Sequence characteristics of potato virus Y recombinants

Hu, Xiaojun; Karasev, Alexander V.; Brown, Celeste J.; Lorenzen, J.

doi:10.1099/vir.0.014142-0

Cited by 62 publications

(39 citation statements)

References 66 publications

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“…This can be explained by a 94 % nucleotide identity shared between PVY-Bzh-1 and PVY Guiding. The development of new variants through mutation and recombination had foster global distribution of the isolates [33]. The phylogenetic analysis of the TMV isolates also confirms the redistribution of the plant viruses across borders.…”

Section: Resultsmentioning

confidence: 88%

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Akinyemi

Wang

Zhou

et al. 2016

Virol J

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BackgroundThe invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses. A survey of plant viruses infecting field-grown Tobacco crop was conducted in Anhui Province of China by the deep sequencing of sRNAs.MethodsSurvey of plant viruses infecting Tobacco was carried based on 104 samples collected across the province. Nine different sRNA libraries was prepared and custom-made bioinformatics pipeline coupled with molecular techniques was developed to sequence, assemble and analyze the siRNAs for plant virus discovery. We also carried out phylogenetic and recombination analysis of the identified viruses.ResultsTwenty two isolates from eight different virus species including Cucumber mosaic virus, Potato virus Y, Tobacco mosaic virus, Tobacco vein banding Mosaic virus, Pepper mottle virus, Brassica yellow virus, Chilli venial mottle virus, Broad bean wilt virus 2 were identified in tobacco across the survey area. The near-complete genome sequence of the 22 new isolates were determined and analyzed. The isolates were grouped together with known strains in the phylogenetic tree. Molecular variation in the isolates indicated the conserved coding regions have majorly a nucleotide sequence identity of 80-94 % with previously identified isolates. Various events of recombination were discovered among some of the isolates indicating that two or more viruses or different isolates of one virus infect the same host cell.ConclusionThis study describes the discovery of a consortium of plant viruses infecting Tobacco that are broadly distributed in Anhui province of China. It also demonstrates the effectiveness of NGS in identifying plant viruses without a prior knowledge of the virus and the genetic diversity that enhanced mixed infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0639-7) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 88%

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Akinyemi

Wang

Zhou

et al. 2016

Virol J

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“…Additional pathological and biological characterization of these isolates is necessary to further type the NTN and N-Wi populations. This would also allow researchers to further categorize the NTN strain into PVY NTNHun (European PVY NTN ) and PVY NTN -Tu 660 (North American PVY NTN ), the two NTN types identified and discussed by several research groups (Thole et al 1993, Nie & Singh 2002, 2003a, b, Piche et al 2004, Chikh Ali et al 2007b, 2010b, Hu et al 2009.…”

Section: Discussionmentioning

confidence: 99%

Potato virus Y (PVY) strains in Belgian seed potatoes and first molecular detection of the N-Wi strain

Kamangar

Smagghe

Maes³

et al. 2014

J Plant Dis Prot

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Potato virus Y (PVY), one of the most important agents causing potato crop losses worldwide, is transmitted by a variety of aphid species in a non-persistent manner. Several PVY strains have been differentiated, all of them causing different symptoms and symptom expression levels on numerous commercial potato cultivars. In Belgium, strains belonging to the N group have been reported as the most prevalent, but no detailed information on the relative importance of the PVY strains in Belgium have been published to date.We report here on a survey performed on Belgian seed potatoes harvested in 2010 in which 2700 individual tubers from 54 seed potato lots originating from 54 farms were screened for presence of PVY. The results revealed a high PVY incidence and substantial strain diversity in some farms. The dominance of the N group in Belgian seed potatoes was confirmed, while the O strain was only found in a few locations. Further characterization using multiplex PCR identified 75% of the isolates as NTN strains and 7.5% as Wilga strain (N-Wi). The presence of the N-Wi strain was confirmed and characterized for the first time in Belgian seed potato production.

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“…It has been well documented that recombination plays an important role in the rapid evolution of potyviruses [24,30,40]. Recombination analysis of all the full genome sequences with the P1, CP and 3 0 -UTR sequences of the 14 …”

Section: Recombination Analysismentioning

confidence: 99%

Characterisation of potato virus Y isolates from Iran

et al. 2010

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A survey of Potato virus Y (PVY) was conducted in cultivated fields in six Iranian provinces between January 2005 to July 2007. Two hundred samples from potato and tomato were collected and analyzed by enzyme-linked immunosorbent assay (ELISA) for potyviruses. Almost one fourth of the samples were found to be infected by PVY. Analysis of these PVY-positive samples using three monoclonal antibodies (MAbs) facilitating the simultaneous detection of three main strains namely the ordinary (PVY(O)), strain (PVY(N)) and C (PVY(C)) strains. However, the fourth strain (PVY(NTN)) and some others recombinant isolates were also identified by molecular methods. Host range and symptoms analysis using sap inoculation of four different strains of PVY onto a range of plants revealed that the four strains showed biological properties that seemed to be consistent with their molecular grouping. Fourteen isolates of PVY were chosen based on the host and geographical location, primer specificity and serology for further biological and molecular characterisation. The coat protein (CP) and P1 genes and 3'-non-translated region (3'NTR) from 14 representative isolates were sequenced and analysed with the sequences available in GenBank. Composite analysis of the P1, CP and 3'-UTR sequences with all full genome sequences of PVY revealed that there are three potential strains of PVY in Iran, PVY(O), PVY(N)-W and PVY(NTN). Isolate KER.SA(N) was the most divergent of all the 14 isolates reacted with PVY(N) specific MAbs but grouped with PVY(O) strains in maximum likelihood phylogentic analysis. The PVY(NTN) isolates from Iran more closely related to the European than North American PVY(NTN) isolates.

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Sequence characteristics of potato virus Y recombinants

Cited by 62 publications

References 66 publications

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Potato virus Y (PVY) strains in Belgian seed potatoes and first molecular detection of the N-Wi strain

Characterisation of potato virus Y isolates from Iran

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