Genetic Variability and Evolutionary Implications of RNA Silencing Suppressor Genes in RNA1 of <i>Sweet Potato Chlorotic Stunt Virus</i> Isolates Infecting Sweetpotato and Related Wild Species

Background The bipartite single-stranded RNA genome of Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus; Closteroviridae) encodes a Class 1 RNase III (RNase3), a putative hydrophobic protein (p7) and a 22-kDa protein (p22) from genes located in RNA1. RNase3 and p22 suppress RNA silencing, the basal antiviral defence mechanism in plants. RNase3 is sufficient to render sweetpotato (Ipomoea batatas) virus-susceptible and predisposes it to development of severe diseases following infection with unrelated virus. The incidence, strains and gene content of SPCSV infecting wild plant species have not been studied. Methodology/Principal Findings Thirty SPCSV isolates were characterized from 10 wild Ipomoea species, Hewittia sublobata or Lepistemon owariensis (family Convolvulaceae) in Uganda and compared with 34 local SPCSV isolates infecting sweetpotatoes. All isolates belonged to the East African (EA) strain of SPCSV and contained RNase3 and p7, but p22 was not detected in six isolates. The three genes showed only limited genetic variability and the proteins were under purifying selection. SPCSV isolates lacking p22 synergized with Sweet potato feathery mottle virus (SPFMV, genus potyvirus; Potyviridae) and caused severe symptoms in co-infected sweetpotato plants. One SPCSV isolate enhanced accumulation of SPFMV, but no severe symptoms developed. A new whitefly-transmitted virus (KML33b) encoding an RNase3 homolog (<56% identity to SPCSV RNase3) able to suppresses sense-mediated RNA silencing was detected in I. sinensis. Conclusions/Significance SPCSV isolates infecting wild species and sweetpotato in Uganda were genetically undifferentiated, suggesting inter-species transmission of SPCSV. Most isolates in Uganda contained p22, unlike SPCSV isolates characterized from other countries and continents. Enhanced accumulation of SPFMV and increased disease severity were found to be uncoupled phenotypic outcomes of RNase3-mediated viral synergism in sweetpotato. A second virus encoding an RNase3-like RNA silencing suppressor was detected. Overall, results provided many novel and important insights into evolutionary biology of SPCSV.背景 甘薯褪绿矮化病毒（Sweet potato chlorotic stunt virus, SPCSV，隶属于长线形病毒科（Closteroviridae）克鲁尼病毒属（Crinivirus））的二分体单链RNA基因组，可从RNA1区段的基因中编码1类RNase III（RNase3）、推定疏水蛋白（p7）以及22 kDa蛋白（p22）。RNase3与p22均可抑制RNA沉默——植物的基础抗病毒防御机制。RNase3足以使甘薯（Ipomoea batatas）对病毒易感，并使其在感染异源病毒后易发展为重症病害。目前针对侵染野生植物物种的SPCSV的发生率、株系及基因组成尚未开展研究。 材料与方法/主要研究结果 本研究从乌干达的10种野生番薯属（Ipomoea）物种、亚球形惠特尼藤（Hewittia sublobata）或Owari银叶藤（Lepistemon owariensis，旋花科Convolvulaceae）中鉴定了30株SPCSV分离株，并与34株本地侵染甘薯的SPCSV分离株进行比对分析。所有分离株均归属于SPCSV的东非（EA）株系，且均携带RNase3与p7，但其中6株未检测到p22。三个基因仅表现出有限的遗传变异，其编码蛋白处于纯化选择压力之下。缺失p22的SPCSV分离株可与甘薯羽状斑驳病毒（Sweet potato feathery mottle virus, SPFMV，隶属于马铃薯Y病毒科（Potyviridae）马铃薯Y病毒属（potyvirus））产生协同侵染效应，并在共侵染的甘薯植株中引发重症症状。另有1株SPCSV分离株可促进SPFMV的积累，但未引发重症症状。本研究还在中国番薯（I. sinensis）中检测到一种新的烟粉虱传病毒（KML33b），其编码的RNase3同源物与SPCSV RNase3的同源性低于56%，且可抑制正义介导的RNA沉默。 结论与意义 乌干达境内侵染野生植物物种与甘薯的SPCSV分离株在遗传上无分化，这表明SPCSV可发生种间传播。与其他国家及大洲已鉴定的SPCSV分离株不同，乌干达境内的多数分离株携带p22。研究发现，SPFMV的积累增强与病害严重程度提升是RNase3介导的病毒协同侵染效应在甘薯中解偶联的两种表型结果。本研究还检测到第二种编码RNase3类RNA沉默抑制因子的病毒。综上，本研究结果为SPCSV的进化生物学研究提供了诸多新颖且重要的见解。