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Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipelin...


Yi ZhengShan GaoPadmanabhan, C.Li, R.Galvez, M.Gutiérrez, D.Fuentes, S.Kai-Shu LingKreuze, J.F.Zhangjun Fei[VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs.]VirusDetect: an automated pipeline for efficient virus discovery using deep sequencing of small RNAs.

Cuéllar, Wilmer J.Galvez, MarcoFuentes, S.Tugume, Joab K.Kreuze, J.F.[Synergistic interactions of begomoviruses with sweet potato chlorotic stunt virus (genus Crinivirus) in sweetpotato (Ipomoea batatas L.)]Synergistic interactions of begomoviruses with sweet potato chlorotic stunt virus (genus Crinivirus) in sweetpotato (Ipomoea batatas L.)

The complete bipartite genome (RNA1 and RNA2) of a new nepovirus infecting potato was obtained using small RNA sequencing and assembly complemented by Sanger sequencing. Each RNA encodes a single polyprotein, flanked by 5’ and 3’ untranslate regions (UTR) and followed by a poly (A) tail. The puta...


Souza, Joao deMuller, G.Pérez, W.Cuéllar, Wilmer J.Kreuze, J.F.[Complete sequence and variability of a new subgroup B nepovirus infecting potato in central Peru]Complete sequence and variability of a new subgroup B nepovirus infecting potato in central Peru

The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680–900 nm long and 11–20 nm wide. There are eight genera, distinguished by the host range, genomic features and phylogeny of the member...


Wylie, S.J.Adams, M.Chalam, C.Kreuze, J.F.López Moya, J.J.Ohshima, K.Praveen, S.Rabenstein, F.Stenger, D.Wang, A.Zerbini, F.M.[ICTV virus taxonomy profile: Potyviridae.]ICTV virus taxonomy profile: Potyviridae.

Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5'- and 3'-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. I...


Niu, X.Sun, Y.Chen, Z.Li, R.Padmanabhan, C.Ruan, J.Kreuze, J.F.Ling, K.S.Fei, Z.J.Gao, S.[Using small RNA-seq data to detect siRNA duplexes induced by plant viruses.]Using small RNA-seq data to detect siRNA duplexes induced by plant viruses.

Kutnjak, D.Rupar, M.Gutiérrez Aguirre, I.Curk, T.Kreuze, J.F.Ravnikar, M.[Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population.]Deep sequencing of virus derived small interfering RNAs and RNA from viral particles shows highly similar mutational landscape of a plant virus population.

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