scholarly journals DNA Barcoding of Two Thymelaeaceae Species: Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2199
Author(s):  
Almuthanna K. Alkaraki ◽  
Maisam A. Aldmoor ◽  
Jamil N. Lahham ◽  
Mohammed Awad
Keyword(s):  
Dna Barcoding ◽  
Plant Species ◽  
Related Species ◽  
Molecular Level ◽  
Dna Barcodes ◽  
Chloroplast Genes ◽  
Human Errors ◽  
Ancient City ◽  
Thymelaea Hirsuta ◽  
Daphne Mucronata

Daphne mucronata Royle and Thymelaea hirsuta (L.) Endl both belong to the Thymelaeaceae family. Both species are used traditionally to treat several diseases along with various daily applications by Jordanian Bedouins. Traditionally, those species are identified through personal proficiency, which could be misleading due to human errors or lack of expertise. This study aims to investigate an effective DNA barcoding method to identify and characterize Daphne mucronata Royle and Thymelaea hirsuta plant species at the molecular level. Daphne mucronata Royle and Thymelaea hirsuta were collected from the ancient city of Petra in the Southern part of Jordan. Sequences of candidate DNA barcodes were amplified (rbcL, matK, and rpoC1), sequenced, and aligned to the blastn database. Moreover, the obtained sequences were compared with available sequences of related species at the GenBank database. Our results showed that DNA barcoding successfully identifies the two plant species using any of chloroplast genes (rbcL, matK, or rpoC1). The results emphasize the ability of DNA barcoding for identifying and characterizing different plant species through the recruitment of different barcode loci in molecular identification.

scholarly journals Assessment of the DNA Barcodes Characteristic of Phalaenopsis deliciosa based on matK, rbcL, and ITS

2020 ◽  
Vol 8 (2) ◽  
pp. 138
Author(s):  
Nada Nisrina Maulidya ◽  
Siti Rohimah ◽  
Zakiyah Ramadany ◽  
Tri Ratnasari ◽  
Mukhamad Su'udi
Keyword(s):  
Dna Barcoding ◽  
Plant Species ◽  
Molecular Identification ◽  
High Specificity ◽  
Morphological Characters ◽  
Flowering Period ◽  
Dna Barcodes ◽  
Alternative Method

Indonesia has high biodiversity for plant species, including orchids with medicinal potential such as Phalaenopsis deliciosa. Generally, morphological characters, especially in flowers are used for orchids identification. However, when the plants are not in the flowering period, the identification becomes difficult. Therefore an alternative method, such as molecular identification (DNA barcoding) needs to be applied for the best solution. This research, which was conducted with three different markers found that the identity level of matK, rbcL, and ITS to other orchids species was 99-98%, 98%, and 94-96%, respectively. Furthermore, matK and ITS showed high specificity for Phalaenopsis deliciosa, and are therefore recommended as the best molecular identification marker of genus Phalaenopsis.

Efficient distinction of invasive aquatic plant species from non‐invasive related species using DNA barcoding

2012 ◽  
Vol 13 (1) ◽  
pp. 21-31 ◽  
Author(s):  
R. Ghahramanzadeh ◽  
G. Esselink ◽  
L. P. Kodde ◽  
H. Duistermaat ◽  
J. L. C. H. Valkenburg ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Plant Species ◽  
Related Species ◽  
Aquatic Plant ◽  
Non Invasive ◽  
Invasive Aquatic Plant

A new species of Tanytarsus van der Wulp, 1874 (Diptera: Chironomidae) and the first Japanese record of Tanytarsus ovatus Johannsen, 1932 with DNA barcodes

Zootaxa ◽  
2018 ◽  
Vol 4422 (4) ◽  
pp. 591
Author(s):  
ATSUYA KODAMA ◽  
KOICHIRO KAWAI ◽  
HIDETOSHI SAITO
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Adult Male ◽  
Related Species ◽  
First Record ◽  
Species Group ◽  
Dna Barcodes ◽  
A New Species

A new species of the genus Tanytarsus van der Wulp, 1874 was described and illustrated based on an adult male. Tanytarsus trichovalis sp. nov. belongs to the eminulus species group, and is closely related to T. tamaundecimus Sasa, 1980, T. okuboi Sasa, 1986, and T. tonebeceus Sasa & Tanaka, 2000. However, the species is distinguished from these species by the morphology of the hypopygium. We also present the first record of T. ovatus Johannsen, 1932 in Japan. In addition, DNA barcoding of 5 species including T. trichovalis sp. nov., T. ovatus, and other morphologically related species was undertaken. A new key of the eleven Japanese eminulus species group was compiled. 

scholarly journals The specific DNA barcodes based on chloroplast genes for species identification of Orchidaceae plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huili Li ◽  
Wenjun Xiao ◽  
Tie Tong ◽  
Yongliang Li ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Plant Species ◽  
Phylogenetic Analyses ◽  
Germplasm Conservation ◽  
Germplasm Resources ◽  
Chloroplast Genes ◽  
Accurate Identification ◽  
Saturation State ◽  
Relationship Analysis

AbstractDNA barcoding is currently an effective and widely used tool that enables rapid and accurate identification of plant species. The Orchidaceae is the second largest family of flowering plants, with more than 700 genera and 20,000 species distributed nearly worldwide. The accurate identification of Orchids not only contributes to the safe utilization of these plants, but also it is essential to the protection and utilization of germplasm resources. In this study, the DNA barcoding of 4 chloroplast genes (matK, rbcL, ndhF and ycf1) were used to provide theoretical basis for species identification, germplasm conservation and innovative utilization of orchids. By comparing the nucleotide replacement saturation of the single or combined sequences among the 4 genes, we found that these sequences reached a saturation state and were suitable for phylogenetic relationship analysis. The phylogenetic analyses based on genetic distance indicated that ndhF and ycf1 sequences were competent to identification at genus and species level of orchids in a single gene. In the combined sequences, matK + ycf1 and ndhF + ycf1 were qualified for identification at the genera and species levels, suggesting the potential roles of ndhF, ycf1, matK + ycf1 and ndhF + ycf1 as candidate barcodes for orchids. Based on the SNP sites, candidate genes were used to obtain the specific barcode of orchid plant species and generated the corresponding DNA QR code ID card that could be immediately recognized by electronic devices. This study provides innovative research methods for efficient species identification of orchids. The standardized and accurate barcode information of Orchids is provided for researchers. It lays the foundation for the conservation, evaluation, innovative utilization and protection of Orchidaceae germplasm resources.

scholarly journals Ancyronyx lianlabangorum sp. nov., a new spider riffle beetle from Sarawak, and new distribution records for A. pulcherrimus Kodada, Jäch & Čiampor based on DNA barcodes (Coleoptera, Elmidae)

ZooKeys ◽  
2020 ◽  
Vol 1003 ◽  
pp. 31-55
Author(s):  
Ján Kodada ◽  
Manfred A. Jäch ◽  
Hendrik Freitag ◽  
Zuzana Čiamporová-Zaťovičová ◽  
Katarína Goffová ◽  
...  
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Related Species ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Dna Barcodes ◽  
Closely Related Species ◽  
Diagnostic Characters ◽  
First Time ◽  
New Distribution

Ancyronyx lianlabangorumsp. nov. (Coleoptera, Elmidae), a new spider riffle beetle from the Kelabit Highlands (Sarawak, northern Borneo), is described. Illustrations of the habitus and diagnostic characters of the new species and the similar, polymorphic A. pulcherrimus Kodada et al. are presented. Differences to closely related species, based on COI nucleotide sequences and morphological characters, are discussed. Ancyronyx pulcherrimus is here recorded from Sarawak for the first time, based on DNA barcoding.

scholarly journals DNA Barcoding of Selected Medicinal Plant Species from Jordan Using matK, rbcL, and rpoC1 Genes

2021 ◽  
Vol 15 ◽  
pp. 376-411
Author(s):  
Almuthanna K. Alkaraki ◽  
Maisam A. Aldmoor ◽  
Jamil N. Lahham ◽  
Shreen D. Nusair
Keyword(s):  
Medicinal Plants ◽  
Medicinal Plant ◽  
Dna Barcoding ◽  
Plant Species ◽  
Related Species ◽  
Dna Barcode ◽  
Dead Sea ◽  
Medicinal Plant Species ◽  
Bioinformatic Tools ◽  
Plant Samples

Medicinal plants play an essential role in preventing and treating several diseases. Classical taxonomic tools generally carry out medicinal plant identification and characterization. Unfortunately, conventional methods need well-trained taxonomists and could give a false identity for closely related species. Jordanian flora is rich in a variety of plant species. The phylogeographic architecture of Jordanian medicinal plant samples was not explored yet. This study aims to recruit DNA barcoding using matK, rbcL, and rpoC1 genes to identify different selected medicinal plants species from Jordan. These are Maerua crassifolia, Ziziphus spina-christi, Balanites aegyptiaca, Senna italica, and Moringa peregrina. Plant samples were collected from the Dead Sea area (Jordan), and three DNA barcode regions were amplified, sequenced, and analyzed using different bioinformatic tools. Twelve sequences were obtained and deposited in Genbank . These sequences showed a very good discrimination capacity with sequences retrieved from related species. The phylogenetic analysis illustrated that DNA barcoding could successfully identify the selected medicinal plant species using different chloroplast genes (rbcL, matK, and rpoC1). Further analysis for other plants species is recommended to explore the genetic relationship and the phylogeographic architecture for Jordanian flora.

DNA Barcoding and Phylogenetic Analysis Sugarcane (Saccharum officinarum L.) Based on matK ( maturase K) Gene

2020 ◽  
Vol 840 ◽  
pp. 162-170
Author(s):  
Ganies Riza Aristya ◽  
Fauzana Putri ◽  
Rina Sri Kasiamdari ◽  
Arni Musthofa
Keyword(s):  
Phylogenetic Tree ◽  
Molecular Level ◽  
Economic Value ◽  
Saccharum Officinarum ◽  
Saccharum Spontaneum ◽  
Dna Barcodes ◽  
Pcr Method ◽  
Hybrid Cultivar ◽  
I Gene ◽  
Sequencing Process

Sugarcane (Saccharum officinarum L.) is an agricultural commodities with a great extent of diversity and high economic value. In Indonesia, the great extent of diversity of sugarcane is evidenced by a large number of cultivars cultivated. Sugarcane diversities at the molecular level can be seen using DNA barcodes, one of which is the matK. The purpose of the study was to identify and characterize matK and reconstruct the phylogenetic tree to determine the phylogeny of 24 sugarcane cultivars Indonesia. matK was amplified using the PCR method with matK F-5’ATGATTAATTAAGAGTAAGAGGAT-3’ and matK R-5’AATGCAAAAATTCGAAGGGT-3. Results showed that the matK gene was successfully amplified as many as 1531 bp. The sequencing process was done to determine the nucleotide sequence and compared with those of the GenBank database. It showed that the samples used had a similarity of 98.87%-99.44% to that of matK in Saccharum officinarum, Saccharum hybrid cultivar and Saccharum spontaneum. Reconstruction of the phylogenetic tree showed that the samples used were located in the same clade with a zero genetic distance, while all the references from NCBI were also located in the same clade. The analysis of genetic variation indicated that it had no haplotype value.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

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