Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination

Ohshima, Kazusato; Tomitaka, Yasuhiro; Wood, Jeffery T.; Minematsu, Y; Kajiyama, Hiromi; Tomimura, Kenta; Gibbs, Adrian

doi:10.1099/vir.0.82335-0

Cited by 129 publications

(129 citation statements)

References 70 publications

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“…The phylogenetic groups of the isolates, namely IRN-1 and IRN-2, closely corresponded to the L and N biological groups, respectively ( Table 2). These data seem to indicate the important role of "host" in the evolution of TYFRV populations, as reported previously for other viruses (Ohshima et al, 2007). The amino acid sequence comparison of nucleoprotein genes of the isolates between the two groups showed 90.8−92.7% identities, which are close to the threshold value used for species determination in the genus Tospovirus (90.0%) (Goldbach and Kuo, 1996).…”

Section: Discussionsupporting

confidence: 60%

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Partial Biological and Molecular Characterization of Tomato yellow fruit ring virus Isolates from Potato

Pourrahim¹,

Golnaraghi²,

Farzadfar³

et al. 2012

The Plant Pathology Journal

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Eight potato-producing provinces of Iran were surveyed during the growing seasons of 2004−2006 to detect the presence of Tomato yellow fruit ring virus (TYFRV), a tentative species in the genus Tospovirus. A total of 1,957 potato leaf samples were collected from plants with tospovirus-like symptoms of chlorotic or necrotic spots, chlorosis and necrosis. The samples were tested by enzyme-linked immunosorbent assay using TYFRVspecific antibodies. Among those tested, 498 samples (25.4%) were found to be infected with the virus. The virus was detected in 72.4% of the potato fields in all provinces surveyed. Thirteen potato isolates of TYFRV were selected for further biological and molecular studies. Based on their reactions on Nicotiana tabacum plants, the isolates were separated into two groups, namely L (local infection) and N (systemic infection). The nucleotide sequences of the nucleoprotein (N) genes of the isolates were determined and compared with the homologous sequences in Genbank. No recombination evidence was found in the isolates using different recombination-detecting programs. In the phylogenetic tree, the potato isolates fell into two major groups: IRN-1 and IRN-2 corresponding to the two biologically separated groups. This study shows for the first time the biological and phylogenetic relationships of geographically distant TYFRV isolates from potatoes in the midEurasian country of Iran.

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Section: Discussionsupporting

confidence: 60%

“…Recombination plays a pivotal role in diversification and evolution of both plant RNA and DNA viruses (Ohshima et al, 2007;Prasanna and Rai, 2007). In this study, none of the TYFRV isolates seemed to be recombinants.…”

Section: Discussionmentioning

confidence: 82%

Partial Biological and Molecular Characterization of Tomato yellow fruit ring virus Isolates from Potato

Pourrahim¹,

Golnaraghi²,

Farzadfar³

et al. 2012

The Plant Pathology Journal

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“…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). The recombinant isolate (GK76-4) obtained in this study was found to have two recombination sites which occurred in the variable N-terminal region and the conserved sequence at the C-terminal regions of the CP gene (Table 4).…”

Section: Discussionmentioning

confidence: 97%

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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“…However, any regions of homology are usually short and may be associated with secondary structures that facilitate the recombination process . Some of the typical properties of sites involved in recombination between viral RNAs include an AU-rich sequence adjacent to a 5' GC-rich region Ohshima et al, 2007;Vives et al, 2005).…”

Section: Incorporation Of Donor Genetic Materialsmentioning

confidence: 99%

Risks from GMOs due to Horizontal Gene Transfer

Keese¹

2008

Environ. Biosafety Res.

135

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Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.

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Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination

Cited by 129 publications

References 70 publications

Partial Biological and Molecular Characterization of Tomato yellow fruit ring virus Isolates from Potato

Partial Biological and Molecular Characterization of Tomato yellow fruit ring virus Isolates from Potato

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

Risks from GMOs due to Horizontal Gene Transfer

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