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https://www.readbyqxmd.com/read/28107413/improving-the-conservation-of-mediterranean-chondrichthyans-the-elasmomed-dna-barcode-reference-library
#1
Alessia Cariani, Silvia Messinetti, Alice Ferrari, Marco Arculeo, Juan J Bonello, Leanne Bonnici, Rita Cannas, Pierluigi Carbonara, Alessandro Cau, Charis Charilaou, Najib El Ouamari, Fabio Fiorentino, Maria Cristina Follesa, Germana Garofalo, Daniel Golani, Ilaria Guarniero, Robert Hanner, Farid Hemida, Omar Kada, Sabrina Lo Brutto, Cecilia Mancusi, Gabriel Morey, Patrick J Schembri, Fabrizio Serena, Letizia Sion, Marco Stagioni, Angelo Tursi, Nedo Vrgoc, Dirk Steinke, Fausto Tinti
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles...
2017: PloS One
https://www.readbyqxmd.com/read/28104454/ecology-of-trypanosoma-cruzi-i-genotypes-across-rhodnius-prolixus-captured-in-attalea-butyracea-palms
#2
Cristina Poveda, Adriana Higuera, Plutarco Urbano, Juan David Ramírez
Trypanosoma cruzi, the agent of Chagas disease exhibits significant genetic diversity. This parasite is divided into six discrete typing units (DTUs) where T. cruzi I (TcI) is the most widespread in the Americas. TcI genotypes have been associated to domestic and sylvatic cycles of transmission (TcIDom and sylvatic TcI). Due to the importance of the enzootic transmission, we determined the frequency of TcI genotypes present in Rhodnius prolixus captured in different regions of the palm A. butyracea to understand the ecology of the disease and the importance of A...
January 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28104086/identification-of-triplophysa-species-from-the-qinghai-tibetan-plateau-qtp-and-its-adjacent-regions-through-dna-barcodes
#3
Jiuxuan Li, Ying Wang, Huifang Jin, Wujiao Li, Chaochao Yan, Pengfei Yan, Xiuyue Zhang, Shunping He, Zhaobin Song
The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28100584/umi-tools-modelling-sequencing-errors-in-unique-molecular-identifiers-to-improve-quantification-accuracy
#4
Tom Sean Smith, Andreas Heger, Ian Sudbery
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR-amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network based methods to account for these errors when identifying PCR duplicates...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28099773/comparison-of-green-and-albino-individuals-of-the-partially-mycoheterotrophic-orchid-epipactis-helleborine-on-molecular-identities-of-mycorrhizal-fungi-nutritional-modes-and-gene-expression-in-mycorrhizal-roots
#5
Kenji Suetsugu, Masahide Yamato, Chihiro Miura, Katsushi Yamaguchi, Kazuya Takahashi, Yoshiko Ida, Shuji Shigenobu, Hironori Kaminaka
Some green orchids obtain carbon from their mycorrhizal fungi, as well as from photosynthesis. These partially mycoheterotrophic orchids sometimes produce fully achlorophyllous, leaf-bearing (albino) variants. Comparing green and albino individuals of these orchids will help to uncover the molecular mechanisms associated with mycoheterotrophy. We compared green and albino Epipactis helleborine by molecular barcoding of mycorrhizal fungi, nutrient sources based on (15) N and (13) C abundances, and gene expression in their mycorrhizae by RNA-seq and cDNA de novo assembly...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28094568/barcode-based-species-delimitation-in-the-marine-realm-a-test-using-hexanauplia-multicrustacea-thecostraca-and-copepoda
#6
Robert G Young, Cathryn L Abbott, Thomas W Therriault, Sarah J Adamowicz
DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value...
October 21, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28089841/the-birth-of-aposematism-high-phenotypic-divergence-and-low-genetic-diversity-in-a-young-clade-of-poison-frogs
#7
Rebecca Dent Tarvin, Emily A Powell, Juan C Santos, Santiago R Ron, David C Cannatella
Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence...
January 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28088131/number-crunching-towards-molecular-barcoding
#8
Soroush Sardari
No abstract text is available yet for this article.
2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28072819/testing-the-efficacy-of-dna-barcodes-for-identifying-the-vascular-plants-of-canada
#9
Thomas W A Braukmann, Maria L Kuzmina, Jesse Sills, Evgeny V Zakharov, Paul D N Hebert
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK...
2017: PloS One
https://www.readbyqxmd.com/read/28059130/rapidly-discriminate-commercial-medicinal-pulsatilla-chinensis-bge-regel-from-its-adulterants-using-its2-barcoding-and-specific-pcr-rflp-assay
#10
Yuhua Shi, Mingming Zhao, Hui Yao, Pei Yang, Tianyi Xin, Bin Li, Wei Sun, Shilin Chen
Pulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that possibly affects medicinal efficacy and safety. We have established an internal transcribed spacer 2 (ITS2) barcode library based on 105 plant samples from 12 Pulsatilla species and 10 common adulterants...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28053872/genetic-identification-of-marine-eels-through-dna-barcoding-from-parangipettai-coastal-waters
#11
Samuel Peninal, Janakiraman Subramanian, Alaganatham Elavarasi, Murugaiyan Kalaiselvam
Anguilliformes, also known as "true eels", are an ecologically diverse group of predominantly marine origin whose members were easily recognized by their extremely elongated bodies with reduced cross-sectional areas and universal lack of pelvic fins. The Marine Eels were collected from landing centres of Parangipettai coastal waters and identified based on their morphometric and meristic characters. The newly recorded species were used for the barcoding analysis. Information on molecular taxonomy of marine eels was very meagre and hence, the present study was aimed to study the barcoding of marine eels which were present along the southeast coast of India...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28052927/dnabarcodes-an-r-package-for-the-systematic-construction-of-dna-sample-tags
#12
Tilo Buschmann
MOTIVATION: DNA barcodes are commonly used for counting and discriminating purposes in molecular and cell biology. Not every set of DNA sequences is equally suitable for this goal. There is a growing demand for more sophisticated barcode designs, with only few tools available. We prepared an R package that combines known algorithms and innovative methods for the efficient, flexible and near-optimal generation of robust barcode sets. RESULTS: Our R-software package 'DNABarcodes' generates sets of DNA barcodes from a few basic input parameters (e...
January 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28052139/application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#13
Tatsuhiko Hoshino, Fumio Inagaki
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28049435/detecting-very-low-allele-fraction-variants-using-targeted-dna-sequencing-and-a-novel-molecular-barcode-aware-variant-caller
#14
Chang Xu, Mohammad R Nezami Ranjbar, Zhong Wu, John DiCarlo, Yexun Wang
BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28018974/hypoxia-sensing-through-%C3%AE-adrenergic-receptors
#15
Hoi I Cheong, Kewal Asosingh, Olivia R Stephens, Kimberly A Queisser, Weiling Xu, Belinda Willard, Bo Hu, Josephine Kam Tai Dermawan, George R Stark, Sathyamangla V Naga Prasad, Serpil C Erzurum
Life-sustaining responses to low oxygen, or hypoxia, depend on signal transduction by HIFs, but the underlying mechanisms by which cells sense hypoxia are not completely understood. Based on prior studies suggesting a link between the β-adrenergic receptor (β-AR) and hypoxia responses, we hypothesized that the β-AR mediates hypoxia sensing and is necessary for HIF-1α accumulation. Beta blocker treatment of mice suppressed hypoxia induction of renal HIF-1α accumulation, erythropoietin production, and erythropoiesis in vivo...
December 22, 2016: JCI Insight
https://www.readbyqxmd.com/read/28011296/bridging-the-gap-between-morphological-species-and-molecular-barcodes-exemplified-by-loricate-choanoflagellates
#16
Nitsche Frank, Thomsen Helge Abuldhauge, Richter Daniel J
Translating the vast amounts of molecular barcodes from global surveys of microbial eukaryotes into ecological insight depends critically on a well-curated reference database with adequate taxonomic coverage. In this respect, the choanoflagellates resemble other eukaryotic lineages: reasonable coverage at higher taxonomic levels, but missing diversity at the species level. The acanthoecid (loricate) choanoflagellates are well-characterized morphologically, with over 115 species described, but less than 10% with any sequence data...
November 9, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/28007566/by-how-much-do-we-underestimate-species-diversity-of-liverworts-using-morphological-evidence-an-example-from-australasian-plagiochila-plagiochilaceae-jungermanniopsida
#17
Matt A M Renner, Margaret M Heslewood, Simon D F Patzak, Alfons Schäfer-Verwimp, Jochen Heinrichs
As a framework for revisionary study of the leafy liverwort Plagiochila in Australia, two methods for species delimitation on molecular sequence data, General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) were applied to a dataset including 265 individuals from Australia, New Zealand, and the Pacific. Groups returned by GMYC and ABGD were incongruent in some lineages, and ABGD tended to lump groups. This may reflect underlying heterogeneity in the history of diversification within different lineages of Plagiochila...
December 19, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28002414/discovery-or-extinction-of-new-scleroderma-species-in-amazonia
#18
Iuri G Baseia, Bianca D B Silva, Noemia K Ishikawa, João V C Soares, Isadora F França, Shuji Ushijima, Nitaro Maekawa, María P Martín
The Amazon Forest is a hotspot of biodiversity harboring an unknown number of undescribed taxa. Inventory studies are urgent, mainly in the areas most endangered by human activities such as extensive dam construction, where species could be in risk of extinction before being described and named. In 2015, intensive studies performed in a few locations in the Brazilian Amazon rainforest revealed three new species of the genus Scleroderma: S. anomalosporum, S. camassuense and S. duckei. The two first species were located in one of the many areas flooded by construction of hydroelectric dams throughout the Amazon; and the third in the Reserva Florestal Adolpho Ducke, a protected reverse by the INPA...
2016: PloS One
https://www.readbyqxmd.com/read/27997843/evolution-plumbing-the-depths-of-diplonemid-diversity
#19
Vojtěch David, John M Archibald
Environmental molecular sequence surveys have opened a window on the hidden riches of the microbial biosphere. Recent genetic 'barcoding' and single-cell genomics studies have provided a snapshot of the biology of diplonemids - abundant, diverse, marine heterotrophic protists whose ecological roles are becoming clearer.
December 19, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27994958/feasibility-of-nuclear-ribosomal-region-its1-over-its2-in-barcoding-taxonomically-challenging-genera-of-subtribe-cassiinae-fabaceae
#20
Priyanka Mishra, Amit Kumar, Vereena Rodrigues, Ashutosh K Shukla, Velusamy Sundaresan
PREMISE OF THE STUDY: The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic relationships ranging from shallow to deep taxonomic levels. Despite several taxonomical revisions in Cassiinae, a stable phylogeny remains elusive at the molecular level, particularly concerning the delineation of species in the genera Cassia, Senna and Chamaecrista...
2016: PeerJ
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