DNA Barcoding

Poecilia reticulata is a freshwater fish from the northeastern part of South America and spread widely to various countries in Asia and other continents. However, research about P. reticulate is limited even though it is a well-known fish species in Indonesia. The purpose of study was to identify the fish species of P. reticulata through DNA barcoding using the COI gene to determine the phylogenetic relationships among fish populations in East Java, Indonesia. In a present study, there were eight samples of P. reticulata from four different freshwater locations in East Java. Extraction, amplification, and sequencing of DNA samples were conducted to obtain the genetic data and construct a phylogenetic tree based on DNA sequences. The COI gene is the most popular markers to study genetic populations and phylogeography among the animal kingdom. Our phylogenetic reconstruction showed a clear that there were two groups of P. reticulata. The first group was obtain through species from Eas...

DNA sequences of cytochrome c oxidase I gene (COI) from Lepidion spp. were employed to test the efficiency of species identification. A sample of 32 individuals from five Lepidion species was sequenced and combined with 26 sequences from other BOLD projects. As a result, 58 Lepidion DNA sequences of the COI gene belonging to eight of the nine recognized Lepidion species were analysed. Sequences were aligned and formed seven clades in a Bayesian phylogenetic tree, where Lepidion lepidion and Lepidion eques grouped jointly. The Kimura 2-parameter genetic distances, among congeners were, on average, 4.28%, 16 times greater than among conspecifics (0.27%). The main diagnostic meristic data of Lepidion spp. were compiled and a detailed morphological revision of the congeneric species L. eques and L. lepidion was made. The eye diameter was significantly different between L. eques and L. lepidion (P < 0.001). The number of anal fin rays ranged from 45 to 51 in L. lepidion and from 47 to 54 in L. eques, but no significant differences were obtained in the mean values of this variable (P = 0.07). According to the morphological and genetic analyses, the results strongly suggest that the Mediterranean codling L. lepidion and the North Atlantic codling L. eques are conspecific, making L. eques a junior synonym of L. lepidion.

Digeneans and cestodes are species-rich taxa and can seriously impact human health, fisheries, aqua-and agriculture, and wildlife conservation and management. DNA barcoding using the COI Folmer region could be applied for species detection and identification, but both 'universal' and taxon-specific COI primers fail to amplify in many flatworm taxa. We found that high levels of nucleotide variation at priming sites made it unrealistic to design primers targeting all flatworms. We developed new degenerate primers that enabled acquisition of the COI barcode region from 100% of specimens tested (n = 46), representing 23 families of digeneans and 6 orders of cestodes. This high success rate represents an improvement over existing methods. Primers and methods provided here are critical pieces towards redressing the current paucity of COI barcodes for these taxa in public databases.

Recently, a novel approach to a highly sensitive and quantitative detection of rare earth element (REE) ions including La3+, Eu3+ and Tb3+, by the polymerase chain reaction (PCR) technique, has been reported. The detection of REE ions is based on the catalytic nature of REE ions targeting the deoxyribonucleic acid (DNA), thus monitoring of the ions can be achieved by reading the level of intact DNA by PCR. Despite of its high sensitivity (at ppb to ppt levels), the conventional PCR-based REE detection protocol requires certain length of time (1-2 hours). In the present study, we modified the PCR-based REE detection protocols by employing the high-speed PCR, and performed the automated and rapid detection of La3+ in small-sized aqueous samples within 5min.

The Brazilian federal government has adopted DNA barcoding (i.e. analysing about 650 base pairs of the COI mitochondrial gene) as a standardised method in a nationwide programme for routine and systematic regulation of processed seafood products. Here, we report rates and trends of a forensic programme which sampled products with twenty-eight commercial fish names (N = 255) confiscated by official governmental officers from 14 states, and which also included imports from 8 countries. A mislabelling rate of 17.3% (44 samples) was recovered when comparing the DNA barcode identification of fish products to the official Brazilian list of species and commercial names. No statistical differences in mislabelling rates between geopolitical regions was detected (G = 2.4, N = 5, p = 0.66). The number of mislabelled samples was not correlated to samples size per commercial name (r = 0.34, N = 29, p = 0.07), but instead, misla-belling was positively correlated to the number of species detected (r = 0.75, N = 29, p < 0.00), suggesting that more surveillance should be given to species with less well-defined commercial names. The programme resulted in financial penalties being applied according to the amount of mislabelling detected. Moreover, companies caught selling mislabelled products were further inspected until the company proved that their production was normalised according to Brazilian labelling regulations. A systematic nationwide forensic governmental programme may lead to more sustainable and trusted fisheries activities allowing consumers to make informed choices when buying seafood products.

The application of DNA barcoding to dietary studies allows prey taxa to be identified in the absence of morphological evidence and permits a greater resolution of prey identity than is possible through direct examination of faecal material. For insectivorous bats, which typically eat a great diversity of prey and which chew and digest their prey thoroughly, DNAbased approaches to diet analysis may provide the only means of assessing the range and diversity of prey within faeces. Here, we investigated the effectiveness of DNA barcoding in determining the diets of bat species that specialize in eating different taxa of arthropod prey. We designed and tested a novel taxon-specific primer set and examined the performance of short barcode sequences in resolving prey species. We recovered prey DNA from all faecal samples and subsequent cloning and sequencing of PCR products, followed by a comparison of sequences to a reference database, provided species-level identifications for 149 ⁄ 207 (72%) clones. We detected a phylogenetically broad range of prey while completely avoiding detection of nontarget groups. In total, 37 unique prey taxa were identified from 15 faecal samples. A comparison of DNA data with parallel morphological analyses revealed a close correlation between the two methods. However, the sensitivity and taxonomic resolution of the DNA method were far superior. The methodology developed here provides new opportunities for the study of bat diets and will be of great benefit to the conservation of these ecologically important predators.

Jacquemontia reclinata House (Convolvulaceae) is a federally listed endangered species endemic to coastal strand habitat of south-eastern Florida. In order to identify the closest relatives of J. reclinata, a phylogenetic reconstruction was performed based on nucleotide sequence data from the internal transcribed spacer region of nuclear ribosomal DNA and from the trnH-psbA intergenic spacer of chloroplast DNA. The three putative relatives of J. reclinata and the majority of Jacquemontia Choicy species known to occur in the Caribbean Islands were included. The strict consensus tree concurs with previous morphological studies, indicating that J. reclinata is closely related to the Caribbean species J. cayensis Britton, J. curtisii Hallier f., and J. havanensis (Jacq.) Urb. These three species and J. reclinata form an unresolved clade. Nucleotide divergence within this clade is low, suggesting that the group is recent, perhaps diversifying after the latest glacial period. These taxa need to be studied further using population-level DNA markers. Most species endemic to the Caribbean Basin form a strongly supported clade. Our phylogeny supports Convolvulus nodiflorus Desr. as part of Jacquemontia. In addition, J. ovalifolia (West) Hallier f. ssp. sandwicensis (A. Gray) K.R. Robertson is sister to the Antillean endemic J. solanifolia (L.) Hallier f. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 443–454.

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter-and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

Explosions and molotov bomb throwing actions have prominent economic, psychological and social effects on the collective memory since they inflict nonrecoverable wounds. One of the prominent purposes of the crime scene investigation is to investigate the fingerprints in order to identify the identity of the offender. The purpose of this study is to determine the impact of heat on the quality of fingerprints on the findings obtained in crime scene and to create the standards to use as a routine investigation method in criminal laboratories of the law enforcers. Few studies have been published and little is known about this subject. The paper aims to discuss these issue. In this study, 720 fingerprint samples, which were created according to the conditions that would exist in the crime scenes after an explosion or handmade incendiary weapons incidents, had been 􀁈􀁛􀁄􀁐􀁌􀁑􀁈􀁇􀀑􀀃 􀂳􀀶􀁘􀁓􀁈􀁕􀀃􀀪􀁏􀁘􀁈􀂴􀀃􀁄􀁑􀁇􀀃 􀂳􀀶􀀳􀀵􀂴􀀃 􀁐􀁈􀁗􀁋􀁒􀁇􀁖􀀃 􀁚􀁈􀁕􀁈􀀃 􀁘􀁖􀁈􀁇􀀃 􀁒􀁑􀀃 􀁐􀁈􀁗􀁄􀁏􀀃 􀁄􀁑􀁇􀀃 􀁊􀁏􀁄􀁖􀁖􀀃 􀁖􀁄􀁐􀁓􀁏􀁈􀁖􀀃 􀁄􀁑􀁇􀀃 􀂳􀀱􀁌􀁑􀁋􀁜􀁇􀁕􀁌􀁑􀂴􀀃 method were used on paper samples in order to create fingerprints. All the samples were exposed to temperatures varying between 50oC-300oC. When different temperatures were taken into consideration, fingerprints suitable for comparison were obtained under all surface and environmental conditions up to 300oC. We are of the opinion that this study which is conducted for the first time in our country would significantly contribute to the identification of attackers and shed light on the incidents, especially in terrorist events.

F; OLIVEIRA, C. DNA barcoding reveals hidden diversity in the neotropical freshwater fish Piabina argentea (Characiformes: Characidae) from the Upper Parana Basin of brazil. Mitochondrial DNA, 2011a PFENNINGER, M.C.; NOWAK, C.; KLEY, D.; STEINKE, D.; STREIT, B. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Molecular Ecology, v. 16, p. Drummond, G. M.;PAGLIA, A. P. (eds.) Livro Vermelho da Fauna Brasileira Ameaçada de Extinção. Belo Horizonte: Fundação Biodiversitas. 2v. 2008. 1420p. SATO, Y. e GODINHO, H. P. Peixes da bacia do rio São Francisco. In: Estudos ecológicos de comunidades de peixes tropicais. Lowe-McConnell (Ed.). Tradução de Vazzoler A.E.A.M.; Agostinho A.A.; & Cunnhingham, P.T.M. EDUSP, São Paulo, 1999. 401-413 p. SATO, Y. e GODINHO, H.P. Migratory fishes of the São Francisco River, p.197-228. In: Carolsfeld, J.; Harvey, B.; Baer, A. (ed.). M i t o c h o n d r i a l phylogeography of the vegetable pest Liriomyza trifolii (Diptera: Agromyzidae): diverged clades and invasive populations. Annals of Entomological Society of America, v. 99, p. 991-998, 2006. SMITH, P.J., MCVEAGH, S.M., e STEINKE, D. DNA barcoding for the identification of smoked fish products. Journal of Fish Biology, v. 72(2), p. 464-471, 2008. SOUSA, A.B.; CARVALHO, D.C.; MELO ,D.C.; SEERIG, A.S.; OLIVEIRA, D.A.A. A utilização de baixo número de matrizes em piscicultura: perda de r e c u r s o s g e n é t i c o s p a r a p r o g r a m a s d e repovoamento. Revista Brasileira de Reprodução Animal, v. 30(3/4), p. 100-104, 2006. VALDEZ-MORENO, M.; IVANOVA, N.V.; ELÍAS-GUTIÉRREZ, M.; CONTRERAS-BALDERAS, S. & HEBERT, P.D.N. Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. Journal of Fish Biology, v. 74, p. 377-402, 2009. VALE DO SÃO FRANCISCO. Disponível em: < h t t p : / / w w w . v a l e d o saofrancisco.com.br/OVale/AspectosFisicos-Potamografica.asp>. Acesso em: 12 jan. 2010. VIERIA , F. e POMPEU, P. Peixamentos, uma alternativa eficiente? Ciência Hoje v. 175, p. 29-33, 2001. VIEIRA, F.; ALVES, C.B.M.; POMPEU, P.S.; VONO, V. Peixes ameaçados de Minas Gerais. In: DRUMMOND, G.M.; MACHADO, A.B.M.; MARTINS, C. S.; MENDONÇA, M.P.; STEHMANN, J.R. (Org.). Listas vermelhas das espécies da fauna e flora ameaçadas de extinção em Minas Gerais. 2a. ed. Belo Horizonte: Fundação Biodiversitas, 2008. WARD, R. D.; ZEMLAK, T. S.; INNES, B. H.; LAST, P. R.; e HEBERT, P. D. N. DNA barcoding Australia's fish species. ZEMLAK, T. S.; MASON, J. A.; WASHINGTON, J. D.; TENGE, B. J.; NGUYEN, N.L.N.; BARNETT, J. D.; SAVARY, W. E.; HILL, W. E.; MOORE, M. M.; FRY, F. S.; RANDOLPH, S. C.; ROGERS, P. L. & HEBERT, P. D. N. The potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia.

We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40% to 70% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.

Characterizing the diet of large herbivores and the determinants of its variation remains a difficult task in wild species. DNA-based techniques have the potential to complement traditional time-consuming methods based on the microhistology of plant cuticle fragments in fecal or rumen samples. Recently, it has been shown that a short chloroplast DNA fragment, the P6 loop of the trnL (UAA) intron, can act as a minimalist barcode. Here, we used the trnL approach with high-throughput pyrosequencing to study diet from feces in a wild herbivore, the alpine chamois (Rupicapra rupicapra) and showed that the fine resolution in plant determination obtained with this method allows exploring subtle temporal shifts and inter-individual variability in diet composition. First, we built a DNA barcoding database of 475 plants species. Seventy-two percent of plant species can be unambiguously identified to species level, 79% to genus level and 100% to family level using the P6 loop. Second, we analysed 74 feces collected from October to November. Based on 47,896 P6 loop sequences, we identified a total of 110 taxa, 96 in October and 76 in November, with a clear diet shift between October and November. We recognized four and two clusters of feces composition in October and November, respectively, revealing different diet categories among individuals within each month. DNA-based diet analysis is faster and more taxonomically precise than studies based on microhistology, and opens new possibilities for analysing plant-herbivore interactions in the wild.

Accurate identification of seafood species in the markets is a growing concern due to the high incidence of species substitution at international level. It is a prime priority for governments to be able to identify the already processed fish products (fish fillets). In this context, DNA barcoding was applied to ascertaining species in fish fillets (tilapia, Nile perch and panga) purchased from Egyptian markets. Ninety commercial samples were analyzed. Sequencing of a short fragment of mitochondrial cytochrome oxidase I (COI) gene revealed 33.3% species substitution in the fish fillets analyzed, 50% Nile perch (Lates niloticus) and 50% basa fish (Pangasius bocourti) being replaced by imported Vietnamese tra fish (Pangasianodon hypophthalmus). These results demonstrate that DNA barcoding is a reliable tool for detecting fish products adulteration in Egypt. We recommend its use for control and law enforcement of seafood quality.

DNA barcoding is a relatively new method developed to provide rapid, accurate and automatable species identification using standardized DNA sequences as tags. Species identification in this way is usually achieved by the repossession of a short DNA sequence, the “barcode” from a standard part of the genome of a given species. An experiment was conducted to identify three species of genus Allium using five barcode regions including ndhJ, rpoC1, rpoB, YCF5 and rbcL. Results indicated that A. ampeloprasum persicum was the only identified species. Barcode region of YCF5 had the highest SRSP with 93.33%. The highest interspecific diversity and intraspecific divergence with 0.8% and 0.4% were observed in region of ndhJ which was the most sufficient barcode region for species identification.

Abstact  Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present

The steroid 5 alpha reductase encoded by SRD5A2 gene plays a critical role in male sex differentiation and mutation happened in the gene might also be one of the major causes of transexualism. In order to make this evident, a small study was designed. Blood samples were collected from normal people as well as transgenders, from which DNA was isolated by Miller’s method. From the DNA samples, the SRD5A2 gene was amplified using site specific primers and the amplified gene products were then sequenced. The sequences from the transgender samples were compared with the respective controls using the Bioedit tool. This study revealed the presence of few previously reported mutations on the transsexuals which clearly states that the mutation in the SRD5A2 gene was one of the vital causes for the transexualism.

The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification. #

FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens. # 2009 CSIRO Journal compilation # 2009 The Fisheries Society of the British Isles

DNA barcoding is a system for fast and accurate species identification. It's creates ecological system more accessible by using short DNA sequence instead of whole genome and is used for eukaryotes and prokaryotes. The short DNA sequence is generated from standard region of genome known as marker. This marker is different for various species like CO1 cytochrome c oxidase 1 for animals, matK and rbcL for plants and Internal Transcribed Spacer (ITS) for fungus. It has many uses in various fields such as agriculture, sustaining natural resources, protecting endangered species, water quality, preserving natural resources, identification of medicinal plants.

Due to the high information content of DNA molecules, a rapid growth in the number of methods of crop molecular genetic analysis using molecular or DNA markers is observed in world scientific practice. The same methods of DNA analysis can be used for genetic certification of crop varieties instead of low-information methods for the protein markers analysis. This review discusses the use of various DNA markers for the identification and evaluation of genetic resources of species, subspecies, varieties and lines of cultivated plants. Some information on the classification of markers and examples of their successful use in certification, selection and phylogenetic studies are presented. Briefly describes the stages of their use, as well as the advantages and disadvantages of different methods. The most effective and inexpensive methods for detecting intraspecies polymorphism can be considered ISSR, SSR and SNP-analyzes. The SNP-analysis method is the most informative, which is most likely to find increasing application in the genetic analysis and selection of cultivated plants. It is noted that different types of markers are suitable for studying polymorphism both within a single species and in higher taxonomic groups (genus, family, etc.). Population and evolutionary studies also noted the need to use several evolving independently markers, for example, nuclear, chloroplast and mitochondrial markers.
For citation: Sukhareva A.S., Kuluev B.R. DNA markers for genetic analysis of crops. Biomics. 2018. 10(1). P. 69-84. DOI: 10.31301/2221-6197.bmcs.2018-15

Species of Orchidaceae are under severe threat of extinction mainly due to overcollection and habitat destruction; accurate identification of orchid species is critical in conservation biology and sustainable utilization of orchids as plant resources. We examined 647 sequences of the cpDNA regions rbcL, matK, atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS from 89 orchid species (95 taxa) and four outgroup taxa to develop an efficient DNA barcode for Orchidaceae in Korea. The five cpDNA barcode regions were successfully amplified and sequenced for all chlorophyllous taxa, but the amplification and sequencing of the same regions in achlorophyllous taxa produced variable results. psbK-psbI IGS showed the highest mean interspecific K2P distance (0.1192), followed by matK (0.0803), atpF-atpH IGS (0.0648), trnH-psbA IGS (0.0460) and rbcL (0.0248). The degree of species resolution for individual barcode regions ranged from 60.5% (rbcL) to 83.5% (trnH-psbA IGS). The degree of species resolution was significantly enhanced in multiregion combinations of the five barcode regions. Of the 26 possible combinations of the five regions, six provided the highest degree of species resolution (98.8%). Among these, a combination of atpF-atpH IGS, psbK-psbI IGS and trnH-psbA IGS, which comprises the least number of DNA regions, is the best option for barcoding of the Korean orchid species.

In this study, 229 DNA sequences of cytochrome oxidase subunit I gene (COI) from 158 marine fishes of Japan were employed to test the efficacy of species identification by DNA barcoding. The average genetic distance was 60-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 17.6% among congeners and only 0.3% among conspecifics. There were no overlaps between intraspecific and interspecific K2P distances, and all sequences formed species units in the neighbor-joining dendrogram. Hybridization phenomena in two species (Kyphosus vaigiensis and Pterocaesio digramma) were also detected through searches in Barcode of Life Data Systems (BOLD). DNA barcoding provides a new way for fish identification.

Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe.
It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative
for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific
nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and
classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential
application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many
bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool
in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology
overcomes the challenges associated with traditional methods along with prospects for future research.

A simple and efficient protocol for isolating genomic DNA from fresh and dry leaves of Vigna aconitifolia and V. trilobata was developed. It involves a modified CTAB procedure using 3% CTAB, 4% -mercaptoethanol, 2 M NaCl and 5% PVP. The extraction was carried out at 70°C. A slight increase in the concentrations of these chemical components and temperature helped in the removal of secondary metabolites and polysaccharides from the DNA preparation. The quantity and purity of isolated DNA was higher when compared with DNA extracted by the methods of and Doyle and Doyle (1990) [9, 13]. The DNA yield ranged from 45 -55 µg per g of leave samples and it was 1.25 times greater in dried than fresh samples. The DNA samples were found suitable for analysis with restriction enzyme digestion and randomamplification of polymorphic DNA (RAPD).

Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA barcoding in food traceability, and to delineate some best practices in the application of DNA barcoding throughout the industrial pipeline. The use of DNA barcoding for food safety and in the identification of commercial fraud is also discussed.

FAIT ACCOMPLI VIA 2-D CARRIER WAVES, AS YOU'LL SEE.  THE MAJOR POINT IS THAT THE IMAGES / INFO THAT CAUSES FULL DIFFERENTIATION IS PRESENT IN OUR AURA, WHICH IS A HUGE COLLECTION OF ANUs FROM ALL OF OUR PAST, PRESENT AND FUTURE LIVES.  IRREFUTABLE PROOF.

The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.

Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

The main purpose of this book is to highlight the research findings, achievements, challenges and perspectives discussed in the 3rd Regional Conference on Biosensors, Biodiagnostics, Biochips and Biotechnology 2016 (3rd RC4Bs-2016). The 3rd RC4Bs-2016 was held at the AIMST University which provided a platform for scientists, researchers, academicians, students and stakeholders to share their knowledge, challenges, recent advances and future perspectives in the multidisciplinary areas of biosensors, biodiagnostics, biochips and biotechnology. This book contains full-length articles, talk abstracts of all invited speakers, and abstracts of all technical papers presented in the conference.

ISBN: 978-983-43522-8-8 (Print version)
eISBN: 978-983-43522-7-1 (e-Book version)

The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.

This study describes the comparison of five DNA extraction methods (urea-SDS-proteinase K; phenolchloroform; salt extraction; SureFood Ò PREP Allergen kit and Wizard Ò Genomic DNA Purification kit) in terms of their ability to extract high yields of pure, readily amplifiable DNA from the muscle tissue of 29 fish species available in South Africa. Although variations in the yield and purity of extracted DNA were observed between methods, all five methods produced DNA suitable for PCR amplification. Overall, the SureFood Ò PREP method was of the simplest and least hazardous to perform, extracting significantly (P < 0.05) higher DNA yields than all other methods evaluated.

Aims: The use of residual synthetic chemicals, although effective against stored product pests, has led to environmental degradation. However, the risk  of target pests developing resistance to insecticides in addition to the high costs of synthetic insecticides has pushed researchers to find alternative control methods. Plant-based insecticides represent a suitable alternative control method because they are less toxic to non-target organisms and biodegradable. The present study  investigates the potency of essential oil and wood ashes in the control of the stored product pest Callosobruchus maculatus(Coleoptera: Bruchidae).
Study Design: Bioassays were performed in glass jars. Insect rearing, oil extraction and wood ash preparation were done according to an established protocol. For each treatment, a randomized complete block design with four replications was used.
Place and Duration of Study: Laboratory of biology of the Faculty of Science, University of Ngaoundere, Cameroon from February 2013 to February2014.
Methodology:Wood ash from two different plants and essential oil were used. We evaluated the single effects of our products before combining each  wood ash at 0.4, 2, 10, 20 and 40 g/kg with the essential oil of  Lippia adoensis at the rate of 0.05 mL/kg on different fitness parameters of C. maculatus. Data on insect mortality rate and adult emergence were assessed.
Results:In single applications, the susceptibility of  C. maculatus was significantly (P= .05) higher to essential oil than wood ash with LC50 values of 2.64 mL/kg and 139.64 g/kg, respectively after the first day exposure. The essential oil was also more effective in reducing egg laying and adult
emergence. However, the combination of wood ash and essential oil caused 98.69±1.32% mortality within six days of exposure, compared to 73.53±3.80%  for wood ash and 77.44±2.91% for
essential oil. The co-toxicity coefficients of the combination of the two substances for mortality (275.9), fecundity (562.61) and fertility (438.92) were higher than 120, suggesting a significant essential oil-ash synergistic interaction.
Conclusion:Essential oil was the most toxic in single applications for all treatments. But when applied in  combination, a lowest dose of wood ash (0.8 mL/kg) instead of 40 g/kg was able to kill 98.69±1.32% of adults. Therefore, combining essential  oil with wood ash could significantly
(P= .05) improve on the efficacy of controlling C. maculatus in storage facilities. Knowledge gained from this study could be exploited by low income farmers as it could provide a cost effective strategy for crop storage without the use of enormous quantities of wood ash.

The rhodopolioid species of Entoloma (subgen. Entoloma) in Norway are presented. The rhodopolioid clade consists of tricholomatoid or collybioid, rarely omphalinoid, ectomycorrhizal species. Altogether 24 species of the rhodopolioid clade were recorded and verified by rDNA ITS sequence data, of which 10 are here reported as new to Norway, including three apparently undescribed species. Four different eco-geographical elements can be distinguished from our material; (i) the southern (boreonemoral) Tilia-Quercus-Corylus element, (ii) the boreal-arctic-alpine Salix-Alnus-Betula element, (iii) the arctic-alpine Salix(-Dryas) element, and (iv) the boreal Betula(-Picea) element. All 24 species are commented in the taxonomic part, arranged according to the five well-supported clades from phylogenetic analyses.

DNA barcoding is a relatively new method developed to provide rapid, accurate and automatable species identification using standardized DNA sequences as tags. Species identification in this way is usually achieved by the repossession of a short DNA sequence, the "barcode" from a standard part of the genome of a given species. An experiment was conducted to identify three species of genus Allium using five barcode regions including ndhJ, rpoC1, rpoB, YCF5 and rbcL. Results indicated that A. ampeloprasum persicum was the only identified species. Barcode region of YCF5 had the highest SRSP with 93.33%. The highest interspecific diversity and intraspecific divergence with 0.8% and 0.4% were observed in region of ndhJ which was the most sufficient barcode region for species identification.

This study presents DNA barcode records for 4118 specimens representing 561 species of bees belonging to the six families of Apoidea (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae and Melittidae) found in Central Europe. These records provide fully compliant barcode sequences for 503 of the 571 bee species in the German fauna and partial sequences for 43 more. The barcode results are largely congruent with traditional taxonomy as only five closely allied pairs of species could not be discriminated by barcodes. As well, 90% of the species possessed sufficiently deep sequence divergence to be assigned to a different Barcode Index Number (BIN). In fact, 56 species (11%) were assigned to two or more BINs reflecting the high levels of intraspecific divergence among their component specimens. Fifty other species (9.7%) shared the same Barcode Index Number with one or more species, but most of these species belonged to a distinct barcode cluster within a particular BIN. The barcode data contributed to clarifying the status of nearly half the examined taxonomically problematic species of bees in the German fauna. Based on these results, the role of DNA barcoding as a tool for current and future taxonomic work is discussed.