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molecular barcoding

Adriana Vella, Noel Vella, Sarah Schembri
The mitochondrial genome, through the application of DNA barcoding, provides a powerful tool for identifying species even when specimens are either incomplete or belong to species that exhibit cryptic diversity. In fisheries management accurate identification of whole or part of the specimens landed is a fundamental requirement for the conservation of species affected directly or indirectly by the fisheries activities. In this study cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) sequences were used to genetically distinguish 36 elasmobranch species collected from Maltese (Central Mediterranean) commercial fisheries landings...
September 8, 2017: Marine Genomics
Vladimir A Lukhtanov
Specimens with intermediate morphology are often considered to be the result of ongoing interspecific hybridization; however, this conclusion is difficult to prove without analysis of chromosomal and/or molecular markers. In the butterfly genus Melitaea, such an intermediacy can be detected in male genitalia, and is more or less regularly observed in localities where two closely related, presumably parental species are found in sympatry. Here I analyze a high altitude Melitaea population from Mt. Hermon in north Israel and show that its male genitalia are clearly differentiated from those found in phenotypically similar M...
2017: Comparative Cytogenetics
Shih-Chieh Lee, Chia-Hsiang Wang, Cheng-En Yen, Chieh Chang
The major aim of made tea identification is to identify the variety and provenance of the tea plant. The present experiment used 113 tea plants [Camellia sinensis (L.) O. Kuntze] housed at the Tea Research and Extension Substation, from which 113 internal transcribed spacer 2 (ITS2) fragments, 104 trnL intron, and 98 trnL-trnF intergenic sequence region DNA sequences were successfully sequenced. The similarity of the ITS2 nucleotide sequences between tea plants housed at the Tea Research and Extension Substation was 0...
April 2017: Journal of Food and Drug Analysis
Nanae Masunaga, Naofumi Kagara, Daisuke Motooka, Shota Nakamura, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). METHODS: The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR)...
September 13, 2017: Breast Cancer Research and Treatment
Dan Jiang, Zhenyu Zhao, Teng Zhang, Wenhao Zhong, Chunsheng Liu, Qingjun Yuan, Luqi Huang
Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine "HuangQin" (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found to contain adulterants in recent years, which may give rise to issues regarding drug efficacy and safety. In this study, we developed valuable chloroplast molecular resources by comparing intraspecific and interspecific chloroplast genome...
September 13, 2017: Genes
Natsumi Kanzaki, Karin Kiontke, Ryusei Tanaka, Yuuri Hirooka, Anna Schwarz, Thomas Müller-Reichert, Jyotiska Chaudhuri, Andre Pires-daSilva
The co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems. Here we describe two new species of nematodes with trioecy, Auanema rhodensis and A...
September 11, 2017: Scientific Reports
Giulia Furfaro, Daniele Salvi, Emiliano Mancini, Paolo Mariottini
Recent molecular studies revealed high level of endemism and numerous cryptic species within opisthobranchs, with Mediterranean taxa clearly understudied. Here we used genetic data from both mitochondrial and nuclear gene fragments as well as morphological data from taxonomically relevant characters to investigate the phylogenetic relationships and systematics of Mediterranean taxa of the Flabellinidae and Piseinotecidae families. Phylogenetic analyses based on Bayesian and Maximum-Likelihood methods indicate that Flabellinidae and Pisenotecidae taxa and species within the genera Flabellina, Calmella and Piseinotecus do not form monophyletic clades...
September 6, 2017: Molecular Phylogenetics and Evolution
J E Palomares-Rius, C Cantalapiedra-Navarrete, A Archidona-Yuste, S A Subbotin, P Castillo
The traditional identification of plant-parasitic nematode species by morphology and morphometric studies is very difficult because of high morphological variability that can lead to considerable overlap of many characteristics and their ambiguous interpretation. For this reason, it is essential to implement approaches to ensure accurate species identification. DNA barcoding aids in identification and advances species discovery. This study sought to unravel the use of the mitochondrial marker cytochrome c oxidase subunit 1 (coxI) as barcode for Longidoridae species identification, and as a phylogenetic marker...
September 7, 2017: Scientific Reports
Diva J Amon, Amanda F Ziegler, Jeffrey C Drazen, Andrei V Grischenko, Astrid B Leitner, Dhugal J Lindsay, Janet R Voight, Mary K Wicksten, Craig M Young, Craig R Smith
BACKGROUND: There is growing interest in mining polymetallic nodules from the abyssal Clarion-Clipperton Zone (CCZ) in the tropical Pacific Ocean. Despite having been the focus of environmental studies for decades, the benthic megafauna of the CCZ remain poorly known. To predict and manage the environmental impacts of mining in the CCZ, baseline knowledge of the megafauna is essential. The ABYSSLINE Project has conducted benthic biological baseline surveys in the UK Seabed Resources Ltd polymetallic-nodule exploration contract area (UK-1)...
2017: Biodiversity Data Journal
Miguel Alcaide, Stephen Yu, Jordan Davidson, Marco Albuquerque, Kevin Bushell, Daniel Fornika, Sarah Arthur, Bruno M Grande, Suzan McNamara, Mathilde Couetoux du Tertre, Gerald Batist, David G Huntsman, Luca Cavallone, Adriana Aguilar, Mark Basik, Nathalie A Johnson, Rebecca J Deyell, S Rod Rassekh, Ryan D Morin
Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straightforward and cost-effective production of barcoded adapters to tag individual DNA molecules before PCR and sequencing, and better control over cross-contamination between experiments. We validated our approach in a cohort of 24 patients with a broad spectrum of cancer diagnoses by targeting and quantifying single-nucleotide variants (SNVs), indels and genomic rearrangements in plasma samples...
September 5, 2017: Scientific Reports
I Bosmali, S A Ordoudi, M Z Tsimidou, P Madesis
Saffron, the spice produced from the red stigmas of the flower of Crocus sativus L. is a frequent target of fraud and mislabeling practices that cannot be fully traced using the ISO 3632 trade standard specifications and test methods. A molecular approach is proposed herein as a promising branding strategy for the authentication of highly esteemed saffron brands such as the Greek Protected Designation of Origin (PDO) "Krokos Kozanis". Specific ISSR (inter-simple sequence repeat) markers were used to assess for the first time, the within species variability of several populations of C...
October 2017: Food Research International
Alexander Dyomin, Valeria Volodkina, Elena Koshel, Svetlana Galkina, Alsu Saifitdinova, Elena Gaginskaya
Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown...
August 30, 2017: Molecular Phylogenetics and Evolution
Tanakorn Suesatpanit, Kitisak Osathanunkul, Panagiotis Madesis, Maslin Osathanunkul
BACKGROUND: A variety of plants in Acanthaceae have long been used in traditional Thai ailment and commercialised with significant economic value. Nowadays medicinal plants are sold in processed forms and thus morphological authentication is almost impossible. Full identification requires comparison of the specimen with some authoritative sources, such as a full and accurate description and verification of the species deposited in herbarium. Intake of wrong herbals can cause adverse effects...
August 31, 2017: BMC Complementary and Alternative Medicine
Rafael E Valentin, Anne L Nielsen, Nik G Wiman, Doo-Hyung Lee, Dina M Fonseca
Human mediated transportation into novel habitats is a prerequisite for the establishment of non-native species that become invasive, so knowledge of common sources may allow prevention. The brown marmorated stink bug (BMSB, Halyomorpha halys) is an East Asian species now established across North America and Europe, that in the Eastern United States of America (US) and Italy is causing significant economic losses to agriculture. After US populations were shown to originate from Northern China, others have tried to source BMSB populations now in Canada, Switzerland, Italy, France, Greece, and Hungary...
August 29, 2017: Scientific Reports
Vittorio Boscaro, Erick R James, Rebecca Fiorito, Elisabeth Hehenberger, Anna Karnkowska, Javier Del Campo, Martin Kolisko, Nicholas A T Irwin, Varsha Mathur, Rudolf H Scheffrahn, Patrick J Keeling
Members of the genus Trichonympha are among the most well-known, recognizable and widely distributed parabasalian symbionts of lower termites and the wood-eating cockroach species of the genus Cryptocercus. Nevertheless, the species diversity of this genus is largely unknown. Molecular data have shown that the superficial morphological similarities traditionally used to identify species are inadequate, and have challenged the view that the same species of the genus Trichonympha can occur in many different host species...
September 2017: International Journal of Systematic and Evolutionary Microbiology
Denise Karamessini, Salomé Poyer, Laurence Charles, Jean-François Lutz
Mixtures of uniform sequence-defined oligourethanes are evaluated as 2D molecular barcodes for labeling three different commodity polymers, namely polystyrene, polyvinylchloride and polyethylene terephthalate. Six different oligourethanes are synthesized by solid-phase iterative synthesis and are coded using a binary monomer alphabet. High-resolution mass spectrometry studies indicate that all oligomers are uniform and sequence-defined. However, instead of using them as individual coded chains, oligomers with different chain-length, mass and sequence are mixed into intentionally polydispersed libraries...
August 21, 2017: Macromolecular Rapid Communications
Javier Pinochet, Jean-Charles Leclerc, Antonio Brante, Claire Daguin-Thiébaut, Christian Díaz, Florence Tellier, Frédérique Viard
Non-native ascidians are important members of the fouling community associated with artificial substrata and man-made structures. Being efficient fouling species, they are easily spread by human-mediated transports (e.g., with aquaculture trade and maritime transports). This is exemplified by the ascidian Asterocarpa humilis which displays a wide distribution in the Southern Hemisphere and has been recently reported in the Northern Hemisphere (NW Europe). In continental Chile, its first report dates back from 2000 for the locality of Antofagasta (23°S)...
2017: PeerJ
Mona Koosha, Mohammad Ali Oshaghi, Mohammad Mehdi Sedaghat, Hassan Vatandoost, Shahyad Azari-Hamidian, Mohammad Reza Abai, Ahmad Ali Hanafi-Bojd, Fatemeh Mohtarami
Members of the Culex (Culex) pipiens assemblage are known vectors of deadly encephalitides, periodic filariasis, and West Nile virus throughout the world. However, members of this assemblage are morphologically indistinguishable or hard to distinguish and play distinct roles in transmission of the diseases. The current study aimed to provide further evidence on utility of the two most popular nuclear (ITS2-rDNA) and mitochondrial (COI barcode region) genetic markers to identify members of the assemblage. Culex pipiens assemblage specimens from different climate zones of Iran were collected and identified to species level based on morphological characteristics...
October 2017: Experimental Parasitology
Ankush Ashok Saddhe, Rahul Arvind Jamdade, Kundan Kumar
The plant DNA barcoding is a complex and requires more than one marker(s) as compared to animal barcoding. Mangroves are diverse estuarine ecosystem prevalent in the tropical and subtropical zone, but anthropogenic activity turned them into the vulnerable ecosystem. There is a need to build a molecular reference library of mangrove plant species based on molecular barcode marker along with morphological characteristics. In this study, we tested the core plant barcode (rbcL and matK) and four promising complementary barcodes (ITS2, psbK-psbI, rpoC1 and atpF-atpH) in 14 mangroves species belonging to 5 families from West Coast India...
2017: PloS One
Xin Sun, Feng Zhang, Yinhuan Ding, Thomas W Davies, Yu Li, Donghui Wu
Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences...
August 15, 2017: Scientific Reports
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