Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Abstract

BackgroundThe invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses. A survey of plant viruses infecting field-grown Tobacco crop was conducted in Anhui Province of China by the deep sequencing of sRNAs.MethodsSurvey of plant viruses infecting Tobacco was carried based on 104 samples collected across the province. Nine different sRNA libraries was prepared and custom-made bioinformatics pipeline coupled with molecular techniques was developed to sequence, assemble and analyze the siRNAs for plant virus discovery. We also carried out phylogenetic and recombination analysis of the identified viruses.ResultsTwenty two isolates from eight different virus species including Cucumber mosaic virus, Potato virus Y, Tobacco mosaic virus, Tobacco vein banding Mosaic virus, Pepper mottle virus, Brassica yellow virus, Chilli venial mottle virus, Broad bean wilt virus 2 were identified in tobacco across the survey area. The near-complete genome sequence of the 22 new isolates were determined and analyzed. The isolates were grouped together with known strains in the phylogenetic tree. Molecular variation in the isolates indicated the conserved coding regions have majorly a nucleotide sequence identity of 80-94 % with previously identified isolates. Various events of recombination were discovered among some of the isolates indicating that two or more viruses or different isolates of one virus infect the same host cell.ConclusionThis study describes the discovery of a consortium of plant viruses infecting Tobacco that are broadly distributed in Anhui province of China. It also demonstrates the effectiveness of NGS in identifying plant viruses without a prior knowledge of the virus and the genetic diversity that enhanced mixed infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0639-7) contains supplementary material, which is available to authorized users.

History of the Emergence and Spatiotemporal Spread of Tobacco Mosaic Virus in China

“…For example, in 1912, Henan Public Agricultural Major School, now known as Henan Agricultural University, located in Zhengzhou, was established in Henan province and it advanced quickly through inter-collegial ties with universities in the United Kingdom, Japan and the United States where the tobacco industry was already very well established and wherefrom, traders were importing tobacco seed and cigarettes into China since the ratification of the Treaty of Tianjin [16]. Also, Chinese agronomic records indicate that tobacco cultivation was introduced into Henan [54], and that Henan was the primary hub of China's tobacco production before being surpassed by Yunnan province in the late-1980s up until today [1,18,32]. This study infers that the expansion of the tobacco cultivation practice throughout and beyond Henan province heralded the genesis of the spatiotemporal diffusion of TMV's progenitor across China from province to municipality and/or autonomous region, until the pathogen achieved its current distribution range.…”

“…China is the world's largest producer and consumer of tobacco (Nicotiana tabacum L. sp), an important economic crop in China and worldwide [1]. Tobacco farming is very labor intensive.…”

“…Currently, these four tobacco production hubprovinces collectively account for over 60% of China's tobacco planting area [1,3]. Nevertheless, the majority of China's state administered tobacco industrial companies are distributed mostly within Yunnan, Hunan, Shanghai, Henan, Jiangsu, Zhejiang, Shandong and Guizhou provinces [29].…”

“…This decision angered tobacco farmers, most of whom continue to argue that the special tax further erodes their already meager proceeds. As a retaliatory response to this action by central government, throughout China, there has been an ongoing increase in substitution of tobacco for other crops and a shift toward mixed-cropping by traditional tobacco farmers [1]. As an example, in a 3-year pilot study that began in 2008 in Yunnan province, more than 450 traditionally tobacco farming families substituted the crop for others such as tomatoes, flowers, vegetables, arrowhead, and grapes and reported earning between 21% and 110% more per acre than they had been earning from tobacco farming alone [32].…”

“…In addition to transmission through susceptible weeds and plant reservoirs, TMV can also be transmitted mechanically through use of contaminated cutting tools, handling, plant cuttings, grafting, contact between plants or other contaminated surfaces, soil and/or potting material [5]. Surveys conducted in China and Turkey have shown that, the risk of MD outbreaks occurring elevates with an increase in TMV reservoirs [1,8]. Mosaic disease (MD) symptoms include, leaf necrosis, curling, malformations, mosaic patterns, stunted growth, and loss of apical dominance which leads to poor flower and fruit development [4,5].…”