scholarly journals Molecular tools for utilization of mitochondrial diversity in faba bean (Vicia faba)

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 745-762
Author(s):  
Jelena Aleksic ◽  
Jovanka Miljus-Djukic ◽  
Zivko Jovanovic ◽  
Branko Tomic ◽  
Bojana Banovic
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Related Species ◽  
In Silico ◽  
Pcr Amplification ◽  
Intraspecific Variability ◽  
Pcr Primers ◽  
Molecular Tools ◽  
Universal Primer ◽  
Centre Of Origin

We performed in silico PCR analyses utilizing complete mitochondrial (mtDNA) genome sequences of faba bean (Vicia faba) and two related species, Vigna angularis and Vigna radiata, currently available in GenBank, to infer whether 15 published universal primer pairs for amplification of all 14 cis-spliced introns in genes of NADH subunits (nad genes) are suitable for V. faba and related species. Then, we tested via PCR reactions whether seven out of 15 primer pairs would generate PCR products suitable for further manipulation in 16 genotypes of V. faba representing all botanical varieties of this species (major, minor, equina and subsp. paucijuga) of various levels of improvement (traditional and improved cultivars) originating from Europe, Africa, Asia and south America. We provide new PCR primers for amplification of nad1 intron 2/3 in V. faba, and demonstrate intraspecific variability in primary nucleotide sequences at this locus. Based on outcomes of both in silico predictions and PCR amplification, we report a set of PCR primers for amplification of five introns in nad genes that are promising molecular tools for future phylogeographic and other studies in this species for which unambiguous data on wild ancestors, centre of origin and domestication are lacking.

scholarly journals Identification of Cladosporium sp. Fungi by in- silico RFLP-PCR

2020 ◽  
Vol 17 (1(Suppl.)) ◽  
pp. 0220 ◽  
Author(s):  
Mohammad Ibrahim Khalil
Keyword(s):  
In Silico ◽  
Restriction Enzymes ◽  
Pathogenic Fungi ◽  
Pcr Primers ◽  
Agarose Gel ◽  
Airborne Spores ◽  
Universal Primer ◽  
Unique Restriction ◽  
Conserved Region ◽  
Short Time

Cladosporium sp. plays an important role in human health, it is one of the pathogenic fungi which cause allergy and asthma and most frequently isolated from airborne spores.  In this study, a couple of universal PCR primers were designed to identify the pathogenic fungi Cladosporium sp. according to conserved region 5.8S, 18S and 28S subunit ribosomal RNA gene in Cladosporium species. In silico RFLP-PCR were used to identify twenty-four Cladosporium strains. The results showed that the universal primer has the specificity to amplify the conserved region in 24 species as a band in virtual agarose gel. They also showed that the RFLP method is able to identify three Cladosporium species by specific and unique restriction enzymes for each one. These species are Cl. halotorenas by the two unique enzymes BsaXI and MobII, the other species is Cl. colrandse by two enzymes BccI and BtsCI, while the third species is Cl. aciculare by one enzyme BceAI. Each enzyme forms two bands in virtual agarose gel as a results of cutting the DNA by the enzyme, where the rest twenty – two species share more than one restriction enzymes. This method is active and rapid for identifying Cladosporium genus and three species by computational bases methods before applying it in the lab for more accuracy, efficiency, and specificity of designed primer to get good results in a short time.

scholarly journals Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia

2021 ◽  
Author(s):  
Masayuki K. Sakata ◽  
Mone U. Kawata ◽  
Atsushi Kurabayashi ◽  
Takaki Kurita ◽  
Masatoshi Nakamura ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Environmental Dna ◽  
Pcr Primers ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Biodiversity Monitoring ◽  
Natural Ecosystems ◽  
Universal Primer ◽  
Primer Sets

Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians ecological traits (e.g., nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding-analysis of extra-organismal DNA released into the environment-allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160-311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata, and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set Amph16S had the highest resolution among the tested sets. Finally, we applied Amph16S to actual metabarcoding and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.

scholarly journals New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

2018 ◽  
Author(s):  
Daniel Marquina ◽  
Anders F. Andersson ◽  
Fredrik Ronquist
Keyword(s):  
In Silico ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
Distinct Species ◽  
Taxonomic Resolution ◽  
Reference Database ◽  
Protein Coding ◽  
Gene Coi ◽  
Reference Databases ◽  
Meaningful Measure

AbstractInsect metabarcoding has been mainly based on PCR amplification of short fragments within the ‘barcoding region’ of the gene COI. However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ECOPRIMERS and DEGEPRIME) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.

Acquisition of desiccation tolerance in faba bean (Vicia Faba) as affected by maturity stages, harvested organ type, and drying method

2018 ◽  
Vol 51 (1) ◽  
Author(s):  
Abdul Majeed Baloch ◽  
Tongtong Zhai ◽  
Abdul Wahid Baloch ◽  
Zhihua Liu ◽  
Xingtang Yang ◽  
...  
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Desiccation Tolerance ◽  
Drying Method ◽  
Maturity Stages ◽  
Organ Type

Assessment of soil fertility augmenting potential of faba bean (Vicia faba L.) germplasm and their performance

2016 ◽  
Vol 3 (3) ◽  
Author(s):  
Anil Kumar Singh ◽  
Rashmi Yadav ◽  
M.K. Meena ◽  
Y.J. Khan
Keyword(s):  
Soil Fertility ◽  
Vicia Faba ◽  
Faba Bean ◽  
Climate Scenario ◽  
Climatic Conditions ◽  
Third Place ◽  
Changing Climate ◽  
Vicia Faba L ◽  
Unique Ability

Faba bean (Vicia faba L.) maintain third place with respect to area and production among legume. Its unique ability to excel under all most all type of climatic conditions, it is one of the best performing crops under changing climate scenario. Its soil fertility augmenting potential and their performance was evaluated for two years with 73 accessions collected from Bihar. This study provides glimpses of scope and magnitude of soil fertility improving potential of faba bean (Vicia faba L.)

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