Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species

2015 ◽  
Vol 15 (4) ◽  
pp. 286-295 ◽  
Author(s):  
Sebastin Raveendar ◽  
Jung-Ro Lee ◽  
Donghwan Shim ◽  
Gi-An Lee ◽  
Young-Ah Jeon ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Resolving Power ◽  
Conservation Strategies ◽  
Species Discrimination ◽  
Dna Barcodes ◽  
Additional Tool ◽  
Germplasm Collections ◽  
Classification Tool ◽  
Individual Locus

AbstractThe genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae (Fabaceae). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK, rbcL and psbA-trnH) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK, psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.

scholarly journals An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family

2020 ◽  
Vol 21 (8) ◽  
Author(s):  
Viet The Ho ◽  
MINH PHUONG NGUYEN
Keyword(s):  
Dna Barcoding ◽  
In Silico ◽  
Genetic Relatedness ◽  
Dna Barcode ◽  
Species Level ◽  
Resolving Power ◽  
Phylogenetic Study ◽  
Dna Barcodes ◽  
Sequence Parameters ◽  
Cucurbitaceae Family

Abstract. Ho VT, Nguyen MP. 2020. An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas 21: 3879-3885. DNA barcodes have been used intensively to discriminate different species in Cucurbitaceae family. The main of this study is to evaluate the effectiveness of rbcL and matK loci for 16 species of Cucurbitaceae family by using in silico approach. For analysis, sequences were firstly retrieved from NCBI and then calculated for sequence parameters. Sequences were then aligned and constructed phylogenetic try and examined for species resolution ability. The obtained data show the variability of resolving capacity among species. rbcL region is suitable for distinguishing five species namely S. edule, M. cochinchinensis, L. aegyptiaca, C. melo, and C. pepo, whereas matK locus is more proper for different five species consisting of M. balsamina, M. cochinchinensis, M. charantia, S. edule, and C. sativus. The resolving power is improved sharply by analyzing the rbcL + matK combination with up to nine species consisting of C. lanatus, B. hispida, C. melo, C. sativus, C. pepo, C. agryrosperma, L. aegyptiaca, S. edule, and M. cochinchinensis. Therefore, the integration of rbcL and matK loci may improve the competence of assessing genetic relatedness at species level of members in Cucurbitaceae family. The obtained information could be important for choosing proper DNA barcode loci for phylogenetic study of this crop family.

scholarly journals Efficiency of ITS1-5.8S-ITS2 region in identifying Cordyceps species

2020 ◽  
Vol 16 (4) ◽  
pp. 705-712
Author(s):  
Le Thi Thu Hien ◽  
Ha Hong Hanh
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nearest Neighbor ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Pcr Amplification ◽  
Cordyceps Sinensis ◽  
Its2 Region ◽  
Dna Barcodes ◽  
Plastid Genomes

Cordyceps genus is a well-known traditional medicine worldwide. It contains abundant physiological active compounds that were demonstrated to perform benefit in reducing progression of cancer as well as protecting human health. Accurately classifying species in this genus is essential in order to prevent commercial counterfeit medicines. Nowadays, a taxonomic classification of species based on DNA sequences can overcome the existed limitation in identifying by using only morphological characteristics of this genus. DNA barcodes are standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to discriminate species in the genus. A variety of loci has been suggested as DNA barcodes for plants, including genes and non-coding regions in the nuclear and plastid genomes such as psbA-trnH, matK, rbcL, and ITS. Thus, the objective of this study was to identify selected species of Cordyceps genus using DNA barcodes. Seven strains of Cordyceps were collected. Total DNA extraction and purification, PCR amplification and DNA sequencing were performed with standard chemicals and kits. The candidate ITS1-5.8S-ITS2 region was amplified and sequenced. Data were analyzed using Bioedit 7.2.6 and MEGA 7 softwares. Analysis of seven obtained DNA barcode sequences of collected samples revealed that the ITS1-5.8S-ITS2 region provided high species discriminating power for Cordyceps genus. Accordingly, phylogenetic trees based on this DNA barcode exhibited six samples had closed relationship to Cordyceps militaris, while another specimen was the nearest neighbor to Cordyceps sinensis with average similarities at 99.82% and 99.81%, respectively. Our results support the identification of valuable medicinal plant species within Cordyceps genus.

LSU rDNA D5 region: the DNA barcode for molecular classification and identification of Demodex

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 295-304 ◽  
Author(s):  
Li Hu ◽  
Yae Zhao ◽  
Yuanjun Yang ◽  
Dongling Niu ◽  
Rui Yang
Keyword(s):  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Its Region ◽  
Molecular Classification ◽  
Ribosomal Genes ◽  
Lsu Rdna ◽  
Dna Barcodes ◽  
Barcoding Gap ◽  
Demodex Folliculorum

Whether ribosomal genes can be used as DNA barcodes for molecular identification of Demodex (Acariformes: Demodicidae) is unclear. To examine this, Demodex folliculorum, D. brevis, D. canis, and D. caprae were collected for DNA extraction, rDNA fragments amplification, sequencing, and analysis. The V2 and V4 regions of SSU rDNA; D5, D6, and D8 regions of LSU rDNA; and ITS region were obtained from the four morphospecies. BLAST analysis showed that the obtained sequences matched those of Demodex or Aplonobia (Acariformes: Tetranychidae) in Raphignathae. Phylogenetic trees derived from V2, V4, D5, D6, and D8 regions, but not from ITS region, showed that the four species of Demodex clustered independently. Sequence divergence analysis further demonstrated that D5, D6, and D8 regions had obvious barcoding gap between intraspecific and interspecific divergences, with the gap of D5 (16.91%) larger than that of D6 (11.82%) and D8 (4.66%). The V2 and V4 regions did not have a barcoding gap, as the intraspecific and interspecific divergences partially overlapped. For the ITS region, intraspecific and interspecific divergences completely overlapped. These results suggest that the D5, D6, and D8 regions of LSU rDNA, especially D5, are suitable DNA barcodes for Demodex.

Applicability of chloroplast DNA barcodes for wood identification between Santalum album and its adulterants

Holzforschung ◽  
2019 ◽  
Vol 73 (2) ◽  
pp. 209-218 ◽  
Author(s):  
Lichao Jiao ◽  
Tuo He ◽  
Eleanor E. Dormontt ◽  
Yonggang Zhang ◽  
Andrew J. Lowe ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Barcode ◽  
Species Discrimination ◽  
Santalum Album ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Discrimination Ability ◽  
East Indian ◽  
Commercial Market ◽  
Increasing Demand

AbstractThe East Indian sandalwood,Santalum albumL., is known for its fragrant heartwood and extractive oils. The increasing demand for the valuable sandalwood products has led to illegal and excessive logging, and there are otherSantalumspecies in the commercial market as substitutes (adulterants). Improved tools for the identification ofSantalumspecies are needed to control this situation. In this study, four chloroplast DNA (cpDNA) regions were screened (matK,psbA-trnH,trnK andtrnL) on 35 vouchered specimens covering fiveSantalumspecies, i.e.Santalum acuminatum,S. album,Santalum lanceolatum,Santalum murrayanumandSantalum spicatum. The goal of this study was to test the species discrimination ability by means of both the TaxonDNA and neighbor-joining (NJ) methods. The results indicate that the combination ofpsbA-trnH+trnK gave the best performance for discrimination (100%) of the studiedSantalumspecies concerning the discrimination ability and recovery rate. Meanwhile, six unvouchered wood specimens were retrieved and accurately identified at the species level based on the recommended DNA barcodes. The DNA barcode method is now ready for application in the monitoring of the trade of this valuable resource, and provides an effective approach for wood species identification and product authentication.

scholarly journals DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

ZooKeys ◽  
2020 ◽  
Vol 921 ◽  
pp. 141-157 ◽  
Author(s):  
Peter Huemer ◽  
Ole Karsholt ◽  
Leif Aarvik ◽  
Kai Berggren ◽  
Oleksiy Bidzilya ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Barcode ◽  
Species Level ◽  
Coi Gene ◽  
Species Discrimination ◽  
Nominal Species ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
First Time

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

The Potentials of Scanning Microscopy

1968 ◽  
Vol 26 ◽  
pp. 352-353
Author(s):  
A. V. Crewe
Keyword(s):  
Salient Feature ◽  
Secondary Emission ◽  
Resolving Power ◽  
X Rays ◽  
Scanning Microscope ◽  
Forming Process ◽  
Additional Tool ◽  
Detection Systems ◽  
Conventional Microscope ◽  
Present Information

If the resolving power of a scanning electron microscope can be improved until it is comparable to that of a conventional microscope, it would serve as a valuable additional tool in many investigations.The salient feature of scanning microscopes is that the image-forming process takes place before the electrons strike the specimen. This means that several different detection systems can be employed in order to present information about the specimen. In our own particular work we have concentrated on the use of energy loss information in the beam which is transmitted through the specimen, but there are also numerous other possibilities (such as secondary emission, generation of X-rays, and cathode luminescence).Another difference between the pictures one would obtain from the scanning microscope and those obtained from a conventional microscope is that the diffraction phenomena are totally different. The only diffraction phenomena which would be seen in the scanning microscope are those which exist in the beam itself, and not those produced by the specimen.

scholarly journals Cryopreservation of Woody Crops: The Avocado Case

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 934
Author(s):  
Chris O’Brien ◽  
Jayeni Hiti-Bandaralage ◽  
Raquel Folgado ◽  
Alice Hayward ◽  
Sean Lahmeyer ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Ex Situ Conservation ◽  
Plant Genetic Resources ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Recalcitrant Seed ◽  
In Vitro Storage ◽  
Germplasm Collections ◽  
Seed Crops

Recent development and implementation of crop cryopreservation protocols has increased the capacity to maintain recalcitrant seeded germplasm collections via cryopreserved in vitro material. To preserve the greatest possible plant genetic resources globally for future food security and breeding programs, it is essential to integrate in situ and ex situ conservation methods into a cohesive conservation plan. In vitro storage using tissue culture and cryopreservation techniques offers promising complementary tools that can be used to promote this approach. These techniques can be employed for crops difficult or impossible to maintain in seed banks for long-term conservation. This includes woody perennial plants, recalcitrant seed crops or crops with no seeds at all and vegetatively or clonally propagated crops where seeds are not true-to-type. Many of the world’s most important crops for food, nutrition and livelihoods, are vegetatively propagated or have recalcitrant seeds. This review will look at ex situ conservation, namely field repositories and in vitro storage for some of these economically important crops, focusing on conservation strategies for avocado. To date, cultivar-specific multiplication protocols have been established for maintaining multiple avocado cultivars in tissue culture. Cryopreservation of avocado somatic embryos and somatic embryogenesis have been successful. In addition, a shoot-tip cryopreservation protocol has been developed for cryo-storage and regeneration of true-to-type clonal avocado plants.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 637 ◽  
Author(s):  
Mengyue Guo ◽  
Yanqin Xu ◽  
Li Ren ◽  
Shunzhi He ◽  
and Xiaohui Pang
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Identification Accuracy ◽  
Dna Barcodes ◽  
Success Rates ◽  
Data Set ◽  
Herba Epimedii ◽  
Potential Risks ◽  
Medicinal Properties ◽  
Species Being

Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.

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