Supplemental Figure S1 from Expressed Barcoding Enables High-Resolution Tracking of the Evolution of Drug Tolerance
Jennifer L. CottonJavier EstradaVivek SagarJulie ChenMichelle PiquetJohn AlfordYoungchul SongXiaoyan LiMarkus RiesterMatthew T. DiMareKatja SchumacherGaylor BoulayKathleen SprouffskeLin FanTyler BurksLeandra MansurJoel P. WagnerHyo‐eun C. BhangOleg IartchoukJohn Reece-HoyesErick J. MorrisPeter S. HammermanDavid A. RuddyJoshua M. KornJeffrey A. EngelmanMatthew J. Niederst
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<p>Supplemental Figure S1 shows barcode enrichment in drug treated cells, copy number segmentation, and xBC library cloning.</p>Keywords:
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DNA barcoding of a group of European liverwort species from the genus Herbertus was undertaken using three plastid (matK, rbcL and trnH-psbA) and one nuclear (ITS) marker. The DNA barcode data were effective in discriminating among the sampled species of Herbertus and contributed towards the detection of a previously overlooked European Herbertus species, described here as H. norenus sp. nov. This species shows clear-cut differences in DNA sequence for multiple barcode regions and is also morphologically distinct. The DNA barcode data were also useful in clarifying taxonomic relationships of the European species with some species from Asia and North America. In terms of the discriminatory power of the different barcode markers, ITS was the most informative region, followed closely by matK. All species were distinguishable by ITS alone, rbcL + matK and various other multimarker combinations.
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Abstract DNA barcoding and mini-barcoding involve Cytochrome Oxidase Subunit I ( COI ) gene in mitochondrial genome and are used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging from 500 to 700 base pairs for fish species in DNA barcoding and from 80 to 650 base pairs for DNA mini-barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method which focuses on the analysis of short-length DNA markers and has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample. They may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini-barcoding and metabarcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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Accurate identification of unknown specimens by means of DNA barcoding is contingent on the presence of a DNA barcoding gap, among other factors, as its absence may result in dubious specimen identifications – false negatives or positives. Whereas the utility of DNA barcoding would be greatly reduced in the absence of a distinct and sufficiently sized barcoding gap, the limits of intraspecific and interspecific distances are seldom thoroughly inspected across comprehensive sampling. The present study aims to illuminate this aspect of barcoding in a comprehensive manner for the animal phylum Annelida. All cytochrome c oxidase subunit I sequences (cox1 gene; the chosen region for zoological DNA barcoding) present in GenBank for Annelida, as well as for "Polychaeta", "Oligochaeta", and Hirudinea separately, were downloaded and curated for length, coverage and potential contaminations. The final datasets consisted of 9782 (Annelida), 5545 ("Polychaeta"), 3639 ("Oligochaeta"), and 598 (Hirudinea) cox1 sequences and these were either (i) used as is in an automated global barcoding gap detection analysis or (ii) further analyzed for genetic distances, separated into bins containing intraspecific and interspecific comparisons and plotted in a graph to visualize any potential global barcoding gap. Over 70 million pairwise genetic comparisons were made and results suggest that although there is a tendency towards separation, no distinct or sufficiently sized global barcoding gap exists in either of the datasets rendering future barcoding efforts at risk of erroneous specimen identifications (but local barcoding gaps may still exist allowing for the identification of specimens at lower taxonomic ranks). This seems to be especially true for earthworm taxa, which account for fully 35% of the total number of interspecific comparisons that show 0% divergence.
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Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0-2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding - the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species - was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to 'variation' or thought to be insignificant for species-level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.
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DNA barcoding has been widely used in species identification and biodiversity research because it has been shown that in many groups, including insects, interspecific variation in DNA sequences of some genes is much higher than intraspecific and this provided an opportunity to use DNA sequences for species identification. Cytochrome oxidase I (COI) barcoding sequences can be used to discover cryptic, closely related and morphologically similar species. DNA barcoding has gained increased recognition as a molecular tool for species identification in various groups of organisms. A study was, therefore, undertaken to barcode five fly species prevalent in poultry farms in and around Bengaluru districts in Karnataka state. The barcoding of COI gene of Musca domestica, Chrysomya megacephala, Hydrotaea capensis, Hermetia illucens and Sarcophaga ruficornis yielded an amplified fragment of 658 bp sequence. Barcode for all 5 species was generated using Bold_Systems v3 and submitted to GenBank and accession numbers were obtained. In the present study, identification of five different fly species based on morphology was also confirmed by DNA barcoding to prove their correct identity.
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DNA barcoding has gained increased recognition as a molecular tool for species identification of insects. Interspecific variation in DNA sequences of some genes is much higher than intraspecific and provides an opportunity to use DNA sequences for species identification. A study was therefore undertaken to barcode 5 commonly prevalent CuliCOIdes species in farming regions of Bengaluru districts in Karnataka state. The barcoding of Cytochrome oxidase I (COI) gene of C. anophelis, C. palpifer, C. huffi, C. innoxius and C. circumscriptus yielded an amplified fragment of 648 bp sequence. Barcode for all 5 species was generated using BoldSystems v3 and submitted to genbank for accession numbers. DNA barcoding enabled exact identification of 5 prevalent species.
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DNA barcoding is a technique proposed by Hebert and co-workers in 2003 for discriminating species through analysis of a single gene barcode locus. It aims to obtain a better taxonomic resolution than that achieved through morphological studies, and to avoid the decline in taxonomic knowledge. Today DNA barcoding is a global enterprise, and the implementation of the idea has seen a rapid rise (more than 1900 papers published to date on different organisms). Nonetheless, controversy still arises regarding barcoding and taxonomy. It is important to note that DNA barcoding does not focus on building a tree-of-life or on doing DNA taxonomy, even though sometimes it has been used for these purposes. DNA barcoding rather focuses on producing a universal molecular identification key based on strong taxonomic knowledge that should be included in the barcode reference library. In the phylum Tardigrada, DNA barcoding represents a recent approach to species identification and to help in solving taxonomic problems, especially considering the diminutive size of these animals and the paucity of morphological characters useful for taxonomy. In the framework of the MoDNA Project (Morphology and DNA), carried out by our research group in collaboration with several colleagues, we are combining the study of a fragment of the mitochondrial cytochrome c oxidase subunit I gene (cox1) with morphological data, in a wide sense (cuticular structures, chromosomes, data on sex ratio and reproduction), to form an integrative taxonomy approach for tardigrade species identification. We believe that without verified reference sequences from voucher specimens that have been authenticated by qualified taxonomists, there is no reliable library for newly generated sequences with which to be compared. Methods and protocols for standardized results are focused on obtaining tight correspondence between tardigrade morphology (and egg shell morphology, when useful), possibly both light and scanning electron microscopy images, and molecular sequence. This approach is particularly useful in describing new species, and important when applied on material collected in species type localities. Results using this approach are presented, primarily focusing on a number of species from the so-called Macrobiotus hufelandi group.
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DNA barcoding has been proposed as a means of quick species identification using a short standardized segment of DNA. Two species (Eleotris fusca and Glossogobius giuris) from the family Gobiidae and Eleotridae were selected for DNA barcoding using samples collected from different regions of Bangladesh. Cytochrome Oxidase Subunit I (COI) gene was sequenced from two different gobi fishes and compared with two previously published similar sequences from the genera Eleotris and Glossogobius. Multiple sequence alignment and the molecular systematic study were performed. The DNA barcode technique identified the two species. The study provides a good example of how DNA barcoding can build upon its primary mission of species identification and use available data to integrate genetic variation investigated at the local scale into a global framework.Bangladesh J. Zool. 44(2): 175-184, 2016
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[Objectives] To explore the feasibility of DNA barcoding and establishing a local DNA barcoding library for the identification of moths, the COⅠ genes of 82 samples from 10 Noctuidae species in Baoding and Langfang(Hebei Province) were amplified using universal barcoding primers. [Methods] Tree-based, distance-based, threshold-based and character-based methods. [Results] The results show that DNA-based classification was generally consistent with that of traditional methods. However, sample LF110802.008 was misclassified as Maliattha signifera, which differs from the morphological results. Using character-based methods to analyze the 28S gene produced results were consistent with the morphological taxonomy. The effect of sample sizes on the number of diagnostic characters was investigated. Character-based methods are relatively effective, even in the case of small sample sizes. We propose the establishment of a local DNA barcoding library in order to make species identification is more effective. [ConcIusion] DNA barcoding produces good classification results and a local DNA barcoding library would be useful for moth identification.
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DNA barcoding involves the sequencing of a single gene region from all species to provide a means for identifying all of life. Although appealing to many scientists, this idea has caused considerable controversy among systematists. We applied a DNA barcoding approach to outbreak populations of invasive Liriomyza spp. leafminer pests in the Philippines to explore the use of barcoding in a relatively well studied, economically important group. We sequenced a 527-bp portion of mitochondrial cytochrome oxidase I (COI) from 258 leafminers from 26 plant host species in the Philippines. Neighbor-joining and parsimony analysis were used to compare COI sequences from the Philippines to an extensive database of COI sequences previously obtained from samples of the invasive leafminers Liriomyza huidobrensis (Blanchard), Liriomyza trifolii (Burgess), and Liriomyza sativae Blanchard from locations around the world. We conclude that although a DNA barcoding approach can provide rapid species identifications, in certain instances it is likely to either overestimate or underestimate the number of species present. Only when placed within the context of considerable other data can DNA barcoding be fully interpreted and used. For economically and medically important species, which can be well studied, DNA barcoding offers a powerful means for rapid identifications.
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