High Variability and Rapid Evolution of a Nanovirus

ABSTRACT Nanoviruses are multipartite single-stranded DNA (ssDNA) plant viruses that cause important diseases of leguminous crops and banana. Little has been known about the variability and molecular evolution of these viruses. Here we report on the variability of faba bean necrotic stunt virus (FBNSV), a nanovirus from Ethiopia. We found mutation frequencies of 7.52 × 10−4 substitutions per nucleotide in a field population of the virus and 5.07 × 10−4 substitutions per nucleotide in a laboratory-maintained population derived thereof. Based on virus propagation for a period of more than 2 years, we determined a nucleotide substitution rate of 1.78 × 10−3 substitutions per nucleotide per year. This high molecular evolution rate places FBNSV, as a representative of the family Nanoviridae, among the fastest-evolving ssDNA viruses infecting plants or vertebrates.

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Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

PeerJ ◽

10.7717/peerj.12106 ◽

2021 ◽

Vol 9 ◽

pp. e12106

Author(s):

Mikhail I. Schelkunov ◽

Maxim S. Nuraliev ◽

Maria D. Logacheva

Keyword(s):

Substitution Rate ◽

Nucleotide Substitution ◽

Nucleotide Substitution Rate ◽

Genomic Comparison ◽

Plant Family ◽

Plastid Genomes ◽

The Family ◽

Unknown Reason ◽

Order Of Magnitude ◽

Insight Into

The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have revealed that plastid genomes of Balanophoraceae exhibit a number of interesting features, one of the most prominent of those being a highly elevated AT content of nearly 90%. Additionally, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is an order of magnitude greater than that of their photosynthetic relatives without signs of relaxed selection. Currently, there are no definitive explanations for these features. Given these unusual features, we hypothesised that the nuclear genomes of Balanophoraceae may also provide valuable information in regard to understanding the evolution of non-photosynthetic plants. To gain insight into these genomes, in the present study we analysed the transcriptomes of two Balanophoraceae species (Rhopalocnemis phalloides and Balanophora fungosa) and compared them to the transcriptomes of their close photosynthetic relatives (Daenikera sp., Dendropemon caribaeus, and Malania oleifera). Our analysis revealed that the AT content of the nuclear genes of Balanophoraceae did not markedly differ from that of the photosynthetic relatives. The nucleotide substitution rate in the genes of Balanophoraceae is, for an unknown reason, several-fold larger than in the genes of photosynthetic Santalales; however, the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in the Balanophoraceae family members. Additionally, we did not observe transcripts of several genes whose products function in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

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Nucleotide Sequence Evolution at the κ-Casein Locus: Evidence for Positive Selection Within the Family Bovidae

Genetics ◽

10.1093/genetics/147.4.1863 ◽

1997 ◽

Vol 147 (4) ◽

pp. 1863-1872

Author(s):

Todd J Ward ◽

Rodney L Honeycutt ◽

James N Derr

Keyword(s):

Amino Acid ◽

Molecular Evolution ◽

Nucleotide Sequence ◽

Positive Selection ◽

Milk Protein ◽

Nucleotide Substitution ◽

Sequence Evolution ◽

Amino Acid Sequence Level ◽

Physiological Processes ◽

The Family

Abstract κ-Casein is a mammalian milk protein involved in a number of important physiological processes. In the gut, the ingested protein is split into an insoluble peptide (para κ-casein) and a soluble hydrophilic glycopeptide (caseinomacropeptide). Caseinomacropeptide is responsible for increased efficiency of digestion, prevention of neonate hypersensitivity to ingested proteins, and inhibition of gastric pathogens. Variation within this peptide has significant effects associated with important traits such as milk production. The nucleotide sequences for regions of κ-casein exon and intron four were determined for representatives of the artiodactyl family Bovidae. The pattern of nucleotide substitution in κ-casein sequences for distantly related bovid taxa demonstrates that positive selection has accelerated their divergence at the amino acid sequence level. This selection has differentially influenced the molecular evolution of the two Kcasein split peptides and is focused within a 34-codon region of caseinomacropeptide.

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Mutation rate and genotype variation of Ebola virus from Mali case sequences

Science ◽

10.1126/science.aaa5646 ◽

2015 ◽

Vol 348 (6230) ◽

pp. 117-119 ◽

Cited By ~ 104

Author(s):

T. Hoenen ◽

D. Safronetz ◽

A. Groseth ◽

K. R. Wollenberg ◽

O. A. Koita ◽

...

Keyword(s):

Public Health ◽

Molecular Diagnostics ◽

Substitution Rate ◽

Ebola Virus ◽

Nucleotide Substitution ◽

Rapid Evolution ◽

Nucleotide Substitution Rate ◽

Outbreak Response ◽

Genotype Variation ◽

Current Outbreak

The occurrence of Ebola virus (EBOV) in West Africa during 2013–2015 is unprecedented. Early reports suggested that in this outbreak EBOV is mutating twice as fast as previously observed, which indicates the potential for changes in transmissibility and virulence and could render current molecular diagnostics and countermeasures ineffective. We have determined additional full-length sequences from two clusters of imported EBOV infections into Mali, and we show that the nucleotide substitution rate (1.3 × 10–3 substitutions per site per year) is consistent with rates observed in Central African outbreaks. In addition, overall variation among all genotypes observed remains low. Thus, our data indicate that EBOV is not undergoing rapid evolution in humans during the current outbreak. This finding has important implications for outbreak response and public health decisions and should alleviate several previously raised concerns.

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Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives

10.1101/2020.09.20.305011 ◽

2020 ◽

Author(s):

Mikhail I. Schelkunov ◽

Maxim S. Nuraliev ◽

Maria D. Logacheva

Keyword(s):

Substitution Rate ◽

Nucleotide Substitution ◽

Nucleotide Substitution Rate ◽

Genomic Comparison ◽

Plant Family ◽

Plastid Genomes ◽

The Family ◽

Unknown Reason ◽

Order Of Magnitude ◽

Insight Into

AbstractThe plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have shown that plastid genomes of Balanophoraceae have a number of interesting features, one of the most prominent of those being a tremendous AT content close to 90%. Also, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is greater by an order of magnitude compared to photosynthetic relatives, without signs of relaxed selection. All these features have no definite explanations.Given these unusual features, we supposed that it would be interesting to gain insight into the characteristics of nuclear genomes of Balanophoraceae. To do this, in the present study we analysed transcriptomes of two species from Balanophoraceae, namely Rhopalocnemis phalloides and Balanophora fungosa, and compared them with transcriptomes of their close photosynthetic relatives Daenikera sp., Dendropemon caribaeus, Malania oleifera.The analysis showed that the AT content of nuclear genes of Balanophoraceae does not markedly differ from that of photosynthetic relatives. The nucleotide substitution rate in genes of Balanophoraceae is for an unknown reason several times larger than in genes of photosynthetic Santalales, though the negative selection in Balanophoraceae is likely stronger.We observed an extensive loss of photosynthesis-related genes in Balanophoraceae. Also, for Balanophoraceae we did not see transcripts of several genes whose products participate in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

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A novel, multipartite, negative-strand RNA virus is associated with the ringspot disease of European mountain ash (Sorbus aucuparia L.)

Journal of General Virology ◽

10.1099/vir.0.82715-0 ◽

2007 ◽

Vol 88 (4) ◽

pp. 1337-1346 ◽

Cited By ~ 57

Author(s):

Nicole Mielke ◽

Hans-Peter Muehlbach

Keyword(s):

Rna Virus ◽

Plant Viruses ◽

Glycoprotein Precursor ◽

Structure Comparison ◽

Viral Rnas ◽

Pathogenic Virus ◽

Mountain Ash ◽

The Family ◽

European Mountain ◽

Novel Virus

Four RNAs from a new plant-pathogenic virus, which we have tentatively named European mountain ash ringspot-associated virus (EMARAV), were identified and sequenced completely. All four viral RNAs could be detected in previous double-stranded RNA preparations. RNA 1 (7040 nt) encodes a protein with similarity to the RNA-dependent RNA polymerase of different members of the Bunyaviridae, a family containing five genera with viruses infecting invertebrates, vertebrates and plants. RNA 2 (2335 nt) encodes a 75 kDa protein containing a conserved motif of the glycoprotein precursor of the genus Phlebovirus. Immunological detection indicated the presence of proteins with the expected size of the precursor and one of its processing products. The amino acid sequence of protein p3 (35 kDa) encoded by RNA 3 shows similarities to a putative nucleocapsid protein of two still unclassified plant viruses. The fourth viral RNA encodes a 27 kDa protein that has no significant homology to any known protein. As is typical for members of the family Bunyaviridae, the 5′ and 3′ ends of all viral RNAs are complementary, which allows the RNA to form a panhandle structure. Comparison of these sequences demonstrates a conserved terminal part of 13 nt, similar to that of the bunyaviral genus Orthobunyavirus. Despite the high agreement of the EMARAV genome with several characteristics of the family Bunyaviridae, there are a few features that make it difficult to allocate the virus to this group. It is therefore more likely that this plant pathogen belongs to a novel virus genus.

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An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera

Molecular Biology and Evolution ◽

10.1093/oxfordjournals.molbev.a025804 ◽

1997 ◽

Vol 14 (6) ◽

pp. 644-653 ◽

Cited By ~ 68

Author(s):

M. Friedrich ◽

D. Tautz

Keyword(s):

Substitution Rate ◽

Nucleotide Substitution ◽

Nucleotide Substitution Rate ◽

Insect Order ◽

Episodic Change

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Nucleotide Substitution: Rate of

Encyclopedia of Life Sciences ◽

10.1038/npg.els.0005109 ◽

2006 ◽

Author(s):

Wen-Hsiung Li

Keyword(s):

Substitution Rate ◽

Nucleotide Substitution ◽

Nucleotide Substitution Rate

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Recovery of NanoLuc Luciferase-Tagged Canine Distemper Virus for Facilitating Rapid Screening of Antivirals in vitro

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.600796 ◽

2020 ◽

Vol 7 ◽

Author(s):

Fuxiao Liu ◽

Qianqian Wang ◽

Yilan Huang ◽

Ning Wang ◽

Youming Zhang ◽

...

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Canine Distemper Virus ◽

Reverse Genetics ◽

Rapid Screening ◽

Canine Distemper ◽

Virus Propagation ◽

The Family ◽

Conventional Methods

Canine distemper virus (CDV), belonging to the genus Morbillivirus in the family Paramyxoviridae, is a highly contagious pathogen, affecting various domestic, and wild carnivores. Conventional methods are too cumbersome to be used for high-throughput screening of anti-CDV drugs. In this study, a recombinant CDV was rescued using reverse genetics for facilitating screening of anti-CDV drug in vitro. The recombinant CDV could stably express the NanoLuc® luciferase (NLuc), a novel enzyme that was smaller and “brighter” than others. The intensity of NLuc-catalyzed luminescence reaction indirectly reflected the anti-CDV effect of a certain drug, due to a positive correlation between NLuc expression and virus propagation in vitro. Based on such a characteristic feature, the recombinant CDV was used for anti-CDV assays on four drugs (ribavirin, moroxydine hydrochloride, 1-adamantylamine hydrochloride, and tea polyphenol) via analysis of luciferase activity, instead of via conventional methods. The result showed that out of these four drugs, only the ribavirin exhibited a detectable anti-CDV effect. The NLuc-tagged CDV would be a rapid tool for high-throughput screening of anti-CDV drugs.

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