scholarly journals A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep

2019 ◽  
Author(s):  
Lele Zhao ◽  
Erik Lavington ◽  
Siobain Duffy
Keyword(s):  
Genomic Diversity ◽  
Bootstrap Support ◽  
Substitution Model ◽  
Reciprocal Monophyly ◽  
Dna Viruses ◽  
Single Origin ◽  
Amino Acid Substitution Model ◽  
Protein Matrices ◽  
Ssdna Viruses ◽  
Best Fit

AbstractAbundant novel circular Rep-encoding ssDNA viruses (CRESS DNA viruses) have been discovered in the past decade, prompting a new appreciation for the ubiquity and genomic diversity of this group of viruses. Although highly divergent in the hosts they infect or are associated with, CRESS DNA viruses are united by the homologous replication-associated protein (Rep). An accurate genealogy of Rep can therefore provide insights into how these diverse families are related to each other. We used a dataset of eukaryote-associated CRESS DNA RefSeq genomes (n=926), which included representatives from all six established families and unclassified species. To assure an optimal Rep genealogy, we derived and tested a bespoke amino acid substitution model (named CRESS), which outperformed existing protein matrices in describing the evolution of Rep. The CRESS model-estimated Rep genealogy resolved the monophyly of Bacilladnaviridae and the reciprocal monophyly of Nanoviridae and the alpha-satellites when trees estimated with general matrices like LG did not. The most intriguing, previously unobserved result is a likely single origin of intron-containing Reps, which causes several geminivirus genera to group with Genomoviridae (bootstrap support 55%, aLRT SH-like support 0.997, 0.91-0.997 in trees estimated with established matrices). This grouping, which eliminates the monophyly of Geminiviridae, is supported by both domains of Rep, and appears to be related to our use of all RefSeq Reps instead of subsampling to get a smaller dataset. In addition to producing a trustworthy Rep genealogy, the derived CRESS matrix is proving useful for other analyses; it best fit alignments of capsid protein sequences from several CRESS DNA families and parvovirus NS1/Rep sequences.

scholarly journals MtOrt: An empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects

2020 ◽  
Author(s):  
Huihui Chang ◽  
Yimeng Nie ◽  
Nan Zhang ◽  
Xue Zhang ◽  
Huimin Sun ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Mitochondrial Protein ◽  
Protein Sequences ◽  
Mitochondrial Genomes ◽  
Substitution Model ◽  
New Model ◽  
Substitution Models ◽  
Amino Acid Substitution Model ◽  
Complete Mitochondrial Genomes

Abstract Background Amino acid substitution models play an important role in inferring phylogenies from mitochondrial proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthoptera-specific mitochondrial amino acid empirical model. Results We sequenced complete mitochondrial genomes of 54 Orthoptera species, and then estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing model, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data. Conclusions The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.

scholarly journals Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Disa Bäckström ◽  
Natalya Yutin ◽  
Steffen L. Jørgensen ◽  
Jennah Dharamshi ◽  
Felix Homa ◽  
...  
Keyword(s):  
Deep Sea ◽  
Genomic Diversity ◽  
Genome Comparison ◽  
Phylogenomic Analysis ◽  
Dna Viruses ◽  
Deep Sea Sediments ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Loki’S Castle ◽  
Virus Genomes

ABSTRACT The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome. IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

scholarly journals Yaravirus: A novel 80-nm virus infectingAcanthamoeba castellanii

2020 ◽  
Vol 117 (28) ◽  
pp. 16579-16586 ◽  
Author(s):  
Paulo V. M. Boratto ◽  
Graziele P. Oliveira ◽  
Talita B. Machado ◽  
Ana Cláudia S. P. Andrade ◽  
Jean-Pierre Baudoin ◽  
...  
Keyword(s):  
Major Capsid Protein ◽  
Amino Acid Level ◽  
Three Dimensional ◽  
Genomic Diversity ◽  
Phylogenetic Distance ◽  
Preliminary Assessment ◽  
Dna Viruses ◽  
Origin And Evolution ◽  
Viral Genomes ◽  
Jelly Roll

Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organisms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible function of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs ofPleurochrysisendemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.

An Overview of Immune Evasion Strategies of DNA and RNA Viruses

2021 ◽  
Vol 21 ◽  
Author(s):  
Sheikh Saba Naz ◽  
Afsheen Aslam ◽  
Taqdees Malik
Keyword(s):  
Immune System ◽  
Rna Viruses ◽  
Adaptor Proteins ◽  
Genomic Diversity ◽  
Host Immune System ◽  
Granule Formation ◽  
Dna Viruses ◽  
Defense Proteins ◽  
Dna And Rna ◽  
Cytokines And Chemokines

A successful viral infection is due to the effective evasion of viruses from the immune system. The entry of viruses is usually detected by different cellular receptors including PRRs. Recognition of the viral genome leads to the production of interferons through a signaling stream. This review article will give brief information about escaping mechanisms of DNA and RNA viruses from the host immune system. Glimpses of these strategies include viral endonuclease activity, cap snatching of host mRNA, the formation of replication organelles, stress granule formation, membrane modifications, action of proteases, and evasion from ISGs. Moreover, we will discuss the strategies of DNA viruses to inhibit immune responses include Subversion of mRNA, transcriptional factors, Adaptor proteins, PRRs, evasion from T lymphocytes, Genomic Diversity, Theft or seize of host defense proteins, Imitation of host factors like affecting cytokines and chemokines of the host, and suppression or inhibition of apoptosis, Proteasomal degradation of host antiviral proteins by DNA Viruses. This knowledge is pivotal in understanding of different methodologies that viruses have created to escape antiviral cellular reactions of the host as well as an understanding of virus-host interactions and the origin of viral pathogenesis. Also, this knowledge is significant for the design of gene targeting vectors, antiviral vaccines, and the development of effective treatments directed against DNA and RNA viruses.

scholarly journals Amplification of Uncultured Single-Stranded DNA Viruses from Rice Paddy Soil

2008 ◽  
Vol 74 (19) ◽  
pp. 5975-5985 ◽  
Author(s):  
Kyoung-Ho Kim ◽  
Ho-Won Chang ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
Min-Soo Kim ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Rice Paddy ◽  
Viral Diversity ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Amplification Method ◽  
Metagenome Sequencing ◽  
Biological Entities ◽  
Related Proteins ◽  
Ssdna Viruses

ABSTRACT Viruses are known to be the most numerous biological entities in soil; however, little is known about their diversity in this environment. In order to explore the genetic diversity of soil viruses, we isolated viruses by centrifugation and sequential filtration before performing a metagenomic investigation. We adopted multiple-displacement amplification (MDA), an isothermal whole-genome amplification method with φ29 polymerase and random hexamers, to amplify viral DNA and construct clone libraries for metagenome sequencing. By the MDA method, the diversity of both single-stranded DNA (ssDNA) viruses and double-stranded DNA viruses could be investigated at the same time. On the contrary, by eliminating the denaturing step in the MDA reaction, only ssDNA viral diversity could be explored selectively. Irrespective of the denaturing step, more than 60% of the soil metagenome sequences did not show significant hits (E-value criterion, 0.001) with previously reported viral sequences. Those hits that were considered to be significant were also distantly related to known ssDNA viruses (average amino acid similarity, approximately 34%). Phylogenetic analysis showed that replication-related proteins (which were the most frequently detected proteins) related to those of ssDNA viruses obtained from the metagenomic sequences were diverse and novel. Putative circular genome components of ssDNA viruses that are unrelated to known viruses were assembled from the metagenomic sequences. In conclusion, ssDNA viral diversity in soil is more complex than previously thought. Soil is therefore a rich pool of previously unknown ssDNA viruses.

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