Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases

He, Zhen; Qin, Lang; Xu, Xiaowei; Ding, Shiwen

doi:10.1016/j.csbj.2022.05.021

Cited by 10 publications

(5 citation statements)

References 132 publications

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“…Codon usage patterns of viruses reflect evolutionary changes, such as adaption, evolution, evasion from host immune systems, and survival [ 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. Now, only limited reports show the codon usage patterns of plant viruses, such as citrus tristeza virus (CTV) [ 50 ], rice strape virus (RSV) [ 51 ], papaya ringspot virus (PRSV) [ 52 ], potato virus M (PVM) [ 53 ], sugarcane mosaic virus (SCMV) [ 54 ], broad bean wilt virus 2 (BBWV2) [ 55 ], rice black-streaked dwarf virus (RBSDV) [ 56 ], narcissus degeneration virus (NDV) [ 57 ], narcissus late season yellows virus (NLSYV) [ 57 ], and narcissus yellow stripe virus (NYSV) [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Qin

Ding

Wang

et al. 2022

Viruses

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Turnip mosaic virus (TuMV), an important pathogen that causes mosaic diseases in vegetable crops worldwide, belongs to the genus Potyvirus of the family Potyviridae. Previously, the areas of genetic variation, population structure, timescale, and migration of TuMV have been well studied. However, the codon usage pattern and host adaptation analysis of TuMV is unclear. Here, compositional bias and codon usage of TuMV were performed using 184 non-recombinant sequences. We found a relatively stable change existed in genomic composition and a slightly lower codon usage choice displayed in TuMV protein-coding sequences. Statistical analysis presented that the codon usage patterns of TuMV protein-coding sequences were mainly affected by natural selection and mutation pressure, and natural selection was the key influencing factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) revealed that TuMV genes were strongly adapted to Brassica oleracea from the present data. Similarity index (SiD) analysis also indicated that B. oleracea is potentially the preferred host of TuMV. Our study provides the first insights for assessing the codon usage bias of TuMV based on complete genomes and will provide better advice for future research on TuMV origins and evolution patterns.

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Section: Discussionmentioning

confidence: 99%

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Qin

Ding

Wang

et al. 2022

Viruses

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“…In line with this hypothesis, analysis of the small peptides that are loaded onto the MHC revealed that these peptides tend to be encoded by A/G-poor coding sequences [ 39 ]. While this is a plausible explanation in the context of mammalian immune systems, viruses that infect plants – which are organisms that lack MHC systems – also present similar A-richness [ 40–42 ]. Since A-rich motifs are often depleted in CLIP/SELEX experiments of human RBPs [ 18–20 , 22 ], an alternative explanation for the bias towards adenosine in RNA viruses is the mere scarcity of human proteins that recognise such motifs, therefore, reducing the changes of detection and manipulation of virus RNA by the immune system.…”

Section: Rna-binding Preferences Of Human Proteinsmentioning

confidence: 99%

Sensing nucleotide composition in virus RNA

Lo,

Gonçalves-Carneiro

2023

Bioscience Reports

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Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host–virus interactions and uncover potential targets for antiviral strategies.

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“…Viruses are not only able to adapt to a variety of environmental situations and new hosts, but can evolve rapidly through mutation, genetic drift, and genetic recombination ( Sanjuán and Domingo-Calap, 2021 ). A number of other factors, including long-term continuous monoculture, climate change, the global trade in plant materials, and the expanding geographical ranges of insect vectors, have also led to an increase in viral diseases ( Elena et al, 2011 , 2014 ; Lefeuvre et al, 2019 ; He et al, 2022 ). Consequently, growers need to identify viruses as early as possible in order to take timely action and implement the necessary sanitary measures ( Wallingford et al, 2015 ; Fuchs, 2020 ; Javaran et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection

et al. 2023

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There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect low-abundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common.

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Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases

Cited by 10 publications

References 132 publications

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Host Plants Shape the Codon Usage Pattern of Turnip Mosaic Virus

Sensing nucleotide composition in virus RNA

NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection

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