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molecular barcoding

H Voglmayr, L A Castlebury, W M Jaklitsch
Molecular phylogenetic analyses of ITS-LSU rDNA sequence data demonstrate that Melanconis species occurring on Juglandaceae are phylogenetically distinct from Melanconis s.str., and therefore the new genus Juglanconis is described. Morphologically, the genus Juglanconis differs from Melanconis by light to dark brown conidia with irregular verrucae on the inner surface of the conidial wall, while in Melanconis s.str. they are smooth. Juglanconis forms a separate clade not affiliated with a described family of Diaporthales, and the family Juglanconidaceae is introduced to accommodate it...
June 2017: Persoonia
Yi Xu, Yan Lu, Hai-Ping Wu, Ying Bu
Snake drugs have high values in clinical medication for anti-inflammatory, analgesia activities and dredging collaterals. However, owing to their deficient resource and substantial profit, many counterfeits for snake drugs have appeared on the market. Traditional methods for Chinese medicine authentication include identification of origin, morphology identification, microscopy and physiochemical identification. But these methods are restricted in application because of their high morphological requirement for specimens, complex process for assays and indeterminate results guided by subjective...
August 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Tae-Ho Yoon, Hye-Eun Kang, Soo Rin Lee, Jae-Bong Lee, Gun Wook Baeck, Hyun Park, Hyun-Woo Kim
Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species...
2017: PeerJ
Christian Schmid-Egger, Kees van Achterberg, Rainer Neumeyer, Jérôme Morinière, Stefan Schmidt
The genus Polistes is revised for the West Palaearctic region based on morphology and DNA barcodes. The revision includes all known West Palaearctic species, raising the number of species in Europe to 14 and to 17 for the West Palaearctic realm. DNA barcodes were recovered from 15 species, 14 of which belong to the subgenus Polistes, and one, P. wattii, to the subgenus Gyrostoma. An integrative taxonomic approach combining morphology and molecular data (DNA barcoding) was employed to resolve longstanding taxonomic problems in this group...
2017: ZooKeys
Yun Song, Yan Chen, Jizhou Lv, Jin Xu, Shuifang Zhu, MingFu Li, Naizhong Chen
Rice is the most important crop in the world as the staple food for over half of the population. The wild species of Oryza represent an enormous gene pool for genetic improvement of rice cultivars. Accurate and rapid identification of these species is critical for effective utilization of the wild rice germplasm. In this study, we developed valuable chloroplast molecular markers by comparing the chloroplast genomes for species identification. Four chloroplast genomes of Oryza were newly sequenced on the Illumina HiSeq platform and other 14 Oryza species chloroplast genomes from Genbank were simultaneously taken into consideration for comparative analyses...
2017: Frontiers in Plant Science
Matteo Cecchetto, Maria Chiara Alvaro, Claudio Ghiglione, Alice Guzzi, Claudio Mazzoli, Paola Piazza, Stefano Schiaparelli
The distributional records of Ophiuroidea stored at the Italian National Antarctic Museum (MNA, Section of Genoa) are presented, corresponding to 1595 individuals that belong to 35 species and 17 genera. Specimens were collected in 106 different sampling stations at depths ranging from 21 to 1652 m in the framework of 14 Antarctic expeditions to the Ross Sea, one to the Antarctic Peninsula, and one to the Falkland Islands (Islas Malvinas). Three species, Amphiura joubini Koehler, 1912, Amphiura (Amphiura) angularis Lyman, 1879, and Ophiura flexibilis (Koehler, 1911), are reported as new records for the Terra Nova Bay area, whose check-list of species increases from 15 to 18 species...
2017: ZooKeys
J Ray Fisher, Danielle M Fisher, Michael J Skvarla, Whitney A Nelson, Ashley P G Dowling
The descriptive biology of torrent mites (Parasitengona: Torrenticolidae: Torrenticola) of North America (north of Mexico) is investigated using integrative methods. Material examined includes approximately 2,300 specimens from nearly 500 localities across the United States and Canada, and a few collections in Mexico and Central America. Species hypotheses are derived from a phylogenetic analysis of the barcoding region of cytochrome c oxidase subunit 1 (COI) for 476 specimens and supported with morphology and biogeography...
2017: ZooKeys
Jinda Wang, Weizhong Wang, Rong Wang, Haotian Zheng, Sanji Gao
The Chilo infuscatellus (Snellen; Lepidoptera: Pyralidae) is the main pest of sugarcane in China. The shortage of easily distinguishable morphological characters especially in early stage make it challenging to diagnosed and promptly take steps for pest management. In the present study, we described a PCR method for the molecular identification of based on barcode region of COI sequences between C. infuscatellus and four other sugarcane borer species. A 285bp fragment was successfully amplified from all life stages and different geographical populations...
September 1, 2017: Journal of Insect Science
Young-Gyu Yoon, Peilun Dai, Jeremy Wohlwend, Jae-Byum Chang, Adam H Marblestone, Edward S Boyden
We here introduce and study the properties, via computer simulation, of a candidate automated approach to algorithmic reconstruction of dense neural morphology, based on simulated data of the kind that would be obtained via two emerging molecular technologies-expansion microscopy (ExM) and in-situ molecular barcoding. We utilize a convolutional neural network to detect neuronal boundaries from protein-tagged plasma membrane images obtained via ExM, as well as a subsequent supervoxel-merging pipeline guided by optical readout of information-rich, cell-specific nucleic acid barcodes...
2017: Frontiers in Computational Neuroscience
Egie E Enabulele, Scott P Lawton, Anthony J Walker, Ruth S Kirk
Lecithodendrium linstowi is one of the most prevalent and abundant trematodes of bats, but the larval stages and intermediate hosts have not been identified. We present the first molecular and morphological characterization of the cercariae of L. linstowi based on a phylogenetic analysis of partial fragments of LSU and ITS2 rDNA. The first intermediate host was incriminated as Radix balthica by DNA barcoding using cox1 and ITS2 sequences, although the snail morphologically resembled Radix peregra, emphasizing the requirement for molecular identification of lymnaeids as important intermediate hosts of medical and veterinary impact...
November 8, 2017: Parasitology
Carmelo Andújar, Paula Arribas, Clare Gray, Katherine Bruce, Guy Woodward, Douglas W Yu, Alfried P Vogler
Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (Southern England)...
November 7, 2017: Molecular Ecology
Rebecca Elyanow, Hsin-Ta Wu, Benjamin J Raphael
Motivation: Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing...
November 3, 2017: Bioinformatics
Manorama Maisnam, Suresh Chandra, Kuldeep K Lal, Rajeev K Singh, Vindhya Mohindra
Four species of the genus Osteobrama collected from five different sampling sites of Chindwin and Barak river basin of North-East India, namely O. belangeri, O. cotio, O. cunma and O. feae, were characterized. Meristic study showed differences in anal fin rays count and lateral line scales. Morphometric analysis revealed significant differences among Osteobrama species. In Truss analysis, a clear pattern of differentiation was observed among the four species with discriminant function analysis assigning 100% correctly to the particular species...
November 2, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Joanne L Birch, Neville G Walsh, David J Cantrill, Gareth D Holmes, Daniel J Murphy
In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species)...
2017: PloS One
Abdelmadjid Djoumad, Audrey Nisole, Reza Zahiri, Luca Freschi, Sandrine Picq, Dawn E Gundersen-Rindal, Michael E Sparks, Ken Dewar, Don Stewart, Halim Maaroufi, Roger C Levesque, Richard C Hamelin, Michel Cusson
The gypsy moth, Lymantria dispar L., is one of the most destructive forest pests in the world. While the subspecies established in North America is the European gypsy moth (L. dispar dispar), whose females are flightless, the two Asian subspecies, L. dispar asiatica and L. dispar japonica, have flight-capable females, enhancing their invasiveness and warranting precautionary measures to prevent their permanent establishment in North America. Various molecular tools have been developed to help distinguish European from Asian subspecies, several of which are based on the mitochondrial barcode region...
October 27, 2017: Scientific Reports
Shanlin Liu, Chentao Yang, Chengran Zhou, Xin Zhou
Over the past decade, biodiversity researchers have dedicated tremendous efforts in constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because the Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also refrained High-Throughput-Sequencing (HTS) based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge...
October 25, 2017: GigaScience
Yan-Hong Du, Yuan-Jun Zhao, Fa-Hui Tang
We analyzed the secondary structure of the small subunit (SSU) rRNA genes of Mobilida (Ciliophora, Peritrichia) and found that the secondary structures of some regions within the SSU-rRNA gene are distinct between the families Trichodinidae and Urceolariidae. Therefore, some of these important regions including H10, H11, H17, H47, H29, H30, H37, E10-1, H45-H46, and V4 (E23-4, E23-7) could be used as the barcodes for classification of these two families. In contrast, V4 (E23-1, E23-2) belongs to a hypervariable region and is not a good barcode at the genus level because of its great inter-specific variation...
October 26, 2017: Current Microbiology
Jorge L Ramirez, Jose L Birindelli, Daniel C Carvalho, Paulo R A M Affonso, Paulo C Venere, Hernán Ortega, Mauricio Carrillo-Avila, José A Rodríguez-Pulido, Pedro M Galetti
Molecular studies have improved our knowledge on the neotropical ichthyofauna. DNA barcoding has successfully been used in fish species identification and in detecting cryptic diversity. Megaleporinus (Anostomidae) is a recently described freshwater fish genus within which taxonomic uncertainties remain. Here we assessed all nominal species of this genus using a DNA barcode approach (Cytochrome Oxidase subunit I) with a broad sampling to generate a reference library, characterize new molecular lineages, and test the hypothesis that some of the nominal species represent species complexes...
2017: Frontiers in Genetics
Eva Masiero, Dipanwita Banik, John Abson, Paul Greene, Adrian Slater, Tiziana Sgamma
Liriope and Ophiopogon species have a long history of use as traditional medicines across East Asia. They have also become widely used around the world for ornamental and landscaping purposes. The morphological similarities between Liriope and Ophiopogon taxa have made the taxonomy of the two genera problematic and caused confusion about the identification of individual specimens. Molecular approaches could be a useful tool for the discrimination of these two genera in combination with traditional methods. Seventy-five Liriope and Ophiopogon samples from the UK National Plant Collections of Ophiopogon and Liriope were analyzed...
October 26, 2017: Plants (Basel, Switzerland)
Lu Zhao, Zhimin Liu, Sasha F Levy, Song Wu
Motivation: Barcode sequencing (bar-seq) is a high-throughput, and cost effective method to assay large numbers of cell lineages or genotypes in complex cell pools. Because of its advantages, applications for bar-seq are quickly growing - from using neutral random barcodes to study the evolution of microbes or cancer, to using pseudo-barcodes, such as shRNAs or sgRNAs to simultaneously screen large numbers of cell perturbations. However, the computational pipelines for bar-seq clustering are not well developed...
October 23, 2017: Bioinformatics
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