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Genomics and Genetics of Plant Viruses
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Genomics and Genetics of Plant Viruses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Viral Genomics".

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 6045

Special Issue Editor

Dr. Zhen He

E-Mail Website
Guest Editor
College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, China
Interests: virus evolution; plant virus interaction

Special Issue Information

Dear Colleagues,

Plant viruses accumulate heritable genetic changes during their lifetime, which can arise from adaptations in response to environmental changes or the immune response of the host. Because of their short generation times and large population sizes, RNA viruses can evolve rapidly. More recently, various breakthroughs have led to the rapid advance of plant virus evolution. Especially, within the devastating global pandemic of SARS-CoV-2, the genomics, genetics, phylogenetics, epidemiology, and evolution of plant viruses have received unprecedented attention. This research topic will present articles and review papers covering plant virus genome and evolution including both computational and experimental approaches. Sub-topics may include (but are not limited to): plant virus identification, plant virus evolution and classification, phylogenetics, epidemiology and surveillance, plant virus experimental evolution, viral metagenomics and ecology, and viral bioinformatics and software.

We welcome original research articles and review papers about the recent advancements and current understanding of plant viruses’ computational and experimental evolution.

Dr. Zhen He
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant virus identification
  • plant viral metagenomics and ecology
  • plant virus evolution
  • phylogenetics
  • epidemiology

Published Papers (5 papers)

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Research

8 pages, 1341 KiB  
Communication
Molecular Characteristics of Bean Common Mosaic Virus Occurring in Inner Mongolia, China
by Jingru Li, Zhengnan Li, Zhanmin Wu, Yu Sun, Suqing Niu, Mengze Guo and Lei Zhang
Genes 2024, 15(1), 133; https://doi.org/10.3390/genes15010133 - 21 Jan 2024
Viewed by 1025
Abstract
Bean common mosaic virus (BCMV) was detected on common bean (Phaseolus vulgaris) plants showing wrinkled and/or narrow leaves, curling, shrinking and chlorosis of leaves, dwarfing of plants, and mottled pods in Inner Mongolia and named BCMV-22Huhe. Its genome has a size [...] Read more.
Bean common mosaic virus (BCMV) was detected on common bean (Phaseolus vulgaris) plants showing wrinkled and/or narrow leaves, curling, shrinking and chlorosis of leaves, dwarfing of plants, and mottled pods in Inner Mongolia and named BCMV-22Huhe. Its genome has a size of 10,062 bp and was deposited in GenBank under the accession number OR778613. It is closely related to BCMV-Az (GenBank accession no. KP903372, in China) in the lineage of AzBMV. A recombination event was detected for BCMV-22Huhe among the 99 BCMV isolates published in the NCBI GenBank database, showing that BCMV-CJ25 (MK069986, found in Mexico) was a potential major parent, and the minor parent is unknown. This work is the first description of the occurrence of BCMV in Inner Mongolia, China. Full article
(This article belongs to the Special Issue Genomics and Genetics of Plant Viruses)
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6 pages, 909 KiB  
Communication
Identification and Genome Characterization of a Dahlia Common Mosaic Virus Isolate from China
by Jing Wang, Jiaying Zhou, Ming Chen, Zhengnan Li and Shuang Song
Genes 2023, 14(10), 1833; https://doi.org/10.3390/genes14101833 - 22 Sep 2023
Viewed by 1029
Abstract
Dahlia (Dahlia variabilis) is a widely cultivated ornamental and medicinal plant in China. Recently, dahlia plants with symptoms of leaf mottling and distortion were collected in Hohhot, Inner Mongolia, China. The presence of dahlia common mosaic virus (DCMV), an unassigned species [...] Read more.
Dahlia (Dahlia variabilis) is a widely cultivated ornamental and medicinal plant in China. Recently, dahlia plants with symptoms of leaf mottling and distortion were collected in Hohhot, Inner Mongolia, China. The presence of dahlia common mosaic virus (DCMV), an unassigned species in the genus Caulimovirus, was confirmed by high-throughput sequencing. Three fragments of DCMV Inner Mongolia isolate (DCMV-IN) were PCR-amplified with specific primers, sequenced and assembled into the complete genome sequence with a GenBank accession number of OR494328. The double-stranded circular DNA genome of DCMV-IN consists of 7949 bp and contains six open reading frames (ORFs). Sequence analysis showed that DCMV-IN shared high sequence identities with other DCMV isolates available in the GenBank database. Phylogenetic analysis of DCMV isolates and other representative caulimoviruses based on genome sequence clustered four DCMV isolates to a single branch which was closest to dahlia mosaic virus (DMV). No recombination event was detected among the four DCMV isolates. Full article
(This article belongs to the Special Issue Genomics and Genetics of Plant Viruses)
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13 pages, 1703 KiB  
Article
Complete Genomic Sequence Analysis of a Sugarcane Streak Mosaic Virus Isolate from Yunnan Province of China
by Xiao-Ling Su, Zhong-Yue Mai, Kun-Jiang Wei, Yang-Jian Huang, Hong-Li Shan and De-Jie Cheng
Genes 2023, 14(9), 1713; https://doi.org/10.3390/genes14091713 - 28 Aug 2023
Cited by 2 | Viewed by 1079
Abstract
In recent years, the sugarcane streak mosaic virus (SCSMV) has been the primary pathogen of sugarcane mosaic disease in southern China. In this study, the complete genome of a sugarcane mosaic sample (named YN-21) from Kaiyuan City, Yunnan Province, was amplified and sequenced. [...] Read more.
In recent years, the sugarcane streak mosaic virus (SCSMV) has been the primary pathogen of sugarcane mosaic disease in southern China. In this study, the complete genome of a sugarcane mosaic sample (named YN-21) from Kaiyuan City, Yunnan Province, was amplified and sequenced. By comparing the amino acid sequences of YN-21 and 15 other SCSMV isolates from the NCBI database, the protease recognition site of SCSMV was determined. YN-21 had the highest nucleotide and amino acid identities of 97.66% and 99.30%, respectively, in comparison with the SCSMV isolate (JF488066). The P1 had the highest variability of 83.38–99.72% in the amino acid sequence, and 6K2 was the most conserved, with 97.92–100% amino acid sequence identity. A phylogenetic analysis of nucleotide and amino acid sequences clustered the 16 SCSMV isolates into two groups. All the Chinese isolates were clustered into the same group, and YN-21 was closely related to the Yunnan and Hainan isolates in China. Recombination analysis showed no major recombination sites in YN-21. Selective pressure analysis showed that the dN/dS values of 11 proteins of SCSMV were less than 1, all of which were undergoing negative selection. These results can provide practical guidance for monitoring SCSMV epidemics and genetics. Full article
(This article belongs to the Special Issue Genomics and Genetics of Plant Viruses)
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16 pages, 4502 KiB  
Article
An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus
by Lingqi Wang, Haiting Zhao, Zhilei Wang, Shiwen Ding, Lang Qin, Runzhou Jiang, Xiaolong Deng, Zhen He and Liangjun Li
Genes 2023, 14(9), 1712; https://doi.org/10.3390/genes14091712 - 28 Aug 2023
Cited by 2 | Viewed by 1093
Abstract
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the [...] Read more.
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism. Full article
(This article belongs to the Special Issue Genomics and Genetics of Plant Viruses)
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12 pages, 3330 KiB  
Article
Screening and Identification of Host Factors Interacting with the Virulence Factor P0 Encoded by Sugarcane Yellow Leaf Virus by Yeast Two-Hybrid Assay
by Kai-Li Liang, Jing-Ying Liu, Ying-Ying Bao, Zhi-Yuan Wang and Xiong-Biao Xu
Genes 2023, 14(7), 1397; https://doi.org/10.3390/genes14071397 - 3 Jul 2023
Cited by 3 | Viewed by 1410
Abstract
Sugarcane yellow leaf virus (SCYLV), a member of the genus Polerovirus in the family Luteoviridae, causes severe damage and represents a great threat to sugarcane cultivation and sugar industry development. In this study, inoculation of Nicotiana benthamiana plants with a potato virus [...] Read more.
Sugarcane yellow leaf virus (SCYLV), a member of the genus Polerovirus in the family Luteoviridae, causes severe damage and represents a great threat to sugarcane cultivation and sugar industry development. In this study, inoculation of Nicotiana benthamiana plants with a potato virus X (PVX)-based vector carrying the SCYLV P0 gene induced typical mosaic, leaf rolling symptoms and was associated with a hypersensitive-like response (HLR) necrosis symptom, which is accompanied with a systemic burst of H2O2 and also leads to higher PVX viral genome accumulation levels. Our results demonstrate that SCYLV P0 is a pathogenicity determinant and plays important roles in disease development. To further explore its function in pathogenic processes, a yeast two-hybrid assay was performed to screen the putative P0-interacting host factors. The recombinant plasmid pGBKT7-P0 was constructed as a bait and transformed into the yeast strain Y2HGold. The ROC22 cultivar (an important parental resource of the main cultivar in China) cDNA prey library was constructed and screened by co-transformation with the P0 bait. We identified 28 potential interacting partners including those involved in the optical signal path, plant growth and development, transcriptional regulation, host defense response, and viral replication. To our knowledge, this is the first time we have reported the host proteins interacting with the P0 virulence factor encoded by sugarcane yellow leaf virus. This study not only provides valuable insights into elucidating the molecular mechanism of the pathogenicity of SCYLV, but also sheds light on revealing the probable new pathogenesis of Polerovirus in the future. Full article
(This article belongs to the Special Issue Genomics and Genetics of Plant Viruses)
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