scholarly journals Identification of two distinct begomoviruses infecting Malvastrum coromandelianum

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Yaqin Wang ◽  
Xinyue Zhang ◽  
Tao Hu ◽  
Xueping Zhou
Keyword(s):  
Yunnan Province ◽  
Phylogenetic Analyses ◽  
Yellow Vein ◽  
Universal Primers ◽  
Genome Sequences ◽  
Sequence Alignments ◽  
Total Dna ◽  
Malvastrum Coromandelianum ◽  
Complete Viral Genome ◽  
Virus Isolates

AbstractMalvastrum coromandelianum is a common weed plant frequently found around agricultural fields. Three virus isolates (Y249, Y278 and Y281) were obtained from M. coromandelianum with yellow vein symptoms in Honghe and Baoshan, Yunnan Province, China. Specific 500 bp products were amplified from total DNA extracts using universal primers for members of the genus Begomovirus. The complete viral genome sequences of both Y278 and Y281 were determined to be 2743 nucleotides, and that of Y249 was determined to be 2740 nucleotides. Sequence alignments and phylogenetic analyses support the proposal of creating new species in the genus Begomovirus, for which the name malvastrum yellow vein Baoshan virus (MaYVBsV) is proposed for Y278 and Y281, and malvastrum yellow vein Honghe virus (MaYVHhV) is proposed for Y249.

scholarly journals Complete Genome Sequences of Chikungunya Viruses Isolated from Plasma Specimens Collected from Haitians in 2014

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Sarah K. White ◽  
J. Glenn Morris ◽  
Maha A. Elbadry ◽  
Valery Madsen Beau De Rochars ◽  
Bernard A. Okech ◽  
...  
Keyword(s):  
Human Plasma ◽  
Complete Genome ◽  
Chikungunya Virus ◽  
Phylogenetic Analyses ◽  
Genomic Sequences ◽  
Genome Sequences ◽  
Chikungunya Fever ◽  
Asian Lineage ◽  
Virus Isolates

ABSTRACT Ten chikungunya virus isolates from human plasma collected in Haiti from May to August 2014, in the midst of a chikungunya fever outbreak, were fully sequenced. The resulting genomic sequences are nearly identical, and phylogenetic analyses indicate they belong to the Asian lineage of the virus.

scholarly journals Molecular Variation of Satellite DNAβ Molecules Associated with Malvastrum yellow vein virus and Their Role in Pathogenicity

2008 ◽  
Vol 74 (6) ◽  
pp. 1909-1913 ◽  
Author(s):  
Wei Guo ◽  
Tong Jiang ◽  
Xian Zhang ◽  
Guixin Li ◽  
Xueping Zhou
Keyword(s):  
Petunia Hybrida ◽  
Yunnan Province ◽  
Geographical Origin ◽  
Geographical Location ◽  
Yellow Vein ◽  
Molecular Variation ◽  
Infectious Clones ◽  
Malvastrum Coromandelianum ◽  
Geographical Locations ◽  
Limited Sequence

ABSTRACT Previous studies have found that the diversity of begomovirus-associated DNAβ satellites is related to host and geographical origin. In this study, we have cloned and sequenced 20 different isolates of DNAβ molecules associated with Malvastrum yellow vein virus (MYVV) isolated from Malvastrum coromandelianum plants in different geographical locations of Yunnan Province, China. Analyses of their molecular variation indicate that the satellites are clustered together according to their geographical location but that they have only limited sequence diversity. Infectivity tests using infectious clones of MYVV and its associated DNAβ molecule indicate that MYVV DNAβ is indispensable for symptom induction in Nicotiana benthamiana, N. glutinosa, Petunia hybrida, and M. coromandelianum plants. Furthermore, we showed that MYVV interacts functionally with heterologous DNAβ molecules in N. benthamiana plants.

scholarly journals GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

2018 ◽  
Author(s):  
Pablo Vinuesa ◽  
Luz Edith Ochoa-Sánchez ◽  
Bruno Contreras-Moreira
Keyword(s):  
Core Genome ◽  
Phylogenetic Analyses ◽  
Superior Performance ◽  
Biological Research ◽  
Species Trees ◽  
Genome Sequences ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Pan Genome ◽  
Link Type

AbstractThe massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.We demonstrate the practical utility of the software by analyzing 170Stenotrophomonasgenome sequences available in RefSeq and 10 new complete genomes of environmentalS. maltophiliacomplex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 14 misclassified RefSeq genome sequences, 12 of them labeled asS. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license athttps://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available athttps://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Correct names of two cultivated mushrooms from the genus Pleurotus in China

Phytotaxa ◽  
2016 ◽  
Vol 260 (1) ◽  
pp. 36 ◽  
Author(s):  
SAMANTHA C. KARUNARATHNA ◽  
PETER E. MORTIMER ◽  
JIE CHEN ◽  
GUO-JIE LI ◽  
MAO-QIANG HE ◽  
...  
Keyword(s):  
Papua New Guinea ◽  
Yunnan Province ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characters ◽  
Universal Primers ◽  
Jiangxi Province ◽  
Rdna Sequence Data ◽  
Cultivated Mushrooms

Two collections of Pleurotus giganteus and one collection of Pl. tuber-regium from Mengsong in Yunnan Province, China, and commercially grown strains of Pl. giganteus and Pl. tuber-regium from Jiangxi Province, China were identified using macro and micro morphological characters. The identification was also confirmed by phylogenetic analysis using Internal Transcribed Spacer (ITS) universal primers. Phylogenetic analyses of ITS-1-5.8S-ITS2 rDNA sequence data of collections of Pl. giganteus from Sri Lanka (epitype), Thailand, Malaysia and Pl. tuber-regium from Australia, Cameroon, China, Ghana, Malaysia, Nigeria, and Papua New Guinea using maximum likelihood, maximum parsimony and Bayesian inference showed that Pl. giganteus forms a strongly supported clade with Thai and Chinese Pl. giganteus, while the Chinese Pl. tuber-regium clade with Cameroon, Ghana and Nigeria samples with strong support. In this paper, we clarify the identifications of the two edible cultivated mushrooms, Pl. giganteus and Pl. tuber-regium in China.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

scholarly journals Respiratory syncytial virus B sequence analysis reveals a novel early genotype

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juan C. Muñoz-Escalante ◽  
Andreu Comas-García ◽  
Sofía Bernal-Silva ◽  
Daniel E. Noyola
Keyword(s):  
Molecular Markers ◽  
Respiratory Syncytial Virus ◽  
Maximum Likelihood ◽  
Respiratory Infections ◽  
Phylogenetic Analyses ◽  
Detection Methods ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Individual Gene ◽  
Syncytial Virus

AbstractRespiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

scholarly journals Whole-Genome Sequences of Influenza A(H1N1)pdm09 Virus Isolates from Kerala, India

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Sara Jones ◽  
Raji Prasad ◽  
Anjana S. Nair ◽  
Sanjai Dharmaseelan ◽  
Remya Usha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Analysis ◽  
Influenza A ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
H1n1 Pandemic ◽  
Genome Sequences ◽  
Influenza A H1n1 ◽  
Virus Isolates ◽  
New Mutations

ABSTRACT We report here the whole-genome sequence of six clinical isolates of influenza A(H1N1)pdm09, isolated from Kerala, India. Amino acid analysis of all gene segments from the A(H1N1)pdm09 isolates obtained in 2014 and 2015 identified several new mutations compared to the 2009 A(H1N1) pandemic strain.

scholarly journals Molecular and Biological Characterisation of Turnip mosaic virus Isolates Infecting Poppy (Papaver somniferum and P. rhoeas) in Slovakia

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 430 ◽  
Author(s):  
Miroslav Glasa ◽  
Katarína Šoltys ◽  
Lukáš Predajňa ◽  
Nina Sihelská ◽  
Slavomíra Nováková ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Turnip Mosaic Virus ◽  
Biological Assays ◽  
Genetic Complexity ◽  
The World ◽  
History Of ◽  
Virus Isolates

In recent years, the accumulated molecular data of Turnip mosaic virus (TuMV) isolates from various hosts originating from different parts of the world considerably helped to understand the genetic complexity and evolutionary history of the virus. In this work, four complete TuMV genomes (HC9, PK1, MS04, MS15) were characterised from naturally infected cultivated and wild-growing Papaver spp., hosts from which only very scarce data were available previously. Phylogenetic analyses showed the affiliation of Slovak Papaver isolates to the world-B and basal-B groups. The PK1 isolate showed a novel intra-lineage recombination pattern, further confirming the important role of recombination in the shaping of TuMV genetic diversity. Biological assays indicated that the intensity of symptoms in experimentally inoculated oilseed poppy are correlated to TuMV accumulation level in leaves. This is the first report of TuMV in poppy plants in Slovakia.

A global phylogenetic analysis of Japanese tonsil-derived Epstein–Barr virus strains using viral whole-genome cloning and long-read sequencing

2021 ◽  
Author(s):  
Misako Yajima ◽  
Risako Kakuta ◽  
Yutaro Saito ◽  
Shiori Kitaya ◽  
Atsushi Toyoda ◽  
...  
Keyword(s):  
Viral Genome ◽  
Epstein Barr Virus ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Regional Distribution ◽  
Genome Sequences ◽  
Barr Virus ◽  
Endemic Areas ◽  
Epstein Barr ◽  
Genome Heterogeneity

Epstein–Barr virus (EBV) establishes lifelong latent infection in the majority of healthy individuals, while it is a causative agent for various diseases, including some malignancies. Recent high-throughput sequencing results indicate that there are substantial levels of viral genome heterogeneity among different EBV strains. However, the extent of EBV strain variation among asymptomatically infected individuals remains elusive. Here, we present a streamlined experimental strategy to clone and sequence EBV genomes derived from human tonsillar tissues, which are the reservoirs of asymptomatic EBV infection. Complete EBV genome sequences, including those of repetitive regions, were determined for seven tonsil-derived EBV strains. Phylogenetic analyses based on the whole viral genome sequences of worldwide non-tumour-derived EBV strains revealed that Asian EBV strains could be divided into several distinct subgroups. EBV strains derived from nasopharyngeal carcinoma-endemic areas constitute different subgroups from a subgroup of EBV strains from non-endemic areas, including Japan. The results could be consistent with biased regional distribution of EBV-associated diseases depending on the different EBV strains colonizing different regions in Asian countries.

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