Complete nucleotide sequence of a Polish strain of Peanut stunt virus (PSV-P) that is related to but not a typical member of subgroup I.

2008 ◽  
Vol 55 (4) ◽  
pp. 731-739 ◽  
Author(s):  
Aleksandra Obrepalska-Steplowska ◽  
Marta Budziszewska ◽  
Henryk Pospieszny
Keyword(s):  
Phylogenetic Analyses ◽  
The Other ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Satellite Rna ◽  
Protein Coding ◽  
Typical Member ◽  
Rna Analysis ◽  
Nucleotide Homology ◽  
Peanut Stunt Virus

Peanut stunt virus (PSV) is a common legume pathogen present worldwide. It is also infectious for many other plants including peanut and some vegetables. Viruses of this species are classified at present into three subgroups based on their serology and nucleotide homology. Some of them may also carry an additional subviral element - satellite RNA. Analysis of the full genome sequence of a Polish strain - PSV-P - associated with satRNA was performed and showed that it may be classified as a derivative of the subgroup I sharing 83.9-87.9% nucleotide homology with other members of this subgroup. A comparative study of sequenced PSV strains indicates that PSV-P shows the highest identity level with PSV-ER or PSV-J depending on the region used for analysis. Phylogenetic analyses, on the other hand, have revealed that PSV-P is related to representatives of the subgroup I to the same degree, with the exception of the coat protein coding sequence where PSV-P is clustered together with PSV-ER.

scholarly journals The complete chloroplast genome sequences of five pinnate-leaved Primula species and phylogenetic analyses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Wenbin Xu ◽  
Boshun Xia ◽  
Xinwei Li
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
The Other ◽  
Trna Genes ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Noncoding Sequences ◽  
Chloroplast Genomes ◽  
Rna Genes

AbstractThe six pinnate-leaved species are a very particular group in the genus Primula. In the present paper, we sequenced, assembled and annotated the chloroplast genomes of five of them (P. cicutarrifolia, P. hubeiensis, P. jiugongshanensis, P. merrilliana, P. ranunculoides). The five chloroplast genomes ranged from ~ 150 to 152 kb, containing 113 genes (four ribosomal RNA genes, 29 tRNA genes and 80 protein-coding genes). The six pinnate-leaved species exhibited synteny of gene order and possessed similar IR boundary regions in chloroplast genomes. The gene accD was pseudogenized in P. filchnerae. In the chloroplast genomes of the six pinnate-leaved Primula species, SSRs, repeating sequences and divergence hotspots were identified; ycf1 and trnH-psbA were the most variable markers among CDSs and noncoding sequences, respectively. Phylogenetic analyses showed that the six Primula species were separated into two distant clades: one was formed by P. filchnerae and P. sinensis and the other clade was consisting of two subclades, one formed by P. hubeiensis and P. ranunculoides, the other by P. merrilliana, P. cicutarrifolia and P. jiugongshanensis. P. hubeiensis was closely related with P. ranunculoides and therefore it should be placed into Sect. Ranunculoides. P. cicutarrifolia did not group first with P. ranunculoides but with P. merrilliana, although the former two were once united in one species, our results supported the separation of P. ranunculoides from P. cicutarrifolia as one distinct species.

scholarly journals Complete Genomic Sequence of Goose-Origin Reovirus from China

2012 ◽  
Vol 86 (18) ◽  
pp. 10257-10257 ◽  
Author(s):  
Tao Yun ◽  
Weicheng Ye ◽  
Zheng Ni ◽  
Liu Chen ◽  
Bin Yu ◽  
...  
Keyword(s):  
New Species ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Full Genome Sequence ◽  
Avian Reovirus ◽  
Complete Genomic Sequence ◽  
Full Genome ◽  
Established Species ◽  
A New Species ◽  
Complete Genomic

We report the full-genome sequence of a goose-origin reovirus (GRV) strain 03G from Zhejiang Province, China. This is the first report of the complete genomic sequence (segments 1 to 10) of GRV. Phylogenetic analyses of the sequence suggest that GRV 03G represents a new species distinct from other established species within the avian reovirus (ARV) group of orthoreoviruses.

scholarly journals Full Genome Evolutionary Studies of Wheat Streak Mosaic-Associated Viruses Using High-Throughput Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Carla Dizon Redila ◽  
Savannah Phipps ◽  
Shahideh Nouri
Keyword(s):  
Mosaic Virus ◽  
Rna Sequencing ◽  
Great Plains ◽  
High Throughput ◽  
Phylogenetic Analyses ◽  
Full Genome Sequence ◽  
Mixed Infections ◽  
Full Genome ◽  
Genome Sequences ◽  
Resistance Breaking

Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.

Peanut stunt virus satellite RNA: Analysis of sequences that affect symptom attenuation in tobacco

Virology ◽  
1992 ◽  
Vol 189 (2) ◽  
pp. 668-677 ◽  
Author(s):  
R.A. Naidu ◽  
G.B. Collins ◽  
S.A. Ghabrial
Keyword(s):  
Satellite Rna ◽  
Rna Analysis ◽  
Peanut Stunt Virus

scholarly journals Mitochondrial genome of Chinese grass shrimp, Palaemonetes sinensis and comparison with other Palaemoninae species

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yingying Zhao ◽  
Xiaochen Zhu ◽  
Yingdong Li ◽  
Zhibin Han ◽  
Weibin Xu ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Grass Shrimp ◽  
The Other ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Basic Characteristics ◽  
Heavy Strand ◽  
Light Strand ◽  
Order Comparison

AbstractThe mitogenome of Chinese grass shrimp, Palaemonetes sinensis, was determined through Illumina sequencing, and the basic characteristics and gene arrangement were analyzed. The mitogenome of P. sinensis was 15955 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and one control region, with tightly packed. 33 of these genes were encoded on the heavy strand, and the remainders encoded on the light strand. The composition of P. sinensis mitogenome presented a strong A + T bias, which account for 66.7%. All PCGs were initiated by a canonical ATN codon, except nad5, which was initiated by GTG. The termination codons of the PCGs were TAA, TAG and T–. The secondary structures of 22 tRNAs of P. sinensis had the typical clover structure, except of trnS1 owing to the lack of dihydroxyuridine (DHU) arm. Gene order comparison of P. sinensis and previously-sequenced Palaemoninae revealed a unique translocation between trnT and trnP in Macrobrachium. The phylogenetic analyses showed that three Exopalaemon species formed a monophyletic group and then clustered with two Palaemon species and P. sinensis successively whereas Macrobrachium clustered with Palaemon capensis in the other clade.

scholarly journals Revisiting the phylogeny of phylum Ctenophora: a molecular perspective

F1000Research ◽  
2017 ◽  
Vol 5 ◽  
pp. 2881
Author(s):  
Luis A. Arteaga-Figueroa ◽  
Valentina Sánchez-Bermúdez ◽  
Nicolás D. Franco-Sierra
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Fluorescent Protein ◽  
Phylogenetic Analyses ◽  
Meta Analysis ◽  
Tyrosine Aminotransferase ◽  
The Other ◽  
Published Data ◽  
Undescribed Species ◽  
Protein Coding

The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora (inside and outside the phylum), are not totally understood. Several loci (protein coding and ribosomal RNA) from organisms belonging to this phylum are currently available on public databases (e.g. GenBank). Previous studies take into account the ribosomal data and the protein data separately. In this study, we perform a meta-analysis of previously published data together. The published data of this phylum have been used in previous phylogenetic analyses inside the phylum and consist in nuclear ribosomal data, such as 18S, 5.8S, ITS1, ITS2, and protein-coding markers such as NFP (non-fluorescent protein). Previous studies concentrate their efforts toward the analyses of ribosomal data or the protein-coding marker separately. Now we take into account these markers together for an upgrade of the phylogenetic analysis of this phylum. We also test several markers such as 28S, IPNS, Tyrosine aminotransferase and HLH domaincontaining protein for the improvement of the study. This markers were analyzed by Bayesian Inference (MrBayes) and Maximum Likelihood (Garli and RAxML), individually and concatenated, showing improvement in the orders placement and presenting new interesting relationship between the paraphyletic order Cydippida and the other ctenophores. These analyses also include sequences from undescribed species that have been reported in GenBank which improved the alignment matrices and support values of some nodes. Adding the undescribed species suggests interesting and well supported clades, the posterior identification of this species would led to an improvement on the ctenophore’s taxonomy.

scholarly journals Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Meng-Yuan Zhao ◽  
Qing-Bo Huo ◽  
Yu-Zhou Du
Keyword(s):  
Ribosomal Rna ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Stem Loop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Noncoding Control Region ◽  
Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

scholarly journals Diversity and evolution of the Cydia pomonella granulovirus

2009 ◽  
Vol 90 (3) ◽  
pp. 662-671 ◽  
Author(s):  
Karolin E. Eberle ◽  
Samy Sayed ◽  
Mohammedreza Rezapanah ◽  
Sharareh Shojai-Estabragh ◽  
Johannes A. Jehle
Keyword(s):  
Phylogenetic Analyses ◽  
Cydia Pomonella ◽  
Codling Moth ◽  
Open Reading Frames ◽  
The Other ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Protein Coding ◽  
Major Genome ◽  
Cydia Pomonella Granulovirus

Eight new field isolates of Cydia pomonella granulovirus (CpGV) originating in Iran and Georgia and one English CpGV isolate were analysed for restriction fragment length polymorphisms (RFLPs) and by partial genome amplification and sequencing. According to the observed RFLPs, most of the predominant genotypes of these isolates could be assigned to those present in previously found isolates originating from Mexico (CpGV-M), England (CpGV-E) and Russia (CpGV-R). We suggest that these isolates should be designated genome A, B and C types, respectively. A fourth genome type was identified in three isolates and is designated D type. The isolates with A, B and D type genomes contained four open reading frames (ORFs) (ORF63–ORF66) not present in C type genomes. The lack of these ORFs in other granuloviruses suggests that the C type genome is evolutionarily ancestral to the other genome types. The B and D type genomes contained an additional insertion of a non-protein coding region of 0.7 kb, which was at different genome locations. Analysis of the partial gene sequences of late expression factor 8 (lef-8), lef-9 and polyhedrin/granulin (polh/gran) genes revealed single nucleotide polymorphisms (SNPs) that corresponded to the RFLP types. Phylogenetic analyses based on these SNPs corroborated the proposed ancestry of the C type genome. C type viruses were also less virulent to neonate codling moth larvae than the other virus types. In conclusion, the known diversity of CpGV isolates can be described by four major genome types, which appear to exist in different isolates as genotype mixtures.

scholarly journals Full-Genome Sequence of an Enterovirus 71 Strain Isolated from a Throat Swab from a Child with Severe Hand-Foot-and-Mouth Disease in Changzhou, China, in 2017

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Qiong Li ◽  
Feng-Ming Wang ◽  
Xu-Jian Mao ◽  
Ping Yao ◽  
Xia Jiang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Throat Swab ◽  
Phylogenetic Analyses ◽  
Enterovirus 71 ◽  
Foot And Mouth Disease ◽  
Human Enterovirus ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Human Enterovirus 71 ◽  
Full Length Genome

ABSTRACT The full-length genome sequence of a human enterovirus 71 (EV71) strain (EV71/CZTN01/CHN/2017) was isolated from a throat swab from a child in Changzhou, China, in 2017. According to the phylogenetic analyses, the full-genome sequence in this study belongs to sub-subgenotype C4a.

scholarly journals Genomic Islands in the Full-Genome Sequence of an NAD-Hemin-Independent Avibacterium paragallinarum Strain Isolated from Peru

2019 ◽  
Vol 8 (16) ◽  
Author(s):  
Luis Tataje-Lavanda ◽  
Ángela Montalván ◽  
Ricardo Montesinos ◽  
Vladimir Morales-Erasto ◽  
Mirko Zimic-Peralta ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Genomic Islands ◽  
Full Genome Sequence ◽  
Full Genome ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Avibacterium Paragallinarum

Here, we report the full-genome sequence of an NAD-hemin-independent Avibacterium paragallinarum serovar C-2 strain, FARPER-174, isolated from layer hens in Peru. This genome contained 12 potential genomic islands that include ribosomal protein-coding genes, a nadR gene, hemocin-coding genes, sequences of fagos, an rtx operon, and drug resistance genes.

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