Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

Park, Dongbin; Goh, Chul Jun; Kim, Hyein; Hahn, Yoonsoo

doi:10.5423/ppj.nt.11.2017.0243

Cited by 26 publications

(14 citation statements)

References 26 publications

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“…Together, these results are compatible with establishing a new Partitiviridae genus that is specific to dinoflagellates, comprising Orion durna-like virus 1, Diktys durna-like virus 1 and the previously identified Ourea durna-like virus. This observation expands the host range reported for this family, already comprising plants, fungi, oomycetes, apicomplexan parasites and green algae 19,[51][52][53][54] . While most of the Partitiviridae do not induce symptoms in their hosts, hypovirulence has been reported in the alpha-, beta-and gammapartitiviruses 55 .…”

Section: A New Partitiviridae Genus Associated With Dinoflagellate Hostssupporting

confidence: 69%

Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures

Charon

Kahlke

Larsson

et al. 2022

Preprint

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Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions on virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimised to detect highly divergent RNA viruses, we identified ten RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a great diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterisation and to investigate the effects of viral infections on microalgal physiology, biology and growth, considering their environmental and industrial roles.ImportanceIn comparison to animals or plants, our knowledge of the diversity of RNA viruses infecting microbial algae – the microalgae – is minimal. Yet describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economical levels because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte and euglena major clades of algae. This work identified ten new divergent RNA virus species, belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.

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Section: A New Partitiviridae Genus Associated With Dinoflagellate Hostssupporting

confidence: 69%

Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures

Charon

Kahlke

Larsson

et al. 2022

Preprint

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“…These selected non-RefSeq CDS sequences were extracted from corresponding genome sequences. In cases where a programmed ribosomal frameshift occurred [ 49 , 50 ], the skipped nucleotide was removed or the repeated nucleotide was added to generate the complete ORF. These sequences were designated as “variant” CDS sequences.…”

Section: Methodsmentioning

confidence: 99%

Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

Park

Hahn

2021

BMC Bioinformatics

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Background RNA viruses possess remarkable evolutionary versatility driven by the high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of proteins, are frequently observed in the coding sequences of various viral genomes. When a secondary indel occurs near the primary indel site, the open reading frame can be restored to produce functional proteins, a phenomenon known as the compensatory frameshift. Results In this study, we systematically analyzed publicly available viral genome sequences and identified compensatory frameshift events in hundreds of viral protein-coding sequences. Compensatory frameshift events resulted in large-scale amino acid differences between the compensatory frameshift form and the wild type even though their nucleotide sequences were almost identical. Phylogenetic analyses revealed that the evolutionary distance between proteins with and without a compensatory frameshift were significantly overestimated because amino acid mismatches caused by compensatory frameshifts were counted as substitutions. Further, this could cause compensatory frameshift forms to branch in different locations in the protein and nucleotide trees, which may obscure the correct interpretation of phylogenetic relationships between variant viruses. Conclusions Our results imply that the compensatory frameshift is one of the mechanisms driving the rapid protein evolution of RNA viruses and potentially assisting their host-range expansion and adaptation.

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“…Particularly in cases like endornaviruses, in which the members do not form classic virions ("capsid-less viruses") [23,32], their naked RNA can go unnoticed while contaminating DNA in dsRNA analysis [32]. Metagenomic studies have accelerated the discovery of new viruses in this category [13,[37][38][39][40][41][42][43][44][45][46]. In addition, the genomes and sequences generated from these studies will improve our understanding of these viruses, including phylogeny, host relation, and transmission.…”

Section: Discussionmentioning

confidence: 99%

Persistent, and Asymptomatic Viral Infections and Whitefly-Transmitted Viruses Impacting Cantaloupe and Watermelon in Georgia, USA

Adeleke

Kavalappara

McGregor

et al. 2022

Viruses

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Cucurbits in Southeastern USA have experienced a drastic decline in production over the years due to the effect of economically important viruses, mainly those transmitted by the sweet potato whitefly (Bemisia tabaci Gennadius). In cucurbits, these viruses can be found as a single or mixed infection, thereby causing significant yield loss. During the spring of 2021, surveys were conducted to evaluate the incidence and distribution of viruses infecting cantaloupe (n = 80) and watermelon (n = 245) in Georgia. Symptomatic foliar tissues were collected from six counties and sRNA libraries were constructed from seven symptomatic samples. High throughput sequencing (HTS) analysis revealed the presence of three different new RNA viruses in Georgia: cucumis melo endornavirus (CmEV), cucumis melo amalgavirus (CmAV1), and cucumis melo cryptic virus (CmCV). Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed the presence of CmEV and CmAV1 in 25% and 43% of the total samples tested, respectively. CmCV was not detected using RT-PCR. Watermelon crinkle leaf-associated virus 1 (WCLaV-1), recently reported in GA, was detected in 28% of the samples tested. Furthermore, RT-PCR and PCR analysis of 43 symptomatic leaf tissues collected from the fall-grown watermelon in 2019 revealed the presence of cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and cucurbit leaf crumple virus (CuLCrV) at 73%, 2%, and 81%, respectively. This finding broadens our knowledge of the prevalence of viruses in melons in the fall and spring, as well as the geographical expansion of the WCLaV-1 in GA, USA.

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Identification of Two Novel Amalgaviruses in the Common Eelgrass (Zostera marina) and in Silico Analysis of the Amalgavirus +1 Programmed Ribosomal Frameshifting Sites

Cited by 26 publications

References 26 publications

Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures

Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures

Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes

Persistent, and Asymptomatic Viral Infections and Whitefly-Transmitted Viruses Impacting Cantaloupe and Watermelon in Georgia, USA

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