TY - JOUR
T1 - Blueberry red ringspot virus genomes from Florida inferred through analysis of blueberry root transcriptomes
AU - Saad, N.
AU - Alcalá-Briseño, R. I.
AU - Polston, J. E.
AU - Olmstead, J. W.
AU - Varsani, A.
AU - Harmon, P. F.
N1 - Funding Information:
This work was supported by the Ministry of Higher Education, Malaysia and the Universiti Putra Malaysia through scholarship funds provided to Norsazilawati Saad. We thank José C. Hughet-Tapía for helpful discussions and consultation on bioinformatic analysis. We thank Heather Capobianco and Camisha Alexis for the assistance during collection and processing of samples. We thank Michael Morrow for the information technology support. Results presented here are from experiments conducted as part of a doctoral dissertation project of N. Saad (2017). Dissertation available at https://ufdc.ufl.edu/UFE0051785/00001.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar ‘Emerald’ (interspecific hybrid of Vaccinium corymbosum and V. darrowi) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences. The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of ‘Emerald’ never developing red ringspot symptoms. Bioinformatic analyses of ‘Emerald’ transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus Soymovirus, family Caulimoviridae). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the ‘Emerald’ root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes.
AB - A growing number of metagenomics-based approaches have been used for the discovery of viruses in insects, cultivated plants, and water in agricultural production systems. In this study, sixteen blueberry root transcriptomes from eight clonally propagated blueberry plants of cultivar ‘Emerald’ (interspecific hybrid of Vaccinium corymbosum and V. darrowi) generated as part of a separate study on varietal tolerance to soil salinity were analyzed for plant viral sequences. The objective was to determine if the asymptomatic plants harbored the latent blueberry red ringspot virus (BRRV) in their roots. The only currently known mechanism of transmission of BRRV is through vegetative propagation; however, the virus can remain latent for years with some plants of ‘Emerald’ never developing red ringspot symptoms. Bioinformatic analyses of ‘Emerald’ transcriptomes using de novo assembly and reference-based mapping approaches yielded eight complete viral genomes of BRRV (genus Soymovirus, family Caulimoviridae). Validation in vitro by PCR confirmed the presence of BRRV in 100% of the ‘Emerald’ root samples. Sequence and phylogenetic analyses showed 94% to 97% nucleotide identity between BRRV genomes from Florida and sequences from Czech Republic, Japan, Poland, Slovenia, and the United States. Taken together, this study documented the first detection of a complete BRRV genome from roots of asymptomatic blueberry plants and in Florida through in silico analysis of plant transcriptomes.
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U2 - 10.1038/s41598-020-68654-3
DO - 10.1038/s41598-020-68654-3
M3 - Article
C2 - 32694553
AN - SCOPUS:85088301650
SN - 2045-2322
VL - 10
JO - Scientific reports
JF - Scientific reports
IS - 1
M1 - 12043
ER -