Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank

Naveed, Khalid; Mitter, Neena; Harper, Artemus; Dhingra, Amit; Pappu, H. R.

doi:10.1016/j.virusres.2014.07.005

Cited by 18 publications

(24 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…7), while for 21-22 nt vsRNAs the enrichment was not significant, even if preference for 5 terminal A and U was observed (not shown). Preference for A/U terminal nucleotides compared to G/C was described in previous vsRNA analyses, for instance for RSV in rice and N. benthamiana plants (Yan et al, 2010;Xu et al, 2012), tomato yellow leaf curl China virus in tomato (Yang et al, 2011), potato virus Y in potato (Naveed et al, 2014), sugarcane mosaic virus in maize (Xia et al, 2014), and TSWV in tomato and N. benthamiana (Mitter et al, 2013;Margaria et al, 2015a). Preferential sorting of small RNAs into AGO complexes has been shown to be directed by the 5 terminal nucleotide (Takeda et al, 2008;Mi et al, 2008;Mallory and Vaucheret, 2010).…”

Section: Sense Vsrnas Are Enriched For Nss But Not For Nsm Genementioning

confidence: 78%

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection

et al. 2016

View full text Add to dashboard Cite

Section: Sense Vsrnas Are Enriched For Nss But Not For Nsm Genementioning

confidence: 78%

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection

et al. 2016

View full text Add to dashboard Cite

“…The PVY strains (PVY-N, PVY-NTN and PVY-O) are known to elicit varied biological responses and differential expression of their genome-derived vsiRNAs [2, 15]. With that in mind, we anticipated varied interaction between PVY strain-specific vsiRNAs and the potato transcripts.…”

Section: Discussionmentioning

confidence: 99%

“…From our previous study [15], we obtained the complete potato specific small RNAs including virus-derived small interfering RNAs (vsiRNAs) profile of three biologically distinct PVY strains (PVY-N, PVY-NTN, PVY-O) infecting the potato cv. Russet Burbank.…”

Section: Methodsmentioning

confidence: 99%

“…Russet Burbank plants, grown under greenhouse conditions as described by Naveed et al 2014 [15], using Trizol reagent (Invitrogen, Carlsbad, CA, USA). Extracted RNA was treated with 2 U of DNase I (Ambion, TX, USA) at 37 °C for 30 min.…”

Section: Methodsmentioning

confidence: 99%

“…A deep sequencing study has revealed the differential accumulation of small RNAs derived from PVY-N, PVY-NTN and PVY-O upon infection of the same potato host cv. Russet Burbank [15]. …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The effects of potato virus Y-derived virus small interfering RNAs of three biologically distinct strains on potato (Solanum tuberosum) transcriptome

Moyo

Ramesh

Kappagantu

et al. 2017

Virol J

Self Cite

View full text Add to dashboard Cite

Background Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions. This study investigated the global effects of PVY vsiRNAs on the host potato transcriptome.MethodsThe strain-specific vsiRNAs of PVY, expressed in high copy number, were analyzed in silico for their proclivity to target potato coding and non-coding RNAs using psRobot and psRNATarget algorithms. Functional annotation of target coding transcripts was carried out to predict physiological effects of the vsiRNAs on the potato cv. Russet Burbank. The downregulation of selected target coding transcripts was further validated using qRT-PCR.ResultsThe vsiRNAs derived from biologically distinct strains of PVY displayed diversity in terms of absolute number, copy number and hotspots for siRNAs on their respective genomes. The vsiRNAs populations were derived with a high frequency from 6 K1, P1 and Hc-Pro for PVY-N, P1, Hc-Pro and P3 for PVY-NTN, and P1, 3′ UTR and NIa for PVY-O genomic regions. The number of vsiRNAs that displayed interaction with potato coding transcripts and number of putative coding target transcripts were comparable between PVY-N and PVY-O, and were relatively higher for PVY-NTN. The most abundant target non-coding RNA transcripts for the strain specific PVY-derived vsiRNAs were found to be MIR821, 28S rRNA,18S rRNA, snoR71, tRNA-Met and U5. Functional annotation and qRT-PCR validation suggested that the vsiRNAs target genes involved in plant hormone signaling, genetic information processing, plant-pathogen interactions, plant defense and stress response processes in potato.ConclusionsThe findings suggested that the PVY-derived vsiRNAs could act as a pathogenicity determinant and as a counter-defense strategy to host RNA silencing in PVY-potato interactions. The broad range of host genes targeted by PVY vsiRNAs in infected potato suggests a diverse role for vsiRNAs that includes suppression of host stress responses and developmental processes. The interactome scenario is the first report on the interaction between one of the most important Potyvirus genome-derived siRNAs and the potato transcripts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-017-0803-8) contains supplementary material, which is available to authorized users.

show abstract

Functional biology of potato-virus interactions

Jeevalatha

Chakrabarti

Khurana

2021

Plant Virus-Host Interaction

View full text Add to dashboard Cite

Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank

Cited by 18 publications

References 47 publications

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection

The effects of potato virus Y-derived virus small interfering RNAs of three biologically distinct strains on potato (Solanum tuberosum) transcriptome

Functional biology of potato-virus interactions

Contact Info

Product

Resources

About