Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches

Abstract

Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.

Known and New Emerging Viruses Infecting Blueberry

“…The advent of high-throughput sequencing and bioinformatics have undoubtedly facilitated the discovery of viruses in blueberry, as shown by characterization of the first complete BRRV genome from Florida [126], as well as the identification of two novel virus species in the family Betaflexiviridae, in within the last 3 years. Interestingly, the metagenomics study which has uncovered the new tepovirus have also led to the discovery of BlLV and BlMaV for the first time in Florida, and the first to demonstrate the occurrence of BlMaV in wild highbush [99].…”

“…After its initial report, the disease has been discovered in various parts of North and South America, as well as Asia, Europe, New Zealand, and South Africa [9,10,96]. Blueberry mosaic has been found in blueberry cultivated areas in the US, including Indiana, Michigan, New Jersey, New York, Oregon, Washington, Kentucky and most recently, Florida [97][98][99]. The highbush cultivars 'Bluecrop', 'Cabot', 'Concord', 'Earliblue', 'Jersey', 'Pioneer', 'Rubel', and 'Stanley' are the most susceptible to blueberry mosaic disease.…”

“…It has been proposed as a possible cause of blueberry mosaic disease [32]. BlMaV has been thought to only infect the highbush and a lowbush dryland blueberry (V. pallidum), until it was recently reported in wild highbush, V. corymbosum in Florida [62,97,99].…”

“…A novel tepovirus, tentatively named as blueberry virus T (BlVT), has been recently discovered through metagenomics approach in blueberry cultivar 'Gulf Coast' and 'Windsor' from Island Grove, Florida [99]. The specific virus symptoms caused by BlVT, however, could not be established yet in blueberry since it was detected in only 3 of the 20 samples tested.…”

“…When a new disease known as blueberry fruit drop disease was detected in the Pacific Northwest (Oregon, Washington, and British Columbia) in the US in the early 2000s, blueberry latent virus (BlLV) was unwittingly discovered [9,42]. BlLV has a broad geographic distribution, as it was initially found in nonsymptomatic and symptomatic plants from Arkansas, Florida, Michigan, New Jersey, and the Pacific Northwest, as well as blueberry germplasm from North America [10,42,99]. It was later shown, however, blueberry infected with single infection of BlLV does not cause any striking symptoms [42].…”