Evolution of rice stripe virus

He, Mei; Guan, Shengyu; He, Cheng-Qiang

doi:10.1016/j.ympev.2017.02.002

Cited by 36 publications

(36 citation statements)

References 33 publications

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“…The continuous survival of viruses is dependent on successful replication, which could be a key driver in ensuring that these genes undergo high purifying selection pressure in spite of recombination and mutations that may occur as observed (Tables 2 and 3) to ensure they maintain these critical functions. These findings are similar to other vector-transmitted RNA viruses such as the Rice stripe virus (RSV) (Wei et al, 2008; He, Guan & He, 2017). A slower rate in the evolution of BCMNV and CABMV could be beneficial to breeding efforts since it would allow for the new BCMNV resistant varieties under development to persist for longer than they would if the viruses were evolving at faster rates.…”

Section: Discussionsupporting

confidence: 78%

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Wainaina

Kubatko

Harvey

et al. 2019

PeerJ

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Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.

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Section: Discussionsupporting

confidence: 78%

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Wainaina

Kubatko

Harvey

et al. 2019

PeerJ

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“…Codon usage plays a significant role in the evolution of animal and human viruses, whereas our understanding of that in the evolution of plant viruses is limited. Until now, the codon usage pattern of citrus tristeza virus (CTV) [60], papaya ringspot virus (PRSV) [61], rice stripe virus (RSV) [62] and begomoviruses [63] had been reported. Low codon usage bias and higher genomic stability were observed from CTV, PRSV and RSV [60,61,62].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Gan

Liang

2019

Viruses

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Potato virus M (PVM) is a member of the genus Carlavirus of the family Betaflexviridae and causes large economic losses of nightshade crops. Several previous studies have elucidated the population structure, evolutionary timescale and adaptive evolution of PVM. However, the synonymous codon usage pattern of PVM remains unclear. In this study, we performed comprehensive analyses of the codon usage and composition of PVM based on 152 nucleotide sequences of the coat protein (CP) gene and 125 sequences of the cysteine-rich nucleic acid binding protein (NABP) gene. We observed that the PVM CP and NABP coding sequences were GC-and AU-rich, respectively, whereas U- and G-ending codons were preferred in the PVM CP and NABP coding sequences. The lower codon usage of the PVM CP and NABP coding sequences indicated a relatively stable and conserved genomic composition. Natural selection and mutation pressure shaped the codon usage patterns of PVM, with natural selection being the most important factor. The codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of PVM was to pepino, followed by tomato and potato. Moreover, similarity Index (SiD) analysis showed that pepino had a greater impact on PVM than tomato and potato. Our study is the first attempt to evaluate the codon usage pattern of the PVM CP and NABP genes to better understand the evolutionary changes of a carlavirus.

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“…This may be explained at least in part by the use of RNP rather than naked RNA as a transcriptional template (490), which is expected to hamper the template switch and some other mechanisms of formation of chimeric genomes. Nevertheless, true intermolecular recombination in these viruses has continuously been demonstrated (491)(492)(493)(494)(495)(496)(497)(498)(499). The error rate (487) and frequency of intermolecular recombination of viruses with doublestranded RNA genomes are relatively low due to peculiarities of their replicative machinery, but again, instances of natural recombination between them have been reported (500)(501)(502)(503).…”

Section: Negative-strand and Double-stranded Rna Virusesmentioning

confidence: 99%

Emergency Services of Viral RNAs: Repair and Remodeling

Agol

Gmyl

2018

Microbiol Mol Biol Rev

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Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.

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Evolution of rice stripe virus

Cited by 36 publications

References 33 publications

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Evolutionary insights ofBean common mosaic necrosis virusandCowpea aphid-borne mosaic virus

Analysis of Synonymous Codon Usage Bias in Potato Virus M and Its Adaption to Hosts

Emergency Services of Viral RNAs: Repair and Remodeling

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