Insights on genetic diversity and phylogenetic analysis of Hop stunt viroid (HSVd) population from symptomatic citrus tree in Tunisia

2011 ◽  
Vol 5 (21) ◽  
Author(s):  
Hamdi I
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Citrus Tree ◽  
Stunt Viroid ◽  
Hop Stunt Viroid

Molecular characterization and phylogenetic analysis of hop stunt viroid isolates from sweet cherry in China

2019 ◽  
Vol 154 (3) ◽  
pp. 705-713
Author(s):  
Li Xu ◽  
Jiawei Wang ◽  
Xin Chen ◽  
Dongzi Zhu ◽  
Hairong Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Sweet Cherry ◽  
Stunt Viroid ◽  
Hop Stunt Viroid

Genetic diversity of hop stunt viroid from symptomatic and asymptomatic citrus trees in Iran

2019 ◽  
Vol 167 (9) ◽  
pp. 484-489
Author(s):  
Ramtin Vamenani ◽  
Heshmatollah Rahimian ◽  
Seyyed Mohammad Alavi ◽  
Ali Pakdin Parizi ◽  
Tarlan Mirza Razzaz
Keyword(s):  
Genetic Diversity ◽  
Stunt Viroid ◽  
Hop Stunt Viroid ◽  
Citrus Trees

scholarly journals Multiplex detection, distribution, and genetic diversity of Hop stunt viroid and Citrus exocortis viroid infecting citrus in Taiwan

2015 ◽  
Vol 12 (1) ◽  
pp. 11 ◽  
Author(s):  
Chun-Yi Lin ◽  
Meng-Ling Wu ◽  
Tang-Long Shen ◽  
Hsin-Hung Yeh ◽  
Ting-Hsuan Hung
Keyword(s):  
Genetic Diversity ◽  
Multiplex Detection ◽  
Stunt Viroid ◽  
Citrus Exocortis Viroid ◽  
Hop Stunt Viroid

Incidence and genetic diversity of Peach latent mosaic viroid and Hop stunt viroid in stone fruits in Serbia

2007 ◽  
Vol 120 (2) ◽  
pp. 167-176 ◽  
Author(s):  
B. Mandic ◽  
M. Al Rwahnih ◽  
A. Myrta ◽  
G. Gomez ◽  
V. Pallás
Keyword(s):  
Genetic Diversity ◽  
Stone Fruits ◽  
Stunt Viroid ◽  
Hop Stunt Viroid

scholarly journals Assessment of Genetic Diversity and Symbiotic Efficiency of Selected Rhizobia Strains Nodulating Lentil (Lens culinaris Medik.)

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 15
Author(s):  
Badreddine Sijilmassi ◽  
Abdelkarim Filali-Maltouf ◽  
Hassan Boulahyaoui ◽  
Aymane Kricha ◽  
Kenza Boubekri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Rhizobium Leguminosarum ◽  
Sequence Similarity ◽  
P Value ◽  
Rrna Gene ◽  
Research Station ◽  
Symbiotic Efficiency ◽  
Rhizobium Strains

A total of 14 Rhizobium strains were isolated from lentil accessions grown at the ICARDA experimental research station at Marchouch in Morocco and used for molecular characterization and symbiotic efficiency assessment. Individual phylogenetic analysis using the 16S rRNA gene, house-keeping genes rpoB, recA, and gyrB, and symbiotic genes nodD and nodA along with Multilocus Sequence Analysis (MLSA) of the concatenated genes (16S rRNA-rpoB-recA-gyrB) was carried out for the identification and clustering of the isolates. The symbiotic efficiency of the strains was assessed on three Moroccan lentil cultivars (Bakria, Chakkouf, and Zaria) based on the number of nodules, plant height, plant dry weight, and total nitrogen content in leaves. The results showed that the individual phylogenetic analysis clustered all the strains into Rhizobium laguerreae and Rhizobium leguminosarum with sequence similarity ranging from 94 to 100%, except one strain which clustered with Mesorhizobium huakuii with sequence similarity of 100%. The MLSA of the concatenated genes and the related percentages of similarity clustered these strains into two groups of Rhizobium species, with one strain as a new genospecies when applying the threshold of 96%. For symbiotic efficiency, the Bakria variety showed the best association with 10 strains compared to its non-inoculated control (p-value ≤ 0.05), followed by Chakkouf and Zaria. The present study concluded that the genetic diversity and the symbiotic efficiency of Rhizobium strains appeared to be mainly under the control of the lentil genotypes.

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

Insights into the genetic diversity and the phylogenetic analysis of Tunisian isolates of Tomato chlorosis virus

2014 ◽  
Vol 43 (1) ◽  
pp. 87-96 ◽  
Author(s):  
Charfeddine Gharsallah ◽  
Amina Ben Halima ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Tomato Chlorosis Virus

scholarly journals SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

2021 ◽  
Author(s):  
Juliana D Siqueira ◽  
Livia R Goes ◽  
Brunna M Alves ◽  
Pedro S de Carvalho ◽  
Claudia Cicala ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cancer Patients ◽  
Disease Severity ◽  
Healthcare Workers ◽  
Viral Population ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Consensus Sequences ◽  
Vulnerable Patients

Abstract Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.

Sign in / Sign up

Export Citation Format

Share Document