scholarly journals The perspectives for DNA barcoding of Rhaponticum carthamoides (Willd.) Iljin using rbcL gene sequence

2021 ◽  
Vol 908 (1) ◽  
pp. 012030
Author(s):  
M V Protopopova ◽  
N A Shvetsova ◽  
V V Pavlichenko
Keyword(s):  
Dna Barcoding ◽  
Large Subunit ◽  
Dna Barcode ◽  
Natural Populations ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Rhaponticum Carthamoides ◽  
South Siberia ◽  
Illegal Harvesting

Abstract The methods of biological species identification using nucleotide sequences of short genome regions (DNA barcoding) are actively developed. The universal DNA barcode for plants remains to be discovered, and one of the leading candidates is the plastid gene of the large subunit of ribulose-bisphosphate carboxylase gene (rbcL). In our study, we estimated the part of rbcL gene as a possible marker for molecular identification of Rhaponticum carthamoides (Willd.) Iljin. Due to its officinal properties, the species is susceptible to uncontrolled and illegal harvesting from natural populations. Today, the species needs to be protected and therefore is included into the Red Data Books of the Russian Federation and certain regions. The study was carried out using plants from the natural populations sampled from the Khamar-Daban Ridge (South Siberia) and considering now as Rh. carthamoides var. chamarense (Peschkova) O S Zhirova. It was shown that rbcL gene can be used to identify Rh. carthamoides at least from the populations of the Khamar-Daban Ridge using a fragment of the maximum length or its 3’ region. Apparently, the 5’ region of the gene (rbcLa) most often used as DNA barcode for plants may be of lesser importance for Rh. carthamoides. The rbcL gene sequences can be also used for the development of approaches for Rh. carthamoides identification in the medicinal preparations and products containing dried tissues to prevent their falsification and illegal harvesting of this species. The combination of rbcL gene with additional markers seems to be highly desirable to create effective DNA barcodes for Rhaponticum species.

scholarly journals DNA Barcoding Dalugha (Cyrtosperma Merkusii) di Kepulauan Talaud dan Minahasa Selatan Berdasarkan Gen rbcL

2021 ◽  
Vol 11 (2) ◽  
pp. 134
Author(s):  
Marlin Bernadet Taariwuan ◽  
Jantje Ngangi ◽  
Yermia Mokosuli ◽  
Sukmarayu Gedoan
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Local Alignment ◽  
Rbcl Gene ◽  
Endemic Plant ◽  
Bisphosphate Carboxylase ◽  
Large Gene ◽  
North Sulawesi ◽  
Barcode Dna ◽  
Search Tool

(Article History: Received June 28, 2021; Revised August 30, 2021; Accepted Sept 3, 2021) ABSTRAKDalugha (Cyrtospera merkusii (Hassk.)Schott) merupakan tanaman endemik Sulawesi Utara yang digunakan sebagai pangan alternatif (penganti beras). Penelitian ini bertujuan untuk membandingkan spesies daluga di Kepulauan Talaud dan Minahasa Selatan menggunakan DNA barcode gen rbcL (ribulose 1,5 bisphosphate carboxylase large). Perbandingan barcode DNA yang dilakukan pada empat sampel yang berbeda lokasi tersebut keduanya menghasilkan tingkat kesamaan 100% (identik). Dengan demikian, tidak ada variasi intra spesies yang ditemukan dari semua sampel yang ada. Selanjutnya, kemiripan sampel-sampel ini telusuri kemiripannya dengan kerabat terdekat yang tercatat di GenBank menggunakan BLAST (Basic Local Alignment Search Tool).  Tanaman dalugha dalam penelitian ini memiliki kemiripan 99,82% dengan tumbuhan Anaphyllopsis americana (AM905753.1), dan kemiripannya 99,63% dengan Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), dan Podolasia stipitata (AM905752.1). Belum ada rekor sekuens DNA gen rbcL dari spesies ini yang dibisa dibandingkan di GenBank.Kata Kunci: Dalugha; DNA barcoding; gen rbcL ABSTRACTDalugha (Cyrtospera merkusii (Hassk.) Schott) is an endemic plant in North Sulawesi that is used as alternative food (substitute for rice). This research aimed to compare the DNA barcode of dalugha in Talaud Islands and in South Minahasa using rbcL (ribulose 1,5 bisphosphate carboxylase large) gene. The DNA barcoding comparison of all four samples in both area resulted in 100% similarity (identical). Therefore, there is no intraspecific variation found in all samples. Furthermore, the similarity of these samples were conducted with BLAST (Basic Local Alignment Search Tool) to compare with its closest relatives in GenBank. The closest relatives of this plant, based on similarity information, are 99.82% with Anaphyllopsis americana (AM905753.1) and all 99.63% with Cyrtosperma macrotum (AM905750.1), Lasimorpha senegalensis (AM905755.1), Pycnospatha arietina (AM905751.1), and Podolasia stipitata (AM905752.1).  There is no record yet of rbcL gene sequence of C. merkusii in GenBank for comparison.Keywords: Dalugha; DNA barcoding; rbcL gene

scholarly journals Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

2022 ◽  
Vol 2022 ◽  
pp. 1-19
Author(s):  
Sarfraz Ahmed ◽  
Muhammad Ibrahim ◽  
Chanin Nantasenamat ◽  
Muhammad Farrukh Nisar ◽  
Aijaz Ahmad Malik ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Species Level ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bacterial Strains ◽  
Accurate Identification ◽  
Bisphosphate Carboxylase ◽  
Parallel Acquisition ◽  
Invertebrate Animal

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

scholarly journals Diel Rhythms in Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase and Glutamine Synthetase Gene Expression in a Natural Population of Marine Picoplanktonic Cyanobacteria (Synechococcusspp.)

1999 ◽  
Vol 65 (8) ◽  
pp. 3651-3659 ◽  
Author(s):  
Michael Wyman
Keyword(s):  
Glutamine Synthetase ◽  
Natural Population ◽  
Nitrogen Assimilation ◽  
Large Subunit ◽  
Natural Populations ◽  
Carbon Assimilation ◽  
Ribulose Bisphosphate Carboxylase ◽  
Temporal Separation ◽  
Bisphosphate Carboxylase ◽  
Carbon And Nitrogen

ABSTRACT Diel periodicity in the expression of key genes involved in carbon and nitrogen assimilation in marine Synechococcus spp. was investigated in a natural population growing in the surface waters of a cyclonic eddy in the northeast Atlantic Ocean.Synechococcus sp. cell concentrations within the upper mixed layer showed a net increase of three- to fourfold during the course of the experiment (13 to 22 July 1991), the population undergoing approximately one synchronous division per day. Consistent with the observed temporal pattern of phycoerythrin (CpeBA) biosynthesis, comparatively little variation was found incpeBA mRNA abundance during either of the diel cycles investigated. In marked contrast, the relative abundance of transcripts originating from the genes encoding the large subunit of ribulose bisphosphate carboxylase/oxygenase (rbcL) and glutamine synthetase (glnA) showed considerable systematic temporal variation and oscillated during the course of each diel cycle in a reciprocal rhythm. Whereas activation of rbcL transcription was clearly not light dependent, expression of glnAappeared sensitive to endogenous changes in the physiological demands for nitrogen that arise as a natural consequence of temporal periodicity in photosynthetic carbon assimilation. The data presented support the hypothesis that a degree of temporal separation may exist between the most active periods of carbon and nitrogen assimilation in natural populations of marine Synecoccoccus spp.

DNA metabarcoding reveals fine scale geographical differences of consumed algae in the Galápagos marine iguanas (Amblyrhynchus cristatus)

2021 ◽  
pp. 1-10
Author(s):  
Sten Anslan ◽  
Denisse Dalgo ◽  
Timm Reinhardt ◽  
Nicolás Peñafiel ◽  
Juan Guayasamin ◽  
...  
Keyword(s):  
Algal Species ◽  
Marine Macroalgae ◽  
Rbcl Gene ◽  
Ribulose Bisphosphate Carboxylase ◽  
Geographical Differences ◽  
Bisphosphate Carboxylase ◽  
Amblyrhynchus Cristatus ◽  
Dna Metabarcoding ◽  
Feeding Activities ◽  
Marine Iguanas

Abstract Galápagos marine iguanas are primarily associated with the marine environment and show special nutritional adaptations. They are the only lizards worldwide that forage on marine macroalgae. Until now, consumed algae have been identified by direct observations during their feeding activities and microscopic identification in faeces samples. In this study, we use a novel DNA metabarcoding approach to identify consumed algal species from the faeces of marine iguanas. We developed primers for the ribulose-bisphosphate carboxylase (rbcL) gene and applied a metabarcoding approach to 25 individual faeces samples collected in four representative sites of two subspecies (Amblyrhynchus cristatus mertensi and A. c. godzilla), found in the San Cristóbal Island. We detected 18 consistently occurring macroalgal operational taxonomic units (OTUs). Most of the OTUs were assigned to Rhodophyta (red algae) and only one OTU to Chlorophyta (green algae). Despite the number of consumed algal species did not differ between two subspecies (OTU richness; P = 0.383), diet overlap level between A. c. mertensi and A. c. godzilla was low (Schoener index = 0.345), suggesting that both subspecies consumed different algal species in their natural environment. Further studies are needed to understand whether the difference of consumed algae reflects disparities in the abundance of algal species between sites, or whether iguanas of the two genetically differentiated subspecies prefer distinct algal species.

Phylogenetic analysis of Aquilaria Lam. (Thymelaeaceae) based on DNA barcoding

Holzforschung ◽  
2019 ◽  
Vol 73 (6) ◽  
pp. 517-523 ◽  
Author(s):  
Tingting Feng ◽  
Qiwei Li ◽  
Yesheng Wang ◽  
Simin Qiu ◽  
Mengling He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationship ◽  
Genetic Distances ◽  
Ribulose Bisphosphate Carboxylase ◽  
Good Discrimination ◽  
Bisphosphate Carboxylase ◽  
Close Match ◽  
Discrimination Ability ◽  
Illegal Harvesting ◽  
Overall Performance

AbstractAquilariaLam. is an important group of trees that produce agarwood, which is widely used for manufacturing medicine, perfumes and incense. The members of the genusAquilariaare close to being extinct due to illegal harvesting and are now protected in many countries. In this study, five DNA barcodes [internal transcribed spacer (ITS), maturase K (matK),psbA-trnH, ribulose bisphosphate carboxylase (rbcL) andtrnL-trnF] and their combinations were evaluated for the discrimination of the major (16 out of 21) species ofAquilariabased on three criteria: sequence variation, genetic distances and the discrimination ability. In addition, we attempted to determine the phylogenetic relationship betweenAquilariaandGyrinopsspecies using three phylogenetic analysis methods. We observed that the combination barcode ITS+trnL-trnF had a good discrimination ability based on the best match and best close match methods, provided more genetic information, and clearly indicated the comprehensive phylogenetic relationship between mostAquilariaandGyrinopsspecies. Considering the overall performance of these barcodes, the ITS+trnL-trnF is a suitable barcode for the identification ofAquilariaspecies.

scholarly journals An Integrated Approach for Efficient and Accurate Medicinal Cuscutae Semen Identification

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1410
Author(s):  
Inkyu Park ◽  
Sungyu Yang ◽  
Goya Choi ◽  
Byeong Cheol Moon ◽  
Jun-Ho Song
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Northeast Asia ◽  
Herbal Medicines ◽  
Integrated Approach ◽  
Rbcl Gene ◽  
Accurate Identification ◽  
Diagnostic Characteristics ◽  
Microscopic Techniques ◽  
Cuscuta Species

To guarantee the safety and efficacy of herbal medicines, accurate identification and quality evaluation are crucial. The ripe dried seeds of Cuscuta australis R.Br. and C. chinensis Lam. are known as Cuscutae Semen (CS) and are widely consumed in Northeast Asia; however, the seeds of other species can be misidentified as CS owing to morphological similarities, leading to misuse. In this report, we propose a multilateral strategy combining microscopic techniques with statistical analysis and DNA barcoding using a genus-specific primer to facilitate the identification and authentication of CS. Morphology-based identification using microscopy revealed that the useful diagnostic characteristics included general shape, embryo exudation, hairiness, and testa ornamentation, which were used to develop an effective identification key. In addition, we conducted DNA barcoding-based identification to ensure accurate authentication. A novel DNA barcode primer was produced from the chloroplast rbcL gene by comparative analysis using Cuscuta chloroplast genome sequences, which allowed four Cuscuta species and adulterants to be discriminated completely. Therefore, this investigation overcame the limitations of universal DNA barcodes for Cuscuta species with high variability. We believe that this integrated approach will enable CS to be differentiated from other species, thereby improving its quality control and product safety in medicinal markets.

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