Molecular variability of sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions

He, Zhen; Li, Wenfeng; Yasaka, Ryosuke; Huang, Ying-Kun; Zhang, Zhixiang; Ohshima, Kazusato; Li, Shifang

doi:10.1007/s00705-013-1854-9

Cited by 26 publications

(32 citation statements)

References 31 publications

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“…More evidence from the recombination detection by RDP4 revealed two recombinant isolates, GK76-4 and GROC7 (Table 4). A previous study reported that the recombinant isolate from China, CB671-1, was distributed from the parents, W23×IND671, and three recombinant isolates (CB740, CB9217-1 and S-8) were distributed from the same parents, THA-NP3×CB671-1 (He et al, 2013). In this study, we found that two recombinant isolates from China (CB671-1 and M55) were distributed from the parents, FUD10-7×IND671 and GRT2007-091×PAK, respectively.…”

Section: Discussionsupporting

confidence: 49%

“…Nucleotide sequence comparison among seven complete genome isolates (THA-NP3, PAK, ID, JP1, JP2, IND671 and TPT) revealed more genetic variations in the P1, HC-Pro and CP genes. These three proteins revealed more genetic variation among SCSMV isolates originally from different sugarcane varieties (Bagyalakshmi et al, 2012;He et al, 2013).…”

Section: Discussionmentioning

confidence: 96%

“…These results suggest that the recombination events occurred in the CP gene among the virus isolates from Thailand, China and India. More results have been reported that the recombination events occurred throughout the HC-Pro gene of SCSMV but not in the P1 gene (Bagyalakshmi et al, 2012;He et al, 2013). Recombination events have been reported as the evolutionary history of single-stranded RNA genome such as Turnip mosaic virus (TuMV), in the P1, HC-Pro, P3, CI, 6K2, VPg, NIa-Pro, NIb and CP genes, except for 6K1 gene (Ohshima et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

“…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. The comparison of these genes revealed high variation among different SCSMV isolates resulting from recombination (Bagyalakshmi et al, 2012;He et al, 2013).…”

mentioning

confidence: 99%

“…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. The comparison of these genes revealed high variation among different SCSMV isolates resulting from recombination (Bagyalakshmi et al, 2012;He et al, 2013). In Thailand, the presence and distribution of SCSMV in Thailand and genetic variations of the existing isolates still have not been recorded so far.…”

mentioning

confidence: 99%

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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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Section: Discussionsupporting

confidence: 49%

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Kasemsin¹,

Chiemsombat²,

Hongprayoon³

2016

MAS

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Biotechnological Approaches to Improve Sugarcane Quality and Quantum Under Environmental Stresses

Sugiharto

Harmoko²,

Sawitri

2022

Agro-Industrial Perspectives on Sugarcane Production Under Environmental Stress

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Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions

Liu

et al. 2015

Arch Virol

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The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.

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Molecular variability of sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions

Cited by 26 publications

References 31 publications

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

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

Biotechnological Approaches to Improve Sugarcane Quality and Quantum Under Environmental Stresses

Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions

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