scholarly journals Phenotypic Characterization and Molecular Phylogenetic Relationship of Erysiphe necator Infecting Grapes (Vitis vinifera)

2019 ◽  
pp. 1-10
Author(s):  
Marimuthu Karthick ◽  
Ayyanar Kamalakannan ◽  
Varagur Ganesan Malathi ◽  
Vaikuntavasan Paranidharan ◽  
Uthandi Sivakumar ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Cytochrome B ◽  
Tamil Nadu ◽  
Gene Segment ◽  
Cytochrome B Gene ◽  
Phenotypic Characterization ◽  
Infected Leaf ◽  
Cyt B ◽  
Erysiphe Necator ◽  
Microscopic Studies

Grapes powdery mildew is caused by the most destructive pathogen Erysiphe necator leading to severe yield losses around the world.  In order to study the phenotypic and molecular characters, the powdery mildew infected leaf samples were collected from eight different places in Coimbatore and Theni districts in the state of Tamil Nadu India. The identity of the pathogen as E. necator was established by microscopic studies and the isolates were further confirmed molecularly by amplification of Internal transcribed spacer (ITS) and Cytochrome b gene (Cyt b). Further molecular confirmation was obtained by characterizing Cytochrome b. An amplicon size of ~ 367 and ~ 470 bp were obtained from amplification with Uncin144 and Uncin511 and Cyt b F and Cyt b R gene primers respectively. The identity for cyt b gene segment was 96 to 98%, similarity with E. necator isolates deposited in NCBI genbank (KY418048.1, KY418049.1). A phylogenetic tree was constructed on the basis of nucleotide sequence of cytochrome b gene of the study isolates as well as E. necator and other Erysiphe species in NCBI database. From the tree it was evident that the study isolates from Tamil Nadu, India were very distinct from other E. necator isolates deposited in NCBI genbank database.

scholarly journals Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh

2019 ◽  
Vol 5 (1) ◽  
pp. 25-30
Author(s):  
RA Begum ◽  
MT Alam ◽  
H Jahan ◽  
MS Alam
Keyword(s):  
Genetic Diversity ◽  
Cytochrome B ◽  
Tissue Sample ◽  
Sequence Similarity ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Multiple Sequence ◽  
Mitochondrial Cytochrome B ◽  
Cyt B Gene

Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to finalize a length of 510 nucleotides which was submitted to NCBI genbank database. Nucleotide BLAST of this sequence at NCBI resulted 100% sequence similarity with L. calbasu sequence of the same region of cyt-b gene. Multiple sequence alignment of the sequence with seven more Labeo species sequences revealed 120 polymorphic sites, which have been mark of diversity among the species and might be used in molecular identification of the Labeo species. A constructed phylogenetic tree has shown relationship among the Labeo species. This research demonstrated the usefulness of mitochondrial DNA-based approach in species identification. Further, the data will provide appropriate background for studying genetic diversity within-species of the Labeo species in general and of L. calbasu in particular. J. Biodivers. Conserv. Bioresour. Manag. 2019, 5(1): 25-30

scholarly journals Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

2018 ◽  
Vol 20 (1) ◽  
pp. 17-22
Author(s):  
TETY HARTATIK ◽  
DWI NUR HAPPY HARIYONO ◽  
YUDI ADINATA
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Gene Sequences ◽  
Cattle Breeds ◽  
Cyt B Gene

Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds.

scholarly journals Occurrence and Molecular Characterization of Strobilurin Resistance in Cucumber Powdery Mildew and Downy Mildew

2001 ◽  
Vol 91 (12) ◽  
pp. 1166-1171 ◽  
Author(s):  
H. Ishii ◽  
B. A. Fraaije ◽  
T. Sugiyama ◽  
K. Noguchi ◽  
K. Nishimura ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Downy Mildew ◽  
Cytochrome B ◽  
Rapid Development ◽  
Single Point ◽  
Cytochrome B Gene ◽  
Single Point Mutation ◽  
Mitochondrial Cytochrome B ◽  
Control Failure ◽  
Pathogen Dna

Between 1998 and 1999, control failure of powdery mildew (Podosphaera fusca) and downy mildew (Pseudoperonospora cubensis) by the strobilurin fungicides azoxystrobin and kresoxim-methyl was observed in cucumber-growing areas of Japan. Results from inoculation tests carried out on intact cucumber plants and leaf disks clearly showed the distribution of pathogen isolates highly resistant to azoxystrobin and kresoximmethyl. Fragments of the fungicide-targeted mitochondrial cytochrome b gene were polymerase chain reaction amplified from total pathogen DNA and their sequences analyzed to elucidate the molecular mechanism of resistance. A single point mutation (GGT to GCT) in the cytochrome b gene, resulting in substitution of glycine by alanine at position 143, was found in resistant isolates of downy mildew. This substitution in cytochrome b seemed to result in high resistance to strobilurins in this pathogen. The same mutation was found in some but not all resistant isolates of powdery mildew. This study suggests that a mutation at position 143 in the target-encoding gene, resulting in an amino acid substitution, was probably a major cause of the rapid development of high strobilurin resistance in these two pathogens.

Phylogenetic Affi nities of the Globodera pallida Inferred From the mtDNA cyt-b Gene Polymorphism

2014 ◽  
Vol 1 (2) ◽  
pp. 3-11
Author(s):  
L. Pylypenko ◽  
V. Blok ◽  
M. Phillips
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variability ◽  
Cytochrome B ◽  
Software Package ◽  
Cytochrome B Gene ◽  
Mitochondrial Cytochrome ◽  
Cyt B ◽  
Sources Of Resistance ◽  
Mitochondrial Cytochrome B ◽  
Mitochondrial Cytochrome B Gene

The mitochondrial cytochrome b gene marker was used to investigate the genetic variability of G. pallida populations of different origins and selection on three sources of resistance. Aim. To sequence the mitochon- drial gene cyt-b and to clarify its application as a genetic marker for intraspecifi c genetic diversity study, phylogenetic analysis and nematode virulence assessment. Methods. The cysts of nematodes were used as a source for DNA extraction. Polymerase chain reaction was performed using the specifi c primers of INRAcytbL and INRAcytbR, followed by the amplifi ed product sequencing. The nucleotide sequences were processed and aligned using software PhredPhrap, CONSED and Clustal W. MEGA-4, DNADIST software package; while PHYLIP and Arlequin were used for statistical analysis. Phylogenetic trees construction and visualization were performed using the software package PHYLIP and TREEVIEW. Results. The phylogenetic analysis based on mitochondrial cytochrome b gene sequences has showed that the Ukrainian populations of G. pallida were almost identical to other populations from the Europe. Limited genetic variability was observed between G. pallida populations distributed in the Europe and Ukraine, accounting for 82.3 per cent (P < 0.05) of the genetic variability inferred from the mitochondrial cytochrome b gene polymorphisms within the populations studied. G. pallida populations selected on three sources of resistance were similar but not identical indicat- ing that changes in mtDNA haploid type frequency had taken place as a result of the selection regime, but the marker used was not yet applicable for virulence monitoring. Conclusions. The obtained data prove the hypothesis that G. pallida populations in Ukraine are the result of the continuing spread of the species within the Europe and not the consequence of additional introduction from the South America.

scholarly journals Population diversity of striped snakehead, Channa striata (Bloch, 1793) from Bekasi, West Java and Barito Kuala, South Kalimantan using Cytochrome B gene

2021 ◽  
Vol 21 (1) ◽  
pp. 61-73
Author(s):  
Gita Kusuma Rahayu ◽  
Dedy Duryadi Solihin ◽  
Nurlisa A Butet
Keyword(s):  
Genetic Distance ◽  
Cytochrome B ◽  
Southern China ◽  
Genetic Relationships ◽  
Population Diversity ◽  
Cytochrome B Gene ◽  
Cyt B ◽  
Channa Striata ◽  
Commercially Important ◽  
Cyt B Gene

Channa striata or striped snakehead is one of species from family Channidae that widely distributed from India, Southern China to Southeast Asia including Indonesia. It is a commercially important freshwater fish because of its taste and health benefits. High demand of this species trigger many efforts to increase its production, one of them is genetic monitoring. This study used complete Cytochrome b gene sequence of mtDNA for determining genetic variation in wild population of C. striata. C. striata samples (n=31) from two different locations in Indonesia were amplified and analyzed using MEGA ver 7.0. Sequences of 1140 bp complete cyt b gene revealed the presence of 2 haplotypes with 1137 bp conserved sites and 3 bp variable sites (0,26%). Overlapping haplotype was observed in samples from Bekasi, however there were only one haplotype in samples from South Borneo. Interspecies genetic were analysed with species from Genebank and showed that C. striata from Indonesia has close genetic relationships with C. striata from Borneo-Indonesia (MN057164.1) with genetic distance 0%. This study also revealed that C. striata from Indonesia were phylogenetically distinct with C. striata from China with 9,2%K2P genetic distance. Complete cyt b gene has been proven for assessing phylogenetic relationships and population diversity of C. striata in Indonesia.

scholarly journals Molecular Characterization of Pyraclostrobin Resistance and Structural Diversity of the Cytochrome b Gene in Botrytis cinerea from Apple

2012 ◽  
Vol 102 (3) ◽  
pp. 315-322 ◽  
Author(s):  
Y. N. Yin ◽  
Y. K. Kim ◽  
C. L. Xiao
Keyword(s):  
Botrytis Cinerea ◽  
Point Mutation ◽  
Cytochrome B ◽  
Genetic Background ◽  
Structural Diversity ◽  
Polymerase Chain Reaction Analysis ◽  
Cytochrome B Gene ◽  
Type I ◽  
Cyt B ◽  
Allele Specific

Botrytis cinerea isolates obtained from apple orchards were screened for resistance to the quinone outside inhibitor (QoI) pyraclostrobin. Of the 220 isolates tested, 43 (19.5%) were resistant to pyraclostrobin. Analysis of partial sequences of the cytochrome b gene (cyt b) in five pyraclostrobin-resistant (PR) and five pyraclostrobin-sensitive (PS) isolates showed that PR isolates harbored the point mutation leading to the substitution of glycine by alanine at codon position 143 in cyt b (G143A). Two pairs of allele-specific primers were designed based on this point mutation, and allele-specific polymerase chain reaction analysis with these primers showed that all 73 PR isolates (including 30 collected from decayed apple fruit) harbored the G143A mutation but PS isolates did not. Six pairs of primers were designed to analyze the presence of various introns in cyt b. There were six types (I to VI) of cyt b present in 247 isolates of B. cinerea collected from various apple-production areas in Washington State. Of the 247 isolates, 23 had type I cyt b containing all four introns (Bcbi-67/68, Bcbi-131/132, Bcbi-143/144, and Bcbi-164), 176 had type II cyt b containing three introns (Bcbi-67/68, Bcbi-131/132, and Bcbi-164), six had type III cyt b containing two introns (Bcbi-67/68 and Bcbi-131/132), one had type IV cyt b containing two introns (Bcbi-131/132 and Bcbi-164), one had type V cyt b containing only the Bcbi-131/132 intron, and 40 had type VI cyt b containing no introns. This is the first report of types III to VI cyt b present in B. cinerea. All 73 PR isolates did not carry the Bcbi-143/144 intron in cyt b. Of the 247 isolates tested, >90% did not carry the Bcbi-143/144 intron in cyt b, suggesting that B. cinerea populations from apple pose a high inherent risk for the development of resistance to QoIs because the presence of this intron in cyt b prevents the occurrence of G143A-mediated resistance. Analysis of genetic background based on three microsatellite primers showed that PR isolates originated from different lineages, and there was no correlation between cyt b types (I, II, and III) and the genetic background of the isolates; however, isolates carrying type VI cyt b might originate from the same lineage.

scholarly journals Halal Food Safety: PCR Based Detection of Porcine DNA in Imported Chocolate

2021 ◽  
pp. 61-71
Author(s):  
Khaleda Akter ◽  
Mahfuza Khandaker ◽  
Md. Abdul Aziz ◽  
Shahriar Mahmud ◽  
Md. Neaz Morshed ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Detection System ◽  
Free Food ◽  
Cytochrome B Gene ◽  
Agarose Gel ◽  
Cyt B ◽  
Two Samples ◽  
Halal Food ◽  
Primer Sets ◽  
Processed Products

Halal food and food products consumption is a major part of living in Muslim community. Pork meat or meat items are not considered halal in Muslim countries and consumers. Ensuring pork-free food items is a challenge for the food industry and exporters to Muslim nations. This study aims to detect porcine DNA in imported chocolate products in Bangladesh for halal safety assurance. The imported chocolate samples were collected from various multi shops in Dhaka. Polymerase chain reaction (PCR) method is used in our research to detect the porcine DNA. Two primer sets are used for the detection of porcine mitochondrial cyt-b (cytochrome-b) gene fragments in chocolate samples. To visualize the amplified DNA, agarose gel (1%) was used. After electrophoresis, DNA band in agarose gel indicated that the gene fragments are amplified properly. In our research, out of 42 chocolate samples, only 2 samples were found positive. The chocolate samples were branded as Wild Berry Flavor Chocolate and Cadbury Milk Tray Chocolate. In comparison with the positive pork sample, these two samples also containing the 165bp and 359bp fragment of the porcine cytochrome b gene. We reported that chocolate products contain the pork contamination were not labeled as halal. While other samples that did not have any halal logo originated from outside Bangladesh and imported also showed negative result. The present study established the DNA-based porcine detection system based on mitochondrial cyt-b that is viable in highly processed products. It can be used in the halal certification process to determine the pork items presence in food and halal safety. Our research also reported that imported chocolates should halal certify before release into the market.

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