Phylogenetic relationships and genetic diversity of Monilinia spp. isolated in Poland based on housekeeping‐ and pathogenicity‐related genes sequence analysis

2021 ◽  
Author(s):  
A. Poniatowska ◽  
M. Michalecka ◽  
J. Puławska
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Relationships

In silico Prediction and Designing of Potential siRNAs to be Used as Antivirals Against SARS-CoV-2

2021 ◽  
Vol 27 ◽  
Author(s):  
Sayed Sartaj Sohrab ◽  
Sherif Aly El-Kafrawy ◽  
Aymn T. Abbas ◽  
Leena H. Bajrai ◽  
Esam Ibraheem Azhar
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Relationships ◽  
In Silico ◽  
Full Genome ◽  
In Silico Prediction ◽  
High Sequence Identity ◽  
Minor Parent ◽  
Sequence Identity ◽  
The City

Background:: The unusual pneumonia outbreak that originated in the city of Wuhan, China in December 2019 was found to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. Methods:: In this work, we have performed an in silico design and prediction of potential siRNAs based on genetic diversity and recombination patterns, targeting various genes of SARS-CoV-2 for antiviral therapeutics. We performed extensive sequence analysis to analyze the genetic diversity and phylogenetic relationships, and to identify the possible source of virus reservoirs and recombination patterns, and the evolution of the virus as well as we designed the siRNAs which can be used as antivirals against SARS-CoV-2. Results:: The sequence analysis and phylogenetic relationships indicated high sequence identity and closed clusters with many types of coronavirus. In our analysis, the full-genome of SARS-CoV-2 showed the highest sequence (nucleotide) identity with SARS-bat-ZC45 (87.7%). The overall sequence identity ranged from 74.3% to 87.7% with selected SARS viruses. The recombination analysis indicated the bat SARS virus is a potential recombinant and serves as a major and minor parent. We have predicted 442 siRNAs and finally selected only 19 functional, and potential siRNAs. Conclusions:: The siRNAs were predicted and selected based on their greater potency and specificity. The predicted siRNAs need to be validated experimentally for their effective binding and antiviral activity.

Genetic Diversity of HIV-1 Non-B Strains in Sicily: Evidence of Intersubtype Recombinants by Sequence Analysis ofgag,pol, andenvGenes

2007 ◽  
Vol 23 (9) ◽  
pp. 1131-1138 ◽  
Author(s):  
Fabio Tramuto ◽  
Filippa Bonura ◽  
Anna Maria Perna ◽  
Salvatrice Mancuso ◽  
Alberto Firenze ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Hiv 1

scholarly journals Assessment of genetic diversity and phylogenetic relationships of endangered endemic plant Barbarea integrifolia DC. (Brassicaceae) in Turkey

2014 ◽  
Vol 38 ◽  
pp. 1169-1181 ◽  
Author(s):  
Ertuğrul FİLİZ ◽  
Etem OSMA ◽  
Ali KANDEMİR ◽  
Hüseyin TOMBULOĞLU ◽  
Güzin TOMBULOĞLU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationships ◽  
Endemic Plant

scholarly journals Sequence Analysis and Classification of Apparent Recombinant Begomoviruses Infecting Tomato in the Nile and Mediterranean Basins

2005 ◽  
Vol 95 (5) ◽  
pp. 549-555 ◽  
Author(s):  
C. M. Fauquet ◽  
S. Sawyer ◽  
A. M. Idris ◽  
J. K. Brown
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Relationships ◽  
Tomato Yellow Leaf ◽  
Viral Diseases ◽  
Yellow Leaf ◽  
Recombination Hotspots ◽  
Molecular Biodiversity ◽  
Leaf Curl Virus ◽  
Leaf Curl

Numerous whitefly-transmitted viral diseases of tomato have emerged in countries around the Nile and Mediterranean Basins the last 20 years. These diseases are caused by monopartite geminiviruses (family Gemini viridae) belonging to the genus Begomovirus that probably resulted from numerous recombination events. The molecular biodiversity of these viruses was investigated to better appreciate the role and importance of recombination and to better clarify the phylogenetic relationships and classification of these viruses. The analysis partitioned the tomato-infecting begomoviruses from this region into two major clades, Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus. Phylogenetic and pairwise analyses together with an evaluation for gene conversion were performed from which taxonomic classification and virus biodiversity conclusions were drawn. Six recombination hotspots and three homogeneous zones within the genome were identified among the tomatoinfecting isolates and species examined here, suggesting that the recombination events identified were not random occurrences.

scholarly journals Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers

2020 ◽  
Author(s):  
R. H. Sammour ◽  
M. A. Karam ◽  
Y. S. Morsi ◽  
R. M. Ali
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Rapa ◽  
Phylogenetic Relationships ◽  
Fixation Index ◽  
Distribution Area ◽  
Enzyme Analysis ◽  
Breeding Programs ◽  
Expected Heterozygosity ◽  
Wide Range

Abstract The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

scholarly journals DNA BARCODING USING COI GENE SEQUENCES OF WILD BETTA FIGHTING FISH FROM INDONESIA: PHYLOGENY, STATUS AND DIVERSITY

2020 ◽  
Vol 26 (2) ◽  
pp. 97
Author(s):  
Melta R. Fahmi ◽  
Eni Kusrini ◽  
Erma P. Hayuningtiyas ◽  
Shofihar Sinansari ◽  
Rudhy Gustiano
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Gene Sequence ◽  
Ornamental Fish ◽  
Coi Gene ◽  
Tree Construction ◽  
In The Wild ◽  
Blast Program

The wild betta fish is a potential ornamental fish export commodity normally caught by traders or hobbyists in the wild. However, the population of wild betta in nature has declined and become a threat for their sustainability. This research was conducted to analyze the genetic diversity, phylogenetic relationships, and molecular identification through DNA COI gene sequence of Indonesian wild betta fish. A total of 92 wild betta fish specimens were collected in this study. Amplification of COI genes was carried out using Fish F1, Fish R1, Fish F2, and Fish R2 primers. The genetic diversity and phylogenetic relationships were analyzed using MEGA version 5 software program. Species identification of the specimen was conducted using BLAST program with 98-100% similarity value of the DNA sequences to indicate the same species. Phylogenetic tree construction showed seven monophyletic clades and showed that Betta smaragdina was the ancestral species of genus Betta in Indonesian waters. Genetic distance among species ranged from 0.02 to 0.30, whereas intra-species genetic distance ranged from 0 to 6.54.

Sign in / Sign up

Export Citation Format

Share Document