Molecular characterization and detection of a new closterovirus identified from blackcurrant by high-throughput sequencing
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Two large contigs with high sequence similarities to several closteroviruses were identified by high-throughput sequencing from a blackcurrant plant. The complete genome of this new virus was determined to be 17,320 nucleotides. Its genome contains ten open reading frames (ORF) that include, in the 5′–3′ direction, a large ORF encoding a putative viral polyprotein (ORF 1a) and nine ORFs that encode RNA-dependent RNA polymerase (RdRp, ORF 1b), p6 (ORF 2), heat shock protein 70-like protein (Hsp70h, ORF 3), Hsp-90-like protein (p61, ORF 4), CP minor (ORF 5), CP (ORF 6), p17 (ORF 7), p11 (ORF 8), and p26 (ORF 9), respectively. BCCV-1 shares nucleotide sequence identities of 43–45% with other 9 closteroviruses at genome sequences. The amino acid sequence identities between BCCV-1 and the closteroviruses were 49–55% (RdRp), 37–41% (Hsp70h), 19–33% (p61), 26–38% (CPm), and 19–28% (CP), respectively. Phylogenetic analysis of Hsp70h sequences placed the new virus with members of genus Closterovirus in the same group. The results indicate that this new virus, which is provisionally named as Blackcurrant closterovirus 1, should represent a new species of the genus Closterovirus. A RT-PCR was developed and used to detect BCCV-1 in more germplasm accessions of Ribes spp.
KeywordsBlackcurrant closterovirus 1 Molecular characterization Ribes spp. RT-PCR detection
This work was supported by U.S. Department of Agriculture, Agriculture Research Service under research project 1215-22000-302-00D “Characterizing and Detecting Pathogens to Ensure Safe Exchange of Plant Germplasm” and the Fujian province scholarship for overseas studies (Grant No. 2016-29).
Study conception and design: RL Acquisition of data: LZ, LW, JP, HL Analysis and interpretation of data: L. Zheng, RL Drafting of manuscript: LZ Critical revision: RL.
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Conflict of interest
All authors declare that they have no conflict of interest.
Research involving human or animal participants
This article does not contain any research involving human or animal participants.
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