Molecular characterization of a new strain of sugarcane streak mosaic virus (SCSMV)

Li, Wenfeng; He, Zhen; Li, Shifang; Huang, Ying‐Kun; Zhang, Zhixiang; Jiang, Dongmei; Wang, Xiaoyan; Luo, Zhi-Ming

doi:10.1007/s00705-011-1090-0

Cited by 46 publications

(37 citation statements)

References 11 publications

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“…In recent years, three SCSMV isolates were found in sugarcane plants imported from Japan and Indonesia, and were allowed to grow in a quarantine zone at the National Nursery for Sugarcane Germplasm Resources in Kaiyuan, Yunnan province (Chen et al 2002). Whole genome sequence analyses indicated that these isolates from China were distinct from the previously described SCSMV-PAK and SCSMV-India isolates suggesting that they represented new strains of SCSMV (Li et al 2011).…”

Section: Introductionmentioning

confidence: 91%

Genetic diversity of viruses associated with sugarcane mosaic disease of sugarcane inter-specific hybrids in China

et al. 2015

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In this study, we investigated 78 sugarcane samples with severe mosaic symptoms collected from four provinces of southern China: Guangxi, Yunnan, Hainan, and Guangdong, which cover nearly 85 % of commercial sugarcane planting zones in China. Using RT-PCR, sequencing and phylogenetic analysis, we identified 72 hybrid sugarcane samples containing causal agents of sugarcane mosaic disease. Among these, 66 virus isolates were identified as Sorghum mosaic virus (SrMV) (84.6 %), four were identified as Sugarcane streak mosaic virus (SCSMV) (5.1 %), and two were identified as Sugarcane mosaic virus (SCMV) (2.6 %). The isolates of SrMV were classified into three subgroups: I, II, and III with a 95 % similarity level. The two largest subgroups, SrMV I containing 36 sugarcane mosaic diseases isolates (46.2 %), and SrMV III containing 20 isolates (25.6 %), were prevalent in Guangdong and Guangxi provinces; however, SrMV II containing five isolates (6.4 %) did not exhibit any close association with geographical distribution. The popular sugarcane cultivar, ROC22, was found Eur J Plant Pathol

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Section: Introductionmentioning

confidence: 91%

Genetic diversity of viruses associated with sugarcane mosaic disease of sugarcane inter-specific hybrids in China

et al. 2015

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“…However, the sequence variation could not be correlated with the geographical origin of the isolates. More recently, four complete genomic sequences of SCSMV isolates were deposited in the GenBank database, and nt sequence analysis revealed variability in the HC-Pro gene [7,8]. Viral gene sequences can be quite useful in revealing population structure, phylogenetic relationships, and the demographic history of their host [12].…”

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confidence: 99%

“…SCSMV has flexuous filamentous particles (890 9 15 nm) containing a single-stranded positive-sense RNA genome of approximately 10 kb. The SCSMV genome has a single open reading frame that is translated in to a large polypeptide and subsequently cleaved into functional proteins [7,8].…”

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Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus

et al. 2012

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Sugarcane streak mosaic virus (SCSMV), a member of the family Potyviridae, is an important viral pathogen affecting sugarcane production in India. The variability in the nucleotide (nt) and amino acid (aa) sequences of helper component proteinase (HC-Pro) of SCSMV isolates from India was investigated and compared with those of previously published virus isolates from different Asian countries. Comparison of all of the sequenced virus isolates revealed a high level of diversity in the HC-Pro gene (72-97% nt sequence identity; 83-99% aa sequence identity), and the Indian isolates were found to be the most divergent (up to 12% variation at the amino acid level). Phylogenetic analysis revealed clustering of 16 SCSMV isolates into two groups. Group I included isolates from India and Pakistan, and group II consisted of isolates from Japan and Indonesia. Recombination analysis revealed nine potentially significant recombination events, and putative recombination sites were identified throughout the HC-Pro gene. Analysis of selection pressure indicated that the HC-Pro gene of SCSMV is under strong negative selection. It is likely that recombination, along with strong negative selection, enhances the speed of elimination of deleterious mutations in the HC-Pro gene.

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“…SCSMV was reported for its devastating effects in Asia, including India (Viswanathan et al, 2008), Pakistan, Sri Lanka, Vietnam, Thailand (Chatenet et al, 2005), China (Li et al, 2011) and Indonesia (Damayanti & Putra, 2011). The identified hosts of SCSMV under natural condition are poaceae plants including sugarcane, maize, sorghum and Egyptian crowfoot grass (Dactylactonium aegypticum) (Hema, Joseph, Gopinath, Sreenivasulu, & Savithri, 1999;Putra, Kristini, Achadian, & Damayanti, 2014;Srinivas, Subba Reddy, Ramesh, Lava Kumar, & Sreenivasulu, 2010).…”

mentioning

confidence: 99%

“…Sequence comparison and a phylogenetic tree of the complete genome revealed that SCSMV was a distinct group from those of other genus in the family Potyviridae, and has been recently named Poacevirus (Xu et al, 2010;ICTV: www.ictvonline.org). More isolates of SCSMV and their complete genome sequences were reported from China (Li et al, 2011) and India (Parameswari, Bagyalakshmi, Viswanathan, & Chinnaraja, 2013). The study on genetic variability of SCSMV has been investigated using the analysis of CP (He et al, 2013), P1 (He et al, 2013) and HC-Pro (Bagyalakshmi et al, 2012) coding regions.…”

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confidence: 99%

Characterization and Genetic Variation of Sugarcane Streak Mosaic Virus, a Poacevirus Infecting Sugarcane in Thailand

Kasemsin¹,

Chiemsombat²,

Hongprayoon³

2016

MAS

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Sugarcane leaves showing yellow streak mosaic symptoms were observed in farmers' fields in Kamphaeng Saen, Nakhon Pathom province, during disease surveys conducted in 2010. Diagnosis of symptomatic leaf samples by RT-PCR for Sugarcane mosaic potyvirus failed, but it revealed the presence of Sugarcane streak mosaic virus (SCSMV). SCSMV-infected sugarcane, designated as THA-NP3, was subjected to RNA extraction and RT-PCR-based viral gene cloning and sequencing. The complete genome of THA-NP3 (JN163911) contained 9,781 nucleotides, excluding 3′ poly (A) tail which encoded a polyprotein of 3,130 amino acid residues. Protein sequence analysis indicated nine putative cleavage sites that yielded ten functional proteins namely P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, NIa-Pro, NIb and CP, and an additional frameshifted PIPO protein. Sequence alignment revealed that THA-NP3 shared 97.84% nucleotide identity with JP2 from China and 81.39-97.78% identities to other recorded SCSMV sequences. Surveys for streak mosaic disease were conducted from 2010 to 2014 at major sugarcane growing areas in five provinces, Nakhon Pathom, Kanchanaburi, Nakhon Ratchasima, Khon Kaen and Udon Thani, and among germplasm collections. The percentages of the infected samples ranged from 43.48-90.91% and 54.17-100% in collected farmers and germplasm fields, respectively. Genetic diversity based on coat protein (CP) coding sequences of 58 Thai SCSMV isolates showed 86.17-100% nucleotide identities among them and 85.70-99.29% identities to isolates from other countries. Phylogenetic analysis of CP sequences indicated two major clusters of virus variants, one in cropping fields and another in germplasm fields. Genetic variations of SCSMV isolates were consistently indicated according to recombination events detected in CP coding regions. These findings represent essential knowledge and should be utilized to improve the SCSMV resistance of sugarcane varieties.

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Molecular characterization of a new strain of sugarcane streak mosaic virus (SCSMV)

Cited by 46 publications

References 11 publications

Genetic diversity of viruses associated with sugarcane mosaic disease of sugarcane inter-specific hybrids in China

Genetic diversity of viruses associated with sugarcane mosaic disease of sugarcane inter-specific hybrids in China

Genetic variability and potential recombination events in the HC-Pro gene of sugarcane streak mosaic virus

Characterization and Genetic Variation of Sugarcane Streak Mosaic Virus, a Poacevirus Infecting Sugarcane in Thailand

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