Genetic changes and host adaptability in sugarcane mosaic virus based on complete genome sequences

He, Zhen; Dong, Zhuozhuo; Gan, Haifeng

doi:10.1016/j.ympev.2020.106848

Cited by 17 publications

(28 citation statements)

References 74 publications

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“…Normally, RNA viruses have low codon usage bias to perform efficient replication in the host by lowering the competition with the host genes [55,[65][66][67][68]. Previous reports showed low codon usage bias from several plant viruses such as CTV, PRSV, PVM, RSV and SCMV [19][20][21][22][23][24]. In our study, a lower codon usage pattern of the BBWV2 genome (the ENC values higher than 35) was also found, indicating a low degree of preference.…”

Section: Discussionsupporting

confidence: 67%

“…CUB in viruses is expected to affect their survival, fitness, evolution, adaption, and avoidance of host cell responses [7,13]. Until now, only several reports have described the influence of codon usage in the evolution of plant viruses, such as begomoviruses [18], citrus tristeza virus (CTV) [19], rice black-streaked dwarf virus (RBSDV) [20], rice strape virus (RSV) [21], papaya ringspot virus (PRSV) [22], potato virus M (PVM) [23], and sugarcane mosaic virus (SCMV) [24].…”

Section: Introductionmentioning

confidence: 99%

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Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Dong

Qin

et al. 2021

Viruses

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Broad bean wilt virus 2 (BBWV-2), which belongs to the genus Fabavirus of the family Secoviridae, is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previously, only limited reports have shown the genetic variation of BBWV2. Meanwhile, the detailed evolutionary changes, synonymous codon usage bias and host adaptation of this virus are largely unclear. Here, we performed comprehensive analyses of the phylodynamics, reassortment, composition bias and codon usage pattern of BBWV2 using forty-two complete genome sequences of BBWV-2 isolates together with two other full-length RNA1 sequences and six full-length RNA2 sequences. Both recombination and reassortment had a significant influence on the genomic evolution of BBWV2. Through phylogenetic analysis we detected three and four lineages based on the ORF1 and ORF2 nonrecombinant sequences, respectively. The evolutionary rates of the two BBWV2 ORF coding sequences were 8.895 × 10−4 and 4.560 × 10−4 subs/site/year, respectively. We found a relatively conserved and stable genomic composition with a lower codon usage choice in the two BBWV2 protein coding sequences. ENC-plot and neutrality plot analyses showed that natural selection is the key factor shaping the codon usage pattern of BBWV2. Strong correlations between BBWV2 and broad bean and pepper were observed from similarity index (SiD), codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses. Our study is the first to evaluate the phylodynamics, codon usage patterns and adaptive evolution of a fabavirus, and our results may be useful for the understanding of the origin of this virus.

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Section: Discussionsupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Dong

Qin

et al. 2021

Viruses

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“…However, the SCMV isolated from canna has been considered a recombinant strain with one parent infecting maize (Li et al 2019). The correlation between SCMV and maize was also higher than the correlation between SCMV and sugarcane in a study based on the codon usage patterns of the virus (He et al 2020). The capacity of maize to host a great diversity of SCMV strains may also be associated with an aphid vector such as the corn leaf aphid Rhopalosiphum maydis, which has a worldwide distribution, is found in cultivated fields and grasslands, and feeds on a wide range of monocots (Blackman and Eastop 2000).…”

Section: Discussionmentioning

confidence: 99%

“…Historically, the CP has often been used for diagnosis of SCMV and characterization of its genetic diversity (Alegria et al 2003;de Souza et al 2012;G omez et al 2009;Handley et al 1998;Marie-Jeanne et al 2000;Moradi et al 2017;Yang and Mirkov 1997). More recently, full genome sequencing has been used to investigate variation within the virus and especially to analyze genomic evolution (Braidwood et al 2019;He et al 2020;Wamaitha et al 2018;Yahaya et al 2019). These studies revealed that SCMV is highly variable, with several recombination hotspots along its genome.…”

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confidence: 99%

Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area

Hincapie

Sood

Mollov³

et al. 2021

Phytopathology®

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Sugarcane mosaic virus (SCMV) was detected by reverse-transcription polymerase chain reaction in eight different species of the Poaceae family in the Everglades Agricultural Area (EAA) of south Florida: Broadleaf signalgrass (Urochloa platyphylla), Columbus grass (Sorghum almum), goosegrass (Eleusine indica), maize (Zea mays), sorghum (Sorghum bicolor), St. Augustine grass (Stenotaphrum secundatum), southern crabgrass (Digitaria ciliaris), and sugarcane (Saccharum interspecific hybrids). Based on their coat protein (CP) gene sequence, 62 isolates of SCMV from Florida and 29 worldwide isolates representing the known genetic diversity of this virus were distributed into eight major phylogenetic groups. SCMV isolates infecting Columbus grass, maize, and sorghum in Florida formed a unique group whereas virus isolates infecting sugarcane in the USA (Florida and Louisiana) clustered with isolates from other countries. Based on the entire genome coding region, SCMV isolates infecting sugarcane in Florida were closest to virus isolates infecting sorghum species or St. Augustine grass. Virus isolates from Columbus grass, St. Augustine grass, and sugarcane showed different virulence patterns after mechanical inoculation of Columbus grass, St. Augustine grass, and sugarcane plants, thus proving that these isolates were different pathogenic strains. Sugarcane was symptomless and tested negative for SCMV by tissue blot immunoassay after inoculation with crude sap from SCMV-infected Columbus grass, indicating that Columbus grass was not a reservoir for SCMV infecting sugarcane in the EAA. Close CP sequence identity between isolates of SCMV from Columbus grass, maize, and sorghum suggested that the same virus strain was naturally spreading among these three plants in south Florida.

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“…A procedure has been developed to assess the presence of potyviruses in samples of infected cereals, followed by identification of the virus species or mix of species (in case of co-infection) of the genus Potyvirus [4]. MDMV and SCMV have been identified in maize plants on all continents [5][6][7][8][9][10][11][12][13][14][15][16], JGMV was found in Johnsongrass (Sorghum halepense), elephant grass (Pennisetum purpureum) and maize in Australia, USA, Brazil and Africa [17,18], and SrMV was identified in maize only in the USA and on sugar cane in China and India [1,3,19,20]. MDMV is the most common pathogen аmong all the viruses that infect maize worldwide [21].…”

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confidence: 99%

First Report of Sugarcane Mosaic Virus in Zea mays L. in Ukraine

Snihur¹,

Харина²,

Kaliuzhna³

et al. 2021

Mikrobiol. Z.

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Maize viral diseases especially maize dwarf mosaic disease (MDMD), which is caused by potyviruses, lead to significant crop losses worldwide. Aim. The aim of this work was to identify the causal agent of mosaic symptoms, observed on maize plants during 2018—2020 in Kyiv region. Methods. Enzyme-linked immunosorbent assay in the DAS-ELISA modification using commercial Loewe Biochemica test systems for Maize dwarf mosaic virus (MDMV), Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) were applied to identify the causal agent of maize disease in collected samples. Transmission electron microscopy was used in order to direct viral particle visualisation. Aphids, which are natural vectors of plant viruses, were found on diseased plants. Results. Plants with typical mosaic symptoms were observed in corn crops of the Kyiv region in early June 2018. The pathogen was transmitted by mechanical inoculation to maize and sweet maize plants with the manifestation of mosaic symptoms. Electron microscopy of the sap from diseased plants revealed the presence of flexible filamentous virions 750 nm long and 13 nm in diameter, typical for the genus Potyvirus. In August, mosaic symptoms and aphids Rhopalosiphum padi were found on previously healthy plants in the same maize crop. In 2020, in the same sown area, maize plants were free of viral infection during inspection in June, but a re-inspection in September revealed mosaic symptoms on maize crop and the presence of aphids in the leaf axils. The presence of SCMV in maize samples collected in June and August/September 2018 and 2020, as well as in inoculated maize and sweet maize plants, was confirmed by ELISA using a commercial test system. The obtained data allow suggesting that Rhopalosiphum padi is a natural vector of SCMV in agrocenoses of Ukraine. It should be noted that co-infection with MDMV and WSMV in the affected plants was not detected. Conclusions. This study presents the first report of SCMV in maize in Ukraine.

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Genetic changes and host adaptability in sugarcane mosaic virus based on complete genome sequences

Cited by 17 publications

References 74 publications

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Phylodynamics and Codon Usage Pattern Analysis of Broad Bean Wilt Virus 2

Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area

First Report of Sugarcane Mosaic Virus in Zea mays L. in Ukraine

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