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Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization.

Pooggin MM.

Front Microbiol. 2018 Nov 20;9:2779. doi: 10.3389/fmicb.2018.02779. eCollection 2018. Review.


Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies.

Massart S, Chiumenti M, De Jonghe K, Glover R, Haegeman A, Koloniuk I, Komínek P, Kreuze J, Kutnjak D, Lotos L, Maclot F, Maliogka V, Maree HJ, Olivier T, Olmos A, Pooggin MM, Reynard JS, Ruiz-García AB, Safarova D, Schneeberger PHH, Sela N, Turco S, Vainio EJ, Varallyay E, Verdin E, Westenberg M, Brostaux Y, Candresse T.

Phytopathology. 2019 Mar;109(3):488-497. doi: 10.1094/PHYTO-02-18-0067-R. Epub 2019 Feb 7.


Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond.

Pooggin MM, Ryabova LA.

Front Microbiol. 2018 Apr 10;9:644. doi: 10.3389/fmicb.2018.00644. eCollection 2018. Review.


Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses.

Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski NE, Pappu HR, Pooggin MM, Richert-Pöggeler KR, Sabanadzovic S, Sanfaçon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH.

J Virol. 2018 May 29;92(12). pii: e00515-18. doi: 10.1128/JVI.00515-18. Print 2018 Jun 15. No abstract available.


Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants.

Turco S, Golyaev V, Seguin J, Gilli C, Farinelli L, Boller T, Schumpp O, Pooggin MM.

Mol Plant Microbe Interact. 2018 Jul;31(7):707-723. doi: 10.1094/MPMI-12-17-0301-R. Epub 2018 May 10.


Revisiting the Roles of Tobamovirus Replicase Complex Proteins in Viral Replication and Silencing Suppression.

Malpica-López N, Rajeswaran R, Beknazariants D, Seguin J, Golyaev V, Farinelli L, Pooggin MM.

Mol Plant Microbe Interact. 2018 Jan;31(1):125-144. doi: 10.1094/MPMI-07-17-0164-R. Epub 2017 Nov 15.


RNAi-mediated resistance to viruses: a critical assessment of methodologies.

Pooggin MM.

Curr Opin Virol. 2017 Oct;26:28-35. doi: 10.1016/j.coviro.2017.07.010. Epub 2017 Jul 25. Review.


Emergence of a Latent Indian Cassava Mosaic Virus from Cassava Which Recovered from Infection by a Non-Persistent Sri Lankan Cassava Mosaic Virus.

Karthikeyan C, Patil BL, Borah BK, Resmi TR, Turco S, Pooggin MM, Hohn T, Veluthambi K.

Viruses. 2016 Sep 28;8(10). pii: E264.


Viral protein suppresses oxidative burst and salicylic acid-dependent autophagy and facilitates bacterial growth on virus-infected plants.

Zvereva AS, Golyaev V, Turco S, Gubaeva EG, Rajeswaran R, Schepetilnikov MV, Srour O, Ryabova LA, Boller T, Pooggin MM.

New Phytol. 2016 Aug;211(3):1020-34. doi: 10.1111/nph.13967. Epub 2016 Apr 27.


MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies.

Seguin J, Otten P, Baerlocher L, Farinelli L, Pooggin MM.

J Virol Methods. 2016 Jul;233:37-40. doi: 10.1016/j.jviromet.2016.03.005. Epub 2016 Mar 16.


Field Trial and Molecular Characterization of RNAi-Transgenic Tomato Plants That Exhibit Resistance to Tomato Yellow Leaf Curl Geminivirus.

Fuentes A, Carlos N, Ruiz Y, Callard D, Sánchez Y, Ochagavía ME, Seguin J, Malpica-López N, Hohn T, Lecca MR, Pérez R, Doreste V, Rehrauer H, Farinelli L, Pujol M, Pooggin MM.

Mol Plant Microbe Interact. 2016 Mar;29(3):197-209. doi: 10.1094/MPMI-08-15-0181-R. Epub 2016 Feb 11.


Interactions of Rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery.

Rajeswaran R, Golyaev V, Seguin J, Zvereva AS, Farinelli L, Pooggin MM.

Mol Plant Microbe Interact. 2014 Dec;27(12):1370-8. doi: 10.1094/MPMI-07-14-0201-R.


Evasion of short interfering RNA-directed antiviral silencing in Musa acuminata persistently infected with six distinct banana streak pararetroviruses.

Rajeswaran R, Seguin J, Chabannes M, Duroy PO, Laboureau N, Farinelli L, Iskra-Caruana ML, Pooggin MM.

J Virol. 2014 Oct;88(19):11516-28. doi: 10.1128/JVI.01496-14. Epub 2014 Jul 23.


De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs.

Seguin J, Rajeswaran R, Malpica-López N, Martin RR, Kasschau K, Dolja VV, Otten P, Farinelli L, Pooggin MM.

PLoS One. 2014 Feb 11;9(2):e88513. doi: 10.1371/journal.pone.0088513. eCollection 2014.


MISIS: a bioinformatics tool to view and analyze maps of small RNAs derived from viruses and genomic loci generating multiple small RNAs.

Seguin J, Otten P, Baerlocher L, Farinelli L, Pooggin MM.

J Virol Methods. 2014 Jan;195:120-2. doi: 10.1016/j.jviromet.2013.10.013. Epub 2013 Oct 14.


How can plant DNA viruses evade siRNA-directed DNA methylation and silencing?

Pooggin MM.

Int J Mol Sci. 2013 Jul 24;14(8):15233-59. doi: 10.3390/ijms140815233. Review.


Silencing and innate immunity in plant defense against viral and non-viral pathogens.

Zvereva AS, Pooggin MM.

Viruses. 2012 Oct 29;4(11):2578-97. doi: 10.3390/v4112578. Review.


Primary and secondary siRNAs in geminivirus-induced gene silencing.

Aregger M, Borah BK, Seguin J, Rajeswaran R, Gubaeva EG, Zvereva AS, Windels D, Vazquez F, Blevins T, Farinelli L, Pooggin MM.

PLoS Pathog. 2012 Sep;8(9):e1002941. doi: 10.1371/journal.ppat.1002941. Epub 2012 Sep 27.


Sequencing of RDR6-dependent double-stranded RNAs reveals novel features of plant siRNA biogenesis.

Rajeswaran R, Aregger M, Zvereva AS, Borah BK, Gubaeva EG, Pooggin MM.

Nucleic Acids Res. 2012 Jul;40(13):6241-54. doi: 10.1093/nar/gks242. Epub 2012 Mar 19.


Short ORF-dependent ribosome shunting operates in an RNA picorna-like virus and a DNA pararetrovirus that cause rice tungro disease.

Pooggin MM, Rajeswaran R, Schepetilnikov MV, Ryabova LA.

PLoS Pathog. 2012;8(3):e1002568. doi: 10.1371/journal.ppat.1002568. Epub 2012 Mar 1.

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