ABSTRACT
Prunus necrotic ringspot virus (PNRSV) is a pathogen that infects Prunus species worldwide, causing major economic losses. Using one and two-step RT-PCR and multiplex RT-PCR, the whole genome of the PNRSV-infecting apricot was obtained and described in this study. Computational approaches were used to investigate the participation of several regulatory motifs and domains of the Replicase1, Replicase2, MP, and CP. A single degenerated reverse and three forward oligo primers were used to amplify PNRSV's tripartite genome. The size of RNA1 was 3.332 kb, RNA2 was 2.591 kb, and RNA3 was 1.952 kb, according to the sequencing analysis. The Sequence Demarcation Tool analysis determined a percentage pair-wise identity ranging between 91 and 99% for RNA1 and 2, and 87-98% for RNA3. Interestingly, the phylogenetic analysis revealed that closely related RNA1, RNA2, and RNA3 sequences of PNRSV strains from various geographical regions of the world are classified into distinct clades or groups. This is the first report on the characterization of the whole genome of PNRSV from India, which provides the cornerstone for further studies on the molecular evolution of this virus. This study will assist in molecular diagnostics and management of the diseases caused by PNRSV.
Subject(s)
Prunus armeniaca , Prunus , Phylogeny , Prunus/genetics , Prunus/virology , Prunus armeniaca/genetics , RNA, Viral/genetics , Whole Genome Sequencing , Plant Diseases/virologyABSTRACT
A nearly complete genome sequence of cherry virus A (CVA), isolated from the Prunus armeniaca plant, is presented in this publication. The genome is 7,380 bases in length and is divided into two open reading frames, with a 54-nucleotide (nt) 5' noncoding region (NCR) and a 297-nt 3' NCR.
ABSTRACT
A biotin-labeled, non-isotopic, novel polyprobe was developed for the simultaneous detection of six viruses viz. apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), apple stem grooving virus (ASGV), cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV) and plum pox virus (PPV) infecting stone and pome fruit trees through dot-blot hybridization assay. The sensitivity of the polyprobe was checked by serial dilutions of total RNA extracted from the tissues of infected trees. ACLSV was detected up to a dilution of 5-5, whereas ApMV, ASGV, CVA, PPV and PNRSV up to 5-4. The developed assay was validated following testing a total of 45 symptomatic leaf samples collected from different geographical regions of Jammu and Kashmir (India), and the presence of the viruses was further confirmed by RT-PCR and sequencing. The polyprobe, designed for performing molecular hybridization assay can be developed quickly and avoid the tedious transformation and cloning procedures. Apart from simultaneously detecting viruses in stone and pome fruit trees, it holds great potential for virus indexing programmes to ascertain the supply of virus-free plant materials to the growers.
ABSTRACT
Cotton leaf curl Burewala virus (CLCuBV, genus Begomovirus) causes devastating cotton leaf curl disease. Among various known virus controlling strategies, RNAi-mediated one has shown potential to protect host crop plants. Micro(mi) RNAs, are the endogenous small RNAs and play a key role in plant development and stress resistance. In the present study we have identified cotton (Gossypium hirsutum)-encoded miRNAs targeting the CLCuBV. Based on threshold free energy and maximum complementarity scores of host miRNA-viral mRNA target pairs, a number of potential miRNAs were annotated. Among them, ghr-miR168 was selected as the most potent candidate, capable of targeting several vital genes namely C1, C3, C4, V1 and V2 of CLCuBV genome. In addition, ghr-miR395a and ghr-miR395d were observed to target the overlapping transcripts of C1 and C4 genes. We have verified the efficacy of these miRNA targets against CLCuBV following suppression of RNAi-mediated virus control through translational inhibition or cleavage of viral mRNA.
