Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

Adriaenssens, Evelien M.; Cowan, Don A.

doi:10.1128/aem.00878-14

Cited by 127 publications

(93 citation statements)

References 110 publications

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“…Sequence-based identification of viral communities, using either multiple gene markers (74) or full-virome sequencing (75), is becoming more routine. In marine virus ecology, the use of conserved viral marker genes such as DNA polymerases (76), ribonucleotide reductases (77), and T4-related structural proteins (78,79) has provided detailed data on viral biodiversity, on intra-and interviral evolutionary relationships, and on oceanic viral turnover rates.…”

Section: Technical Recommendations and Future Researchmentioning

confidence: 99%

Diversity and Ecology of Viruses in Hyperarid Desert Soils

Zablocki

Adriaenssens

Cowan

2016

Appl Environ Microbiol

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101

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In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ϳ33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.

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Section: Technical Recommendations and Future Researchmentioning

confidence: 99%

Diversity and Ecology of Viruses in Hyperarid Desert Soils

Zablocki

Adriaenssens

Cowan

2016

Appl Environ Microbiol

Self Cite

101

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“…Host-derived metabolic genes are commonly found in cyanophages, but not other phages infecting non-cyanobacteria and, consequently, provide ideal molecular markers to investigate the genetic diversity and evolutionary history of cyanophages in nature [99]. In contrast to viral structural genes, the use of host-like metabolic genes as candidate marker genes would enable a deeper understanding of the ecological relationship and molecular diversity of cyanophages in response to specific environments.…”

Section: Signature Markers For Cyanophage Evolutionmentioning

confidence: 99%

Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution

Gao

Huang

Ning

2016

Genes

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Cyanophages, a group of viruses specifically infecting cyanobacteria, are genetically diverse and extensively abundant in water environments. As a result of selective pressure, cyanophages often acquire a range of metabolic genes from host genomes. The host-derived genes make a significant contribution to the ecological success of cyanophages. In this review, we summarize the host-derived metabolic genes, as well as their origin and roles in cyanophage evolution and important host metabolic pathways, such as the light-dependent reactions of photosynthesis, the pentose phosphate pathway, nutrient acquisition and nucleotide biosynthesis. We also discuss the suitability of the host-derived metabolic genes as potential diagnostic markers for the detection of genetic diversity of cyanophages in natural environments.

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“…The unrestricted distribution of plant diseases and emerging infectious disease poses serious threat to food sustenance. A high percentage of this loss is caused by viruses because of their abundant presence in most environments among the biological entities [2]. Early identification of these plant pathogens remains the focal point in the field of virology, aimed at preventing the spread of the viruses as well as developing ways of combating and reducing their effects on agricultural yield.…”

Section: Introductionmentioning

confidence: 99%

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Akinyemi

Wang

Zhou

et al. 2016

Virol J

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BackgroundThe invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses. A survey of plant viruses infecting field-grown Tobacco crop was conducted in Anhui Province of China by the deep sequencing of sRNAs.MethodsSurvey of plant viruses infecting Tobacco was carried based on 104 samples collected across the province. Nine different sRNA libraries was prepared and custom-made bioinformatics pipeline coupled with molecular techniques was developed to sequence, assemble and analyze the siRNAs for plant virus discovery. We also carried out phylogenetic and recombination analysis of the identified viruses.ResultsTwenty two isolates from eight different virus species including Cucumber mosaic virus, Potato virus Y, Tobacco mosaic virus, Tobacco vein banding Mosaic virus, Pepper mottle virus, Brassica yellow virus, Chilli venial mottle virus, Broad bean wilt virus 2 were identified in tobacco across the survey area. The near-complete genome sequence of the 22 new isolates were determined and analyzed. The isolates were grouped together with known strains in the phylogenetic tree. Molecular variation in the isolates indicated the conserved coding regions have majorly a nucleotide sequence identity of 80-94 % with previously identified isolates. Various events of recombination were discovered among some of the isolates indicating that two or more viruses or different isolates of one virus infect the same host cell.ConclusionThis study describes the discovery of a consortium of plant viruses infecting Tobacco that are broadly distributed in Anhui province of China. It also demonstrates the effectiveness of NGS in identifying plant viruses without a prior knowledge of the virus and the genetic diversity that enhanced mixed infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0639-7) contains supplementary material, which is available to authorized users.

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Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity

Cited by 127 publications

References 110 publications

Diversity and Ecology of Viruses in Hyperarid Desert Soils

Diversity and Ecology of Viruses in Hyperarid Desert Soils

Metabolic Genes within Cyanophage Genomes: Implications for Diversity and Evolution

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

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