scholarly journals Erratum to: Genomic classification of betanodavirus by molecular phylogenetic analysis of the coat protein gene

2013 ◽  
Vol 158 (7) ◽  
pp. 1595-1595
Author(s):  
C. P. Binesh ◽  
C. Greeshma ◽  
K. P. Jithendran
Keyword(s):  
Phylogenetic Analysis ◽  
Coat Protein ◽  
Coat Protein Gene ◽  
Protein Gene ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic

Redefining the generic limits of Winthemia (Diptera : Tachinidae)

2016 ◽  
Vol 30 (3) ◽  
pp. 274 ◽  
Author(s):  
Diego J. Inclán ◽  
John O. Stireman ◽  
Pierfilippo Cerretti
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Systematic Study ◽  
Type Species ◽  
Genetic Evidence ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
Phylogenetic Affinities

One of the major problems hindering the systematic study of tachinid flies is that genera are often poorly defined, making it difficult to unambiguously assign species among closely related genera. Within the tribe Winthemiini, an example of this problem is represented by the unstable classification of the Afrotropical species most recently classified as Smidtia capensis (Schiner). This species has been previously assigned to four different genera on the basis of limited examination and evidence. Here, we evaluate the identity and phylogenetic affinities of this species and other members of the tribe Winthemiini using morphological and molecular phylogenetic analysis. We demonstrate that S. capensis actually belongs to the genus Winthemia Robineau-Desvoidy. We also find that Winthemia is paraphyletic with respect to two monotypic genera, Crypsina (type species Crypsina prima Brauer & Bergenstamm) and Hemiwinthemia (type species Hemiwinthemia calva Villeneuve). On the basis of morphological and genetic evidence, we propose to extend the generic limits of Winthemia to include W. londti, sp. nov. (South Africa), W. capensis (Schiner), comb. nov. (South Africa), W. prima (Brauer & Bergenstamm), comb. nov. (China, Japan, Australia) and W. calva (Villeneuve), comb. nov. (D.R. Congo), thus synonymising with Winthemia the generic names Crypsina, syn. nov. and Hemiwinthemia, syn. nov.

Phylogenetic analysis of coat protein gene of BYDV-MAV strain from wheat

2013 ◽  
Vol 46 (14) ◽  
pp. 1747-1755
Author(s):  
Kamran Saleem ◽  
Shahid Hameed ◽  
Irfan Ul-Haque
Keyword(s):  
Phylogenetic Analysis ◽  
Coat Protein ◽  
Coat Protein Gene ◽  
Protein Gene

Novelties towards a phylogenetic infrageneric classification of Baccharis (Asteraceae, Astereae)

Phytotaxa ◽  
2016 ◽  
Vol 289 (3) ◽  
pp. 285 ◽  
Author(s):  
GUSTAVO HEIDEN ◽  
JOSÉ RUBENS PIRANI
Keyword(s):  
Phylogenetic Analysis ◽  
New Taxa ◽  
New World ◽  
Molecular Phylogenetic Analysis ◽  
New Combinations ◽  
Infrageneric Classification ◽  
Molecular Phylogenetic ◽  
Genus Two

Names of new taxa, new combinations and names at new rank are proposed for subgenera and sections in Baccharis to move towards a phylogenetic infrageneric classification of this New World genus. Two earlier segregated genera and two previously recognised sections are moved to the subgeneric rank (as B. subgen. Coridifoliae, B. subgen. Heterothalamus, B. subgen. Heterothalamulopsis, and B. subgen. Oblongifoliae). Three new combinations and/or names at new rank are proposed for the following sections: B. sect. Axillares (assigned to B. subgen. Baccharis), B. sect. Heterothalamulopsis (assigned to B. subgen. Heterothalamulopsis), and B. sect. Pluricephalae (assigned to B. subgen Coridifoliae). Four new sections are described to accommodate taxa not corresponding to any previously described section: B. sect. Andina and B. sect. Illinitae (assigned to B. subgen. Baccharis), B. sect. Bradeanae (assigned to B. subgen. Heterothalamus), and B. sect. Polifoliae (assigned to B. subgen. Molina). All taxa here recognized correspond to monophyletic groups based on highly supported clades in a recent molecular phylogenetic analysis.

scholarly journals Presence and molecular characterization of alfalfa mosaic virus on tobacco in Serbia

2011 ◽  
Vol 26 (3) ◽  
pp. 229-243 ◽  
Author(s):  
Ivana Stankovic ◽  
Ana Vucurovic ◽  
Aleksandra Bulajic ◽  
Danijela Ristic ◽  
Janos Berenji ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Coat Protein ◽  
Mosaic Virus ◽  
Coat Protein Gene ◽  
Protein Gene ◽  
Rna Extraction ◽  
Alfalfa Mosaic Virus ◽  
Lower Percentage ◽  
Rt Pcr ◽  
Plant Host

Three-year investigation of the presence and distribution of tobacco viruses in Serbia revealed that Alfalfa mosaic virus (AMV) appeared every year with different frequency in tobacco crops. During 2008, the presence of AMV was detected in most of the tested samples (58.82%) and it was the second most common compared to all other viruses which presence was confirmed in Serbia. In 2006 and 2007, AMV was detected in a significantly lower percentage (2.80% and 13.64%, respectively). This study showed that Alfalfa mosaic virus was more commonly found in multiple infections with two, three or even four detected viruses. Single infections were detected only in 2006, in one tobacco field in the locality of Futog. During this investigation, a rapid and simple protocol was optimized and developed for molecular detection of AMV in tobacco leaves, using primers CPAMV1/CPAMV2 and commercially available kits for total RNA extraction as well as for RT-PCR (reverse transcription - polymerase chain reaction). Using RT-PCR and these primers that flank the AMV coat protein gene, a DNA fragment of 751 bp was amplified, sequenced, and compared with the sequences available in GenBank database. The sequence of isolate 196-08 (GenBank Acc. No. FJ527749) proved to be identical at the nucleotide level of 99 to 93% with those from other parts of the world. Phylogenetic analysis of 27 isolates based on 528 bp sequences of the coat protein gene did not show correlation of the isolates with their geographic origin or plant host and showed that these isolates fall into four molecular groups of strains. Serbian AMV isolate from tobacco belongs to group IV, the group that includes most of the isolates selected for phylogenetic analysis.

scholarly journals Phylogenetic analysis of coat protein gene of tomato mosaic virus isolates circulating in Ukraine

2019 ◽  
Vol 77 (1) ◽  
pp. 44-50
Author(s):  
I. Pozhylov ◽  
T. Rudnieva ◽  
T. Shevchenko ◽  
O. Shevchenko ◽  
V. Tsvigun
Keyword(s):  
Phylogenetic Analysis ◽  
Coat Protein ◽  
Mosaic Virus ◽  
Coat Protein Gene ◽  
Protein Gene ◽  
Tomato Mosaic Virus ◽  
Chinese Isolate ◽  
Plant Host ◽  
High Level ◽  
Virus Isolates

Tomato mosaic virus (ToMV) induces highly infectious disease of vegetables, whereas use of virus-contaminated seed may lead to complete yield loss. This work was aimed at studying phylogenetic relationships of Ukrainian tomato isolates of ToMV with its known isolates by comparing nucleotide sequence of coat protein gene. ELISA, TEM, RT-PCR, sequence analysis using MEGA 5 software, and statistical methods. cDNAs of two novel Ukrainian isolates ToMV-ukr-5 and ToMV-ukr-10 corresponding to coat protein (CP) gene were sequenced and compared with other published ToMV sequences. On the constructed phylogenetic tree, ToMV isolates were grouped into two separate clusters. In addition to novel Ukrainian isolates ToMV-ukr-5 and ToMV-ukr-10, the first and larger cluster contained nearly all virus isolates used in this study with high (96-98,9 %) level of homology to Ukrainian isolates. The larger cluster was clearly separated into two subclusters: one grouping isolates with over 96,7 % identity with Ukranian isolates, and the other containing three strains and isolates with 96,1 % identity (tomato isolate SL-1, strain camellia isolated from a decorative plant, and isolate Dahlemense DSMZ PV-0135).Two novel Ukrainian isolates ToMV-ukr-5 and ToMV-ukr-10 have been isolated from tomato plants cultivated in open field conditions in different regions of Ukraine. Phylogenetic analysis confirmed high identity of Ukrainian isolates between themselves and with other published ToMV sequences. Ukrainian isolates were most homologous (>98 %) to Brazilian isolate Hemerocallis, to Chinese isolate G2, and to the following tomato isolates: AH4, Queensland, ToMV-tom and Ls-K, S14, and FERA_160205. The high level of homology was traced independently of the source of virus isolation, its plant host and their geography.

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