Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

Sun-Jung Kwon,Ioannis E Tzanetakis,Thien Ho,Tyler Dang,Sohrab Bodaghi,Anne E Simon,Kiran R Gadhave,Maher Al Rwahnih,Georgios Vidalakis,Fatima Osman

doi:10.3389/fmicb.2021.683130

Abstract

Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.

Highlights

Subviral RNAs are one of the smallest plant pathogens (Shimura and Masuta, 2016)
The identified sequence gaps were filled by real-time polymerase chain reaction (RT-PCR), and the 3' and 5' ends were determined by RACE–PCR based on terminal deoxynucleotide transferase poly(G)-tailed cDNA (Kwon et al, 2014)
ORF1 extends from 9 to 581 nt and encodes a protein of 190 aa with a predicted molecular weight of 21.5 kDa, whereas ORF2 extends from 9 to 2,191 nt and is predicted to be translated via a −1 ribosomal frameshift leading to a fusion protein product of 717 aa (81 kDa)

Summary

Introduction

Subviral RNAs are one of the smallest plant pathogens (Shimura and Masuta, 2016). They vary in length, complexity, and functions, in that they rely on helper viruses for at least one of the functions: replication, encapsidation, or in planta movement. Non-coding satellite RNAs are incapable of all three functions (Badar et al, 2020), translated RNAs are capable of encapsidation, but lack the ability to replicate and move in plants (Gnanasekaran and Chakraborty, 2018), whereas coat protein-dependent RNA replicons are capable of synthesizing RNA-dependent RNA polymerase (RdRp) but rely on helper viruses for at least encapsidation (Campbell et al, 2020). Umbraviruses typically rely on the coat protein of a helper virus, for both encapsidation and transmission.

Methods

Results

Conclusion