Development of chloroplast-specific microsatellite markers for molecular characterization of alloplasmic lines and phylogenetic analysis in wheat

2013 ◽  
Vol 133 (1) ◽  
pp. 12-18 ◽  
Author(s):  
Ram Sewak S. Tomar ◽  
Rupesh K. Deshmukh ◽  
Bhojaraja Naik K. ◽  
Shiv Mangal S. Tomar ◽  
Vinod
Keyword(s):  
Phylogenetic Analysis ◽  
Microsatellite Markers ◽  
Molecular Characterization ◽  
Alloplasmic Lines

Morphological, histological and molecular characterization of Myxidium cf. rhodei infecting the kidney of Rutilus rutilus

2020 ◽  
Vol 141 ◽  
pp. 39-46
Author(s):  
MD Dorjievna Batueva ◽  
X Pan ◽  
J Zhang ◽  
X Liu ◽  
W Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rutilus Rutilus ◽  
Longitudinal Axis ◽  
Suture Line ◽  
Present Species ◽  
Supplementary Data

In the present study, we provide supplementary data for Myxidium cf. rhodei Léger, 1905 based on morphological, histological and molecular characterization. M. cf. rhodei was observed in the kidneys of 918 out of 942 (97%) roach Rutilus rutilus (Linnaeus, 1758). Myxospores of M. cf. rhodei were fusiform with pointed ends, measuring 12.7 ± 0.1 SD (11.8-13.4) µm in length and 4.6 ± 0.1 (3.8-5.4) µm in width. Two similar pear-shaped polar capsules were positioned at either ends of the longitudinal axis of the myxospore: each of these capsules measured 4.0 ± 0.1 (3.1-4.7) µm in length and 2.8 ± 0.1 (2.0-4.0) µm in width. Polar filaments were coiled into 4 to 5 turns. Approximately 18-20 longitudinal straight ridges were observed on the myxospore surface. The suture line was straight and distinctive, running near the middle of the valves. Histologically, the plasmodia of the present species were found in the Bowman’s capsules, and rarely in the interstitium of the host. Phylogenetic analysis revealed that M. cf. rhodei was sister to M. anatidum in the Myxidium clade including most Myxidium species from freshwater hosts.

scholarly journals Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258318
Author(s):  
Marta Antas ◽  
Monika Olech ◽  
Anna Szczotka-Bochniarz
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Economic Losses ◽  
High Morbidity ◽  
Antigenic Analysis ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

Molecular characterization of the first human G15 rotavirus strain of zoonotic origin from the bovine species

2021 ◽  
Vol 102 (4) ◽  
Author(s):  
Takeshi Tsugawa ◽  
Yoshiki Fujii ◽  
Yusuke Akane ◽  
Saho Honjo ◽  
Kenji Kondo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Human Infection ◽  
Potential Reservoir ◽  
Group A Rotaviruses ◽  
Paediatric Outpatient ◽  
Group A ◽  
Human Infections ◽  
Bovine Species

Group A rotaviruses (RVAs) infect a wide variety of mammalian and avian species. Animals act as a potential reservoir to RVA human infections by direct virion transmission or by contributing genes to reassortants. Here, we report the molecular characterization of a rare human RVA strain Ni17-46 with a genotype G15P[14], isolated in Japan in 2017 during rotavirus surveillance in a paediatric outpatient clinic. The genome constellation of this strain was G15-P[14]-I2-R2-C2-M2-A13-N2-T9-E2-H3. This is the first report of an RVA with G15 genotype in humans, and sequencing and phylogenetic analysis results suggest that human infection with this strain has zoonotic origin from the bovine species. Given the fact that this strain was isolated from a patient with gastroenteritis and dehydration symptoms, we must take into account the virulence of this strain in humans.

Molecular characterization of small and medium segments of Crimean-Congo hemorrhagic fever virus in Turkey

2020 ◽  
Vol 15 (4) ◽  
pp. 247-254
Author(s):  
Murat Karamese ◽  
Erkan Ozmen ◽  
Hakan Aydin ◽  
Mehmet Ozkan Timurkan ◽  
Mesud Fakirullahoglu
Keyword(s):  
Infectious Disease ◽  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Molecular Characterization ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
Crimean Congo Hemorrhagic Fever ◽  
Hemorrhagic Fever Virus ◽  
Relationship Of

Aim: The objective was to investigate the genotypic relationship of S and M segments in Crimean-Congo hemorrhagic fever virus (CCHFV) by phylogenetic analysis in 25 patients from seven endemic cities in Turkey. Materials & methods: A total of 25 samples from patients with CCHF were included between 2012 and 2015. Phylogenetic tree analyses were inferred using MEGA version-6.0 and distances were calculated by Kimura’s 2-parameter. Results: Phylogenetic analysis showed that all isolated viruses (n = 25) were in the predicted clades such as clade V- Europe-1 regarding both S and M segments of the CCHFV. Conclusion: Further epidemiological, molecular and phylogenic studies should be performed in both reservoir animals/vectors and humans to determine the incidence of tick-borne infectious disease and to help to develop vaccines for prevention of the disease.

scholarly journals Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wild Ruminant ◽  
Genome Sequence Analysis ◽  
Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

scholarly journals Microsatellite markers for identification of a group of italian olive accessions

2009 ◽  
Vol 66 (5) ◽  
pp. 685-690 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Francesca Stefanizzi ◽  
Amelia Salimonti ◽  
Rosanna Falabella ◽  
Enzo Perri
Keyword(s):  
Microsatellite Markers ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Olea Europaea ◽  
Fruit Trees ◽  
Ssr Primers ◽  
Olive Cultivars ◽  
Olea Europaéa

Cultivar characterization for fruit trees certification requires fast, efficient and reliable techniques. Microsatellite markers (SSR) were used in the molecular characterization of 23 genotypes of Olea europaea subsp europaea. The DNA from the olive cultivars was analyzed using nine pre-selected SSR primers (GAPU59, GAPU71A, GAPU71B, GAPU103A, UDO99-01, UDO99-12, UDO99-28 and UDO99-39) and revealed 29 alleles, which allowed each genotype to be identified. In the dendrogram, the nine primers allowed the 23 olive genotypes to be grouped into subgroups corresponding to the same cultivar denominations. SSR markers proved to be efficient and reliable for the molecular characterization of Italian olive cultivars.

scholarly journals Molecular characterization of Lotus corniculatus cultivars using transferable microsatellite markers

2011 ◽  
Vol 38 (3) ◽  
pp. 453-461 ◽  
Author(s):  
Diego Alem ◽  
Rafael Narancio ◽  
Paola Díaz Dellavalle ◽  
Mónica Rebuffo ◽  
Rodrigo Zarza ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Molecular Characterization ◽  
Lotus Corniculatus

scholarly journals Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 830 ◽  
Author(s):  
Yuliya Kleschenko ◽  
Danyil Grybchuk ◽  
Nadezhda S. Matveeva ◽  
Diego H. Macedo ◽  
Evgeny N. Ponirovsky ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cutaneous Leishmaniasis ◽  
Molecular Characterization ◽  
Leishmania Major ◽  
Geographical Origin ◽  
Rna Virus ◽  
Viral Sequences

Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.

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