scholarly journals Identification and Molecular Characterization of Nuclear Citrus leprosis virus, a Member of the Proposed Dichorhavirus Genus Infecting Multiple Citrus Species in Mexico

2015 ◽  
Vol 105 (4) ◽  
pp. 564-575 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Jonathan Shao ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Infected Plant ◽  
Amino Acid Sequences ◽  
N Gene ◽  
Infected Leaf ◽  
N Protein ◽  
A Genome ◽  
Citrus Leprosis

Citrus leprosis is one of the most destructive diseases of Citrus spp. and is associated with two unrelated virus groups that produce particles primarily in either the cytoplasm or nucleus of infected plant cells. Symptoms of leprosis, including chlorotic spots surrounded by yellow haloes on leaves and necrotic spots on twigs and fruit, were observed on leprosis-affected mandarin and navel sweet orange trees in the state of Querétaro, Mexico. Serological and molecular assays showed that the cytoplasmic types of Citrus leprosis virus (CiLV-C) often associated with leprosis symptomatic tissues were absent. However, using transmission electron microscopy, bullet-shaped rhabdovirus-like virions were observed in the nuclei and cytoplasm of the citrus leprosis-infected leaf tissues. An analysis of small RNA populations from symptomatic tissue was carried out to determine the genome sequence of the rhabdovirus-like particles observed in the citrus leprosis samples. The complete genome sequence showed that the nuclear type of CiLV (CiLV-N) present in the samples consisted of two negative-sense RNAs: 6,268-nucleotide (nt)-long RNA1 and 5,847-nt-long RNA2, excluding the poly(A) tails. CiLV-N had a genome organization identical to that of Orchid fleck virus (OFV), with the exception of shorter 5′ untranslated regions in RNA1 (53 versus 205 nt) and RNA2 (34 versus 182 nt). Phylogenetic trees constructed with the amino acid sequences of the nucleocapsid (N) and glycoproteins (G) and the RNA polymerase (L protein) showed that CiLV-N clusters with OFV. Furthermore, phylogenetic analyses of N protein established CiLV-N as a member of the proposed genus Dichorhavirus. Reverse-transcription polymerase chain reaction primers for the detection of CiLV-N were designed based on the sequence of the N gene and the assay was optimized and tested to detect the presence of CiLV-N in both diseased and symptom-free plants.

scholarly journals Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution

2020 ◽  
Author(s):  
Ilias Georgakopoulos-Soares ◽  
Ofer Yizhar Barnea ◽  
Ioannis Mouratidis ◽  
Martin Hemberg ◽  
Nadav Ahituv
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Significant Proportion ◽  
Scoring Function ◽  
Amino Acid Sequences ◽  
Dna Fingerprints ◽  
Functional Categories ◽  
Coding Sequences ◽  
A Genome ◽  
Genomic Characterization

AbstractNullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be that they have a detrimental impact on an organism. Here, we identified all possible nullomers and nullpeptides in the genomes and proteomes of over thirty species and show that a significant proportion of these sequences are under negative selection. We assign nullomers to different functional categories (coding sequences, exons, introns, 5’UTR, 3’UTR and promoters) and show that nullomers from coding sequences and promoters are most likely to be selected against. Utilizing variants in the human population, we annotate variant-associated nullomers, highlighting their potential use as DNA ‘fingerprints’. Phylogenetic analyses of nullomers and nullpeptides across evolution shows that they could be used to build phylogenetic trees. Our work provides a catalog of genomic and proteome derived absent k-mers, together with a novel scoring function to determine their potential functional importance. In addition, it shows how these unique sequences could be used as DNA ‘fingerprints’ or for phylogenetic analyses.

scholarly journals Characterization of a Novel Emaravirus Affecting Ash Species (Fraxinus spp.) in Europe

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1574
Author(s):  
Thomas R. Gaskin ◽  
Max Tischendorf ◽  
Ines Günther ◽  
Marius Rehanek ◽  
Carmen Büttner ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Leaf Tissue ◽  
Spherical Particles ◽  
Infected Leaf ◽  
Rt Pcr ◽  
Glycoprotein Precursor ◽  
A Genome ◽  
Leaf Deformation ◽  
Novel Virus

We identified a novel virus in diseased European ash (Fraxinus excelsior) and manna ash (F. ornus) trees exhibiting chlorotic ringspots, mottle and leaf deformation such as curling and shoestring symptoms. High-throughput sequencing (HTS, Illumina RNASeq) of total RNA isolated from diseased leaf material in combination with RT-PCR-based amplification techniques and Sanger sequencing determined five complete genome segments, each encoding a single open reading frame. Sequence analyses of RNA1–RNA5 revealed a genome organization typical for emaraviruses, i.e., (i) conserved and complementary terminal 5′and 3′termini of each genome segment (ii) proteins showing significant homologies to the RNA-dependent RNA polymerase (RdRP) encoded by RNA1, the glycoprotein precursor (GPP) encoded by RNA2, the viral nucleocapsid protein (N, RNA3), the movement protein (MP, RNA4), and a protein of 26 kDA (P26, RNA5) highly similar to proteins of unknown function encoded by other emaraviruses. Furthermore, we identified spherical particles (double-membrane bodies, DMB) of different sizes (70–80 nm in diameter) which are typical for emaraviruses exclusively in virus-infected leaf tissue exhibiting mottle and leaf deformation. Sequence comparison and phylogenetic analyses confirmed the identified novel virus as a new member of the genus Emaravirus. We established a species-specific RT-PCR detection protocol and could associate the observed disease symptoms with the infection of the novel emaravirus in F. excelsior and F. ornus. Therefore, we propose the name ash shoestring-associated emaravirus (ASaV). Investigation of ASaV-infected sample trees originating from different locations in Switzerland, Germany, Italy and Sweden provided a wide geographical distribution of the virus in affected ash species. To our knowledge, this is the first confirmation of an emaravirus affecting ash tree species with shoestring symptoms of leaves in Europe.

scholarly journals Using nucleocapsid proteins to investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses

2020 ◽  
Author(s):  
Noah Avery Schuster
Keyword(s):  
Nucleocapsid Protein ◽  
Vaccine Development ◽  
Close Association ◽  
Phylogenetic Analyses ◽  
N Gene ◽  
Nucleocapsid Proteins ◽  
Nucleocapsid Gene ◽  
N Protein ◽  
Global Pandemic ◽  
The Relationship

An initial outbreak of coronavirus disease 2019 (COVID-19) in China has resulted in a massive global pandemic causing well over 16,500,000 cases and 650,000 deaths worldwide. The virus responsible, SARS-CoV-2, has been found to possess a very close association with Bat-CoV RaTG13 and Pangolin-CoV MP789. The nucleocapsid protein can serve as a decent model for determining phylogenetic, evolutionary, and structural relationships between coronaviruses. Therefore, this study uses the nucleocapsid gene and protein to further investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses. Sequence and phylogenetic analyses have revealed the nucleocapsid gene and protein in SARS-CoV-2 are both closely related to those found in Bat-CoV RaTG13 and Pangolin-CoV MP789. Evidence of recombination was detected within the N gene, along with the presence of a double amino acid insertion found in the N-terminal region. Homology modeling for the N-Terminal Domain revealed similar structures but distinct electrostatic surfaces and topological variations in the β-hairpin that likely reflect specific adaptive functions. In respect to SARS-CoV-2, two amino acids (S37 and A267) were found to exist only in its N protein, along with an extended β-hairpin that bends towards the nucleotide binding site. Collectively, this study strengthens the relationship among SARS-CoV-2, Bat-CoV RaTG13, and Pangolin-CoV MP789, providing additional insights into the structure and adaptive nature of the nucleocapsid protein found in these coronaviruses. Furthermore, these data will enhance our understanding of the complete history behind SARS-CoV-2 and help assist in antiviral and vaccine development.

scholarly journals Differences of nucleotide and amino acid sequences of nucleoprotein (N) gene between wild-type measles virus and vaccine virus in Indonesia

2008 ◽  
Vol 48 (2) ◽  
pp. 81
Author(s):  
Made Setiawan ◽  
Agus Sjahrurachman ◽  
Fera Ibrahim ◽  
Agus Suwandono
Keyword(s):  
Amino Acid ◽  
Measles Virus ◽  
Protein Analysis ◽  
Rna Replication ◽  
Vaccine Virus ◽  
Amino Acid Sequences ◽  
N Gene ◽  
Wild Type ◽  
N Protein ◽  
Nucleoprotein N

Background Measles virus is a member of genus morbiliviruswhich belongs to family paramyxovirus with negative, single-strand RNA genome. RNA is packed by nucleocapsid (N) protein.The N protein is very important for RNA replication andtranslation. Abnormality in N protein will induce abnormality invirus replication.Objective This study aimed to explore the differences ofnucleotide sequence of N gene and amino acid sequences of Nprotein between wild-type measles virus (G2, G3 and D9) andvaccine virus (CAM-70, Schwarz and Edmonston-wt)Methods The exctraction and amplification of the gene wereconducted in the laboratory using biomolecular technology. Thegene and protein analysis were conducted using the bioinformatictechnology.Results The results showed that more differences were foundbetween nucleotide sequences of N gene of wild-type measlesvirus against CAM-70 vaccine virus (77 – 79 nucleotides)compared against Schwarz and Edmonston-wt vaccine virus (71-74 nucleotides). Likewise, more differences were also observedbetween amino acid sequences of N protein of wild-type measlesvirus against CAM-70 vaccine virus (18-24 residues) comparedagainst Schwarz and Edmonston-wt vaccine virus (17-23 residues).

scholarly journals First Report of Capsicum chlorosis virus Infecting Amaryllis and Blood Lily in Taiwan

Plant Disease ◽  
2009 ◽  
Vol 93 (12) ◽  
pp. 1346-1346 ◽  
Author(s):  
C. C. Chen ◽  
C. H. Huang ◽  
Y. H. Cheng ◽  
T. C. Chen ◽  
S. D. Yeh ◽  
...  
Keyword(s):  
Chenopodium Quinoa ◽  
Amino Acid Sequences ◽  
N Gene ◽  
First Report ◽  
N Protein ◽  
Calla Lily ◽  
Field Samples ◽  
Local Lesions ◽  
Plant Pathol ◽  
Capsicum Chlorosis Virus

Capsicum chlorosis virus (CaCV), a thrips-transmitted, tentative species in the genus Tospovirus, family Bunyaviridae, was first identified in solanaceous crops, but also infects several ornamental crops such as orchid (4), gloxinia (3), and calla lily (1). From 2005 to 2007, virus-like yellow ringspots were observed on the leaves of amaryllis (Hippeastrum hybridum Hort.) and blood lily (Haemanthus multiflorus Martyn.) plants cultured in screenhouses and a private garden, respectively. Three of several hundred amaryllis plants in screenhouses from two places were observed as showing yellow ringspot symptoms and one of six blood lily plants was observed as showing similar yellow ringspot symptoms. Sap extracts from symptomatic leaves were inoculated to Chenopodium quinoa Willd. and the resulting local lesions were passaged three successive times to C. quinoa for virus isolation. Using the tospovirus genus-specific primers gL3637 and gL4435c designed from the conserved region in the L RNA (2), DNA fragments of the expected size of 800 bp were amplified by reverse transcription (RT)-PCR from field samples and local lesions from C. quinoa. Extracts from the diseased plants and local lesions of C. quinoa reacted strongly with antiserum against the nucleocapsid (N) protein of CaCV in ELISA and western blotting. To confirm the identity of this virus, we amplified the N gene from three amaryllis and one blood lily source using primer pair WN2328 and WN3534 designed from the S RNA of Watermelon silver mottle virus (1), and these products were cloned and sequenced. The sequence from each virus isolate was determined from three independent clones. The nucleotide and deduced amino acid sequences of N genes for the blood lily isolate (GenBank Accession No. EF101344) and three amaryllis isolates (GenBank Accession Nos. EF101343, EF137177, and FJ185170) had identities greater than 97% with that of a CaCV isolate infecting Capsicum spp. found in Australia (GenBank Accession No. AY036057). Phylogenetic analysis using maximum parsimony showed that these sequences clustered with CaCV. These results show that the virus identified from amaryllis and blood lily that were expressing yellow ringspot symptoms are isolates of CaCV. To our knowledge, this is the first report of CaCV naturally infecting amaryllis and blood lily and it could become an important threat to ornamental production in Taiwan. References: (1) C. C. Chen et al. Plant Dis. 91:1201, 2007. (2) F. H. Chu et al. Phytopathology 91:361, 2001. (3) H. T. Hsu et al. J. Gen. Plant Pathol. 66:167, 2000. (4) Y. X. Zheng et al. Eur. J. Plant Pathol. 120:199, 2008.

The complete mitochondrial genome of the Eurasian wryneck Jynx torquilla (Aves: Piciformes: Picidae) and its phylogenetic inference

Zootaxa ◽  
2020 ◽  
Vol 4810 (2) ◽  
pp. 351-360
Author(s):  
CHAO DU ◽  
LI LIU ◽  
YUNPENG LIU ◽  
ZHAOHUI FU
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Amino Acid Sequences ◽  
Protein Coding ◽  
Jynx Torquilla ◽  
Monophyletic Lineage ◽  
Phylogeny And Evolution

The Eurasian Wryneck is a species of wryneck woodpecker breeding in temperate regions of Europe and Asia. We sequenced the mitochondrial genome of Jynx torquilla (Aves, Piciformes, Picidae) using the next generation sequencing. The circular genome is 16,832 bp long, encoding 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two control regions. Gene order and orientation are similar to the most common type suggested as ancestral for birds but have a 1,221 bp control region and a 60 bp remnant control region. Phylogenetic analyses of 17 piciform taxa, based on both nucleotide and amino acid sequences of mitochondrial PCGs, strongly support the monophyly of Picidae. All phylogenetic trees indicate that the subfamily Jynginae is a monophyletic lineage sister to other woodpeckers, including monophyletic Picinae. Only the Bayes inferred tree based on the nucleotide dataset, recovered Picumninae as monophyletic. These findings will be helpful for the understanding of the phylogeny and evolution of Picidae. 

scholarly journals A short guide to phylogeny reconstruction

2008 ◽  
Vol 53 (No. 10) ◽  
pp. 442-446 ◽  
Author(s):  
E. Michu
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Amino Acid Sequences ◽  
Short Introduction ◽  
Closely Related Species ◽  
Origin And Evolution ◽  
Anatomical Characters

This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

scholarly journals Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites

2020 ◽  
Vol 48 (22) ◽  
pp. 12604-12617
Author(s):  
Pengpeng Long ◽  
Lu Zhang ◽  
Bin Huang ◽  
Quan Chen ◽  
Haiyan Liu
Keyword(s):  
Genome Sequence ◽  
Energy Function ◽  
Structural Information ◽  
Structural Data ◽  
P Values ◽  
A Genome ◽  
Z Scores ◽  
Transcription Regulators ◽  
Dna Specificity ◽  
Tetracycline Repressor

Abstract We report an approach to predict DNA specificity of the tetracycline repressor (TetR) family transcription regulators (TFRs). First, a genome sequence-based method was streamlined with quantitative P-values defined to filter out reliable predictions. Then, a framework was introduced to incorporate structural data and to train a statistical energy function to score the pairing between TFR and TFR binding site (TFBS) based on sequences. The predictions benchmarked against experiments, TFBSs for 29 out of 30 TFRs were correctly predicted by either the genome sequence-based or the statistical energy-based method. Using P-values or Z-scores as indicators, we estimate that 59.6% of TFRs are covered with relatively reliable predictions by at least one of the two methods, while only 28.7% are covered by the genome sequence-based method alone. Our approach predicts a large number of new TFBs which cannot be correctly retrieved from public databases such as FootprintDB. High-throughput experimental assays suggest that the statistical energy can model the TFBSs of a significant number of TFRs reliably. Thus the energy function may be applied to explore for new TFBSs in respective genomes. It is possible to extend our approach to other transcriptional factor families with sufficient structural information.

scholarly journals Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 545
Author(s):  
Gédéon Prince Manouana ◽  
Paul Alvyn Nguema-Moure ◽  
Mirabeau Mbong Ngwese ◽  
C.-Thomas Bock ◽  
Peter G. Kremsner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Preventive Measures ◽  
Phylogenetic Analyses ◽  
Enteric Viruses ◽  
Study Cohort ◽  
Viral Agent ◽  
A Genome ◽  
Stool Samples ◽  
Pcr Techniques ◽  
High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

Sign in / Sign up

Export Citation Format

Share Document