Abstract
BackgroundViral diseases are the second most significant biotic stress for sweet potato, with yield losses reaching 20% to 40%. Over 30 viruses have been reported to infect sweet potato around the world, and 11 of these have been detected in China. Most of these viruses were detected by traditional detection approaches that show disadvantages in detection throughput. Next-generation sequencing technology provides a novel, high sensitive method for virus detection and diagnosis.Methodology/Principal FindingsWe report the polyadenylated RNA virome of three sweet potato cultivars using a high throughput RNA sequencing approach. Transcripts of 15 different viruses were detected, 11 of which were detected in cultivar Xushu18, whilst 11 and 4 viruses were detected in Guangshu 87 and Jingshu 6, respectively. Four were detected in sweet potato for the first time, and 4 were found for the first time in China. The most prevalent virus was SPFMV, which constituted 88% of the total viral sequence reads. Virus transcripts with extremely low expression levels were also detected, such as transcripts of SPLCV, CMV and CymMV. Digital gene expression (DGE) and reverse transcription polymerase chain reaction (RT-PCR) analyses showed that the highest viral transcript expression levels were found in fibrous and tuberous roots, which suggest that these tissues should be optimum samples for virus detection.Conclusions/SignificanceA total of 15 viruses were presumed to present in three sweet potato cultivars growing in China. This is the first insight into the sweet potato polyadenylated RNA virome. These results can serve as a basis for further work to investigate whether some of the 'new' viruses infecting sweet potato are pathogenic.
Highlights
The sweet potato [Ipomoea batatas L. (Lam.)] originated in South America and was transported across the pacific by Polynesians [1]
All of the following samples were collected from symptomless plants: Fibrous roots (FR) at one month after planting; young leaves (YL), mature leaves (ML), stems and initial tuberous roots (ITR) at 1.5 months; expanding tuberous roots at 3 months; harvested tuberous roots at 5 months; newly opened flowers were collected from symptomless drought-treated plants at 4 months
Virus Identification via Next-generation Sequencing Seven vegetative tissues were collected from sweet potato cv
Summary
The sweet potato [Ipomoea batatas L. (Lam.)] originated in South America and was transported across the pacific by Polynesians [1]. (Lam.)] originated in South America and was transported across the pacific by Polynesians [1] It has been cultivated by humans for up to 8,000 years, and today it is widely grown around the world due to its strong adaptability, easy management, rich nutrient content and multiple usages. China is the biggest producer in the world, accounting for 80% of the global sweet potato production [4]. Compared to other staple food crops sweet potato needs fewer inputs, but produces more biomass [5]. Over 30 viruses have been reported to infect sweet potato around the world, and 11 of these have been detected in China. Most of these viruses were detected by traditional detection approaches that show disadvantages in detection throughput. Next-generation sequencing technology provides a novel, high sensitive method for virus detection and diagnosis
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