Preprint Article Version 1 This version is not peer-reviewed

Blackcurrant Leaf Chlorosis Associated Virus: Next-Generation Sequencing Reveals an Extraordinary Virus with Multiple Genomic Components Including Evidence of Circular RNA

Version 1 : Received: 30 March 2018 / Approved: 30 March 2018 / Online: 30 March 2018 (11:40:46 CEST)

A peer-reviewed article of this Preprint also exists.

James, D.; Phelan, J.; Sanderson, D. Blackcurrant Leaf Chlorosis Associated Virus: Evidence of the Presence of Circular RNA during Infections. Viruses 2018, 10, 260. James, D.; Phelan, J.; Sanderson, D. Blackcurrant Leaf Chlorosis Associated Virus: Evidence of the Presence of Circular RNA during Infections. Viruses 2018, 10, 260.

Journal reference: Viruses 2018, 10, 260
DOI: 10.3390/v10050260

Abstract

Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and proposed as a new and distinct species in the genus Idaeovirus. Genomic components of BCLCaV that were detected and confirmed include: 1) RNA-1 that is monocistronic and encodes the replicase complex; 2) a bicistronic RNA-2 that encodes a movement protein (MP) and the coat protein (CP) of the virus, with open reading frames (ORF) that overlap by a single adenine (A) nucleotide (nt) representing the third position of an opal stop codon of the MP ORF2a and the first position of the start codon of the CP ORF2b; 3) a subgenomic form of RNA-2 (RNA-3) that contains ORF2b; and 4) a concatenated form of RNA-2 that consists of a complementary and inverted RNA-3 conjoined to the full-length RNA-2. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3’-terminus and 5’-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments with denaturation at 95 oC preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.

Subject Areas

Idaeovirus; Blackcurrant leaf chlorosis associated virus; next-generation sequencing (NGS); bridge reads; abutting primers; RNase R digestion; circular RNA; concatenated RNA

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