocystis was chosen to compare sequence divergence and morphological similarity. Acanthocystis nichollsi, an easily identifiable and well outlined species, was isolated from four remote locations; A. costata; A. takahashii (2 strains) and A. turfacea were studied as well. Detailed light- and electron-microscopic data were obtained and a fragment of 18S rDNA (mostly V5 to V8 regions) was cloned and multiple clones were sequenced...
October 14, 2016: Protist
I V Zvyagin, I Z Mamedov, O V Tatarinova, E A Komech, E E Kurnikova, E V Boyakova, V Brilliantova, L N Shelikhova, D N Balashov, M Shugay, A L Sycheva, S A Kasatskaya, Y B Lebedev, A A Maschan, M A Maschan, D M Chudakov
αβT-cell depleted allogeneic hematopoietic cells transplantation holds promise for the safe and accessible therapy of both malignant and non-malignant blood disorders. Here we employed molecular barcoding-normalized T-cell receptor (TCR) profiling to quantitatively track T-cell immune reconstitution after TCRαβ/CD19-depleted transplantation in children. We demonstrate that seemingly early reconstitution of αβT-cell counts two months after transplantation is based on only several hundred rapidly expanded clones originating from non-depleted graft cells...
November 4, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
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