Exploring the Polyadenylated RNA Virome of Sweet Potato through High-Throughput Sequencing

PLOS ONE, Dec 2019

Background Viral 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 Findings We 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/Significance A 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.

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Exploring the Polyadenylated RNA Virome of Sweet Potato through High-Throughput Sequencing

Zhang Y-Z (2014) Exploring the Polyadenylated RNA Virome of Sweet Potato through High-Throughput Sequencing. PLoS ONE 9(6): e98884. doi:10.1371/journal.pone.0098884 Exploring the Polyadenylated RNA Virome of Sweet Potato through High-Throughput Sequencing Ying-Hong Gu 0 Xiang Tao 0 Xian-Jun Lai 0 Hai-Yan Wang 0 Yi-Zheng Zhang 0 Darren P. Martin, Institute of Infectious Disease and Molecular Medicine, South Africa 0 1 College of Life Sciences, Sichuan University, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Center for Functional Genomics and Bioinformatics , Chengdu, Sichuan , People's Republic of China, 2 Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu, Sichuan , People's Republic of China Background: Viral 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 Findings: We 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/Significance: A 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. - Funding: This work was financially supported by the National Science & Technology Pillar Program of China (No. 2007BAD78B03) and the Eleven-Five Key Project of Sichuan Province (No. 07SG111-003-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. The sweet potato [Ipomoea batatas L. (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. Sweet potato is the fifth most important food crop in developing countries. About 130 million metric tons of tuberous roots are produced globally each year on about 9 million hectares of land [2,3]. 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]. A few researchers have shown interest in sweet potato mainly because of its complex hexaploid inheritance [6]. Recently, the growing awareness of health benefits attributed to sweet potato has stimulated renewed interest in this crop [3]. Viral diseases are the second most significant biotic stress for sweet potato after the sweet potato weevil [7]. Usually, sweet potato viruses will co-infect the plants and severely limit root production [8]. Yield losses caused by these viral diseases reach 20% to 40%, but this can reach near 100% in some African countries [912]. Over 30 viruses have been reported to infect sweet potato worldwide, but most of them are asymptomatic [3,13]. Eleven of these viruses have been detected in China [14], including Sweet potato C6 virus (SPC6V) [15], Sweet potato chlorotic fleck virus (SPCFV) [15], Sweet potato chlorotic stunt virus (SPCSV) [1517], Sweet potato collusive virus (SPCV, synonym Sweet potato caulimolike virus) [10], Sweet potato feathery mottle virus (SPFMV) [15,1820], Sweet potato leaf curl virus (SPLCV) [21], Sweet potato latent virus (SwPLV) [19,20], Sweet potato mild mottle virus (SPMMV) [15], Sweet potato mild speckling virus (SPMSV) [15], Sweet potato virus G (SPVG) [20,22 (...truncated)


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Ying-Hong Gu, Xiang Tao, Xian-Jun Lai, Hai-Yan Wang, Yi-Zheng Zhang. Exploring the Polyadenylated RNA Virome of Sweet Potato through High-Throughput Sequencing, PLOS ONE, 2014, 6, DOI: 10.1371/journal.pone.0098884