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molecular barcoding

Jahir Orozco, Elisa Villa, Carmem-Lara Manes, Linda K Medlin, Delphine Guillebault
Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques...
December 1, 2016: Talanta
Vernon G Thomas, Robert H Hanner, Alex V Borisenko
Managing invasive alien species in Canada requires reliable taxonomic identification as the basis of rapid-response management. This can be challenging, especially when organisms are small and lack morphological diagnostic features. DNA-based techniques, such as DNA barcoding, offer a reliable, rapid, and inexpensive toolkit for taxonomic identification of individual or bulk samples, forensic remains, and even environmental DNA. Well suited for this requirement, they could be more broadly deployed and incorporated into the operating policy and practices of Canadian federal departments and should be authorized under these agencies' articles of law...
July 19, 2016: Genome Génome / Conseil National de Recherches Canada
Saroj Rajvanshi, Kirti Choudhary, Nirupama Agrawal
The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools...
October 17, 2016: Experimental Parasitology
Nhu Nguyen, Else C Vellinga, Thomas D Bruns, Peter Kennedy
The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. Here we present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available in public databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America...
October 19, 2016: Mycologia
Jedsada Sukantamala, Kong-Wah Sing, Narong Jaturas, Raxsina Polseela, John-James Wilson
Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity...
October 19, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Sundar Poovitha, Nithaniyal Stalin, Raju Balaji, Madasamy Parani
The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2...
September 14, 2016: Genome Génome / Conseil National de Recherches Canada
E Leyva-Cruz, L Vásquez-Yeomans, L Carrillo, M Valdez-Moreno
In the waters surrounding Banco Chinchorro in the Mexican Caribbean are spawning and nursery areas for many types of fish. In this natural environment, as opposed to under controlled laboratory conditions, it is almost impossible to link an individual egg to the adult that laid it. This makes identifying the species of the eggs difficult. However, DNA barcodes have made this easier. In the present study, 300 eggs were processed for molecular analysis, from which 139 sequences were obtained. We identified 42 taxa (33 species with their binomial names), 35 genera, and 24 families...
May 17, 2016: Genome Génome / Conseil National de Recherches Canada
Steven D Leavitt, Theodore L Esslinger, Pradeep K Divakar, Ana Crespo, H Thorsten Lumbsch
Molecular data provide unprecedented insight into diversity of lichenized fungi, although morphologically cryptic species-level lineages circumscribed from sequence data often remain undescribed even in well-studies groups. Using diagnostic characters from DNA sequence data and support from the multispecies coalescent model, we formally describe a total of eleven new species and resurrect two others in the hyperdiverse lichen-forming fungal family Parmeliaceae. These include: four in the genus Melanelixia - M...
November 2016: Fungal Biology
Mikko Pentinsaari, Heli Salmela, Marko Mutanen, Tomas Roslin
DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function...
October 13, 2016: Scientific Reports
Tatyana Darienko, Lydia Gustavs, Thomas Pröschold
The genera Elliptochloris and Pseudochlorella were erected for Chlorella-like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either free-living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and sometimes lack of characteristic features. The taxonomic and nomenclatural status of these species therefore remains unclear. In this study, 34 strains were investigated using an integrative approach...
October 13, 2016: Journal of Phycology
Charles Girardot, Jelle Scholtalbers, Sajoscha Sauer, Shu-Yi Su, Eileen E M Furlong
BACKGROUND: The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI...
October 8, 2016: BMC Bioinformatics
Yvonne Ukamaka Ajamma, Enock Mararo, David Omondi, Thomas Onchuru, Anne W T Muigai, Daniel Masiga, Jandouwe Villinger
Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the Anopheles gambiae and Culex pipiens complexes...
2016: F1000Research
Antonio R Pérez-Asso, Rayner Núñez-Aguila, Julio A Genaro
The predominantly Greater Antillean endemic genus Calisto Hübner, 1823 is highly diversified on several islands being more species rich on Hispaniola. We conducted expeditions during five years in the Dominican Republic resulting in new findings related with lyceius species group. Material belonging to this group was examined following the traditional morphological characters employed in genus taxonomy, and the COI barcode sequences obtained were analyzed through different approaches: Neighbor Joining clustering, ABGD, Maximum Likelihood (ML), and Bayesian Inference (BI)...
September 26, 2016: Zootaxa
Ying Wang, Qing-Song Zhou, Hui-Jie Qiao, Ai-Bing Zhang, Fang Yu, Xu-Bo Wang, Chao-Dong Zhu, Yan-Zhou Zhang
With the recent development of molecular approaches to species delimitation, a growing number of cryptic species have been discovered in what had previously been thought to be single morpho-species. Molecular methods, such as DNA barcoding, have greatly enhanced our knowledge of taxonomy, but taxonomy remains incomplete and needs a formal species nomenclature and description to facilitate its use in other scientific fields. A previous study using DNA barcoding, geometric morphometrics and mating tests revealed at least two cryptic species in the Encyrtus sasakii complex...
October 4, 2016: Scientific Reports
Rachael J M Bashford-Rogers, Anne L Palser, Clare Hodkinson, Joanna Baxter, George A Follows, George S Vassiliou, Paul Kellam
Chronic lymphocytic leukaemia (CLL) is characterised by the accumulation of clonally-derived mature CD5(high) B-cells, however the cellular origin of CLL is still unknown. Patients with CLL also harbour variable numbers of CD5(low) B-cells, but the clonal relationship of these cells to the bulk disease is unknown and can have important implications for monitoring, treating and understanding the biology of CLL. Here we use B-cell receptors (BCRs) as molecular barcodes to first show that the great majority of CD5(low) B-cells in the blood of CLL patients are clonally related to CD5(high) CLL B-cells by single-cell BCR sequencing...
September 27, 2016: Experimental Hematology
Dhivya Shanmughanandhan, Subramanyam Ragupathy, Steven G Newmaster, Saravanan Mohanasundaram, Ramalingam Sathishkumar
INTRODUCTION: India is considered the 'medicinal garden' of the world, with 8000 medicinal plants of which 960 are commercial species that are traded nationally and globally. Although scientific studies estimate herbal product adulteration as 42-66 % in North America, India does not have any published marketplace studies and subsequent estimates of adulteration in an industry facing considerable supply demands. OBJECTIVES: The goal of this project is to provide an initial assessment of herbal product authentication and adulteration in the marketplace in India by (1) developing a biological reference material (BRM) herbal DNA library for Indian herbal species using DNA barcode regions (ITS2 and rbcL) in order to facilitate accurate species resolution when testing the herbal products; and (2) assessing herbal product identification using our BRM library; and (3) comparing the use of our BRM library to identify herbal products with that of GenBank...
September 29, 2016: Drug Safety: An International Journal of Medical Toxicology and Drug Experience
Xiu-Feng Li, Chong Han, Cai-Rong Zhong, Jun-Qiu Xu, Jian-Rong Huang
Sphaeroma terebrans, a wood-boring isopoda, is distributed worldwide in tropical and subtropical mangroves. The taxonomy of S. terebrans is usually based on morphological characteristics, with its molecular identification still poorly understood. The number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod are considered as the major morphological characteristics in S. terebrans, which can cause difficulty in regards to accurate identification. In this study, we identified S...
September 18, 2016: Dong Wu Xue Yan Jiu, Zoological Research
Alexandre Dos Santos Rodrigues, José Henrique Souza Galdino Brandão, Jamille de Araújo Bitencourt, Ricardo Jucá-Chagas, Iracilda Sampaio, Horácio Schneider, Paulo Roberto Antunes de Mello Affonso
Lignobrycon myersi is a threatened freshwater fish species and endemic of a few coastal rivers in northeastern Brazil. Even though the Brazilian laws prohibit the fisheries of threatened species, L. myersi is occasionally found in street markets, being highly appreciated by local population. In order to provide a reliable DNA barcode dataset for L. myersi, we compared mitochondrial sequences of cytochrome c oxidase subunit I (COI) from fresh, frozen, and salt-preserved specimens. Phylogenetically related species (Triportheus spp...
2016: TheScientificWorldJournal
Ralf Thiel, Thomas Knebelsberger
Accurate stock assessments for each of the dominant species of sand lances in the northeast Atlantic Ocean and adjacent areas are not available due to the lack of a reliable identification procedure; therefore, appropriate measures of fisheries management or conservation of sand lances cannot be implemented. In this study, detailed morphological and molecular features are assessed to discriminate between four species of sand lances belonging to the genera Ammodytes and Hyperoplus. Morphological characters described by earlier authors as useful for identification of the genera are confirmed, and two additional distinguishing characters are added...
2016: ZooKeys
Sheng-Tai Hsiao, Shin-Chang Chuang, Kao-Sung Chen, Ping-Ho Ho, Chi-Lun Wu, Chaolun Allen Chen
The Pacific cupped oyster, Crassostrea gigas, is one of the major aquacultural shellfish species that has been introduced to Europe and America from its native source in the West Pacific. In Taiwan, the cultivated cupped oysters along the west coast have been identified as C. gigas for over centuries; however, several molecular phylogenetic studies have cast doubt upon the existence of this species in Taiwan and adjacent waters. Indeed, our analyses of mitochondrial cytochrome oxidase I (COI) sequences from 313 Crassostrea collected from 12 locations along Taiwanese and southern Chinese coastlines confirm that all samples were the Portuguese oyster, C...
September 26, 2016: Scientific Reports
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