Abstract Solanum quitoense Lam. is a solanaceous fruit shrub native to South America that produces a tomato-sized fruit popular in the preparation of fresh juice, fermented beverages, nectars, ice cream and fruit concentrates. Unfortunately, this crop is highly susceptible to insects, nematodes, fungi, oomycetes, bacteria, and a wide range of viral diseases. With the arrival of High-Throughput Sequencing (HTS) methods, our understanding of the viruses affecting this crop has increased at a steady pace. In this work, we investigate the virome of S. quitoense in Antioquia (Colombia) using the Illumina HTS platform and analyze the effect of using ribosomal RNA depleted total RNA and dsRNA templates. Our results suggest that total RNA outputs a larger amount of viral sequences but fails to detect viruses present at lower loads. Both templates allowed detection and assembly of Potato leafroll virus (PLRV), Potato yellow vein virus (PYVV), and Potato mop-top virus (PMTV); however, the dsRNA input was more sensitive for detection of Potato virus Y (PVY), Potato virus X (PVX), Potato virus S (PVS), and Bell pepper alphaendornavirus (BPEV). These results suggest that the combination of different RNA inputs in HTS studies of plant viromes can give a more complete picture of the real virus diversity.

中文翻译：

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通过使用总和双链 RNA 输入的高通量测序 (HTS) 检测茄属植物中的 RNA 病毒

摘要 Solanum Quitoense 林。是一种原产于南美洲的茄科水果灌木，可生产番茄大小的水果，常用于制备新鲜果汁、发酵饮料、花蜜、冰淇淋和浓缩水果。不幸的是，这种作物对昆虫、线虫、真菌、卵菌、细菌和各种病毒病非常敏感。随着高通量测序 (HTS) 方法的出现，我们对影响这种作物的病毒的了解稳步增加。在这项工作中，我们使用 Illumina HTS 平台研究了安蒂奥基亚（哥伦比亚）的基托链霉菌病毒组，并分析了使用核糖体 RNA 耗尽的总 RNA 和 dsRNA 模板的影响。我们的结果表明，总 RNA 输出了大量的病毒序列，但无法检测到以较低负载量存在的病毒。两种模板都允许检测和组装马铃薯卷叶病毒 (PLRV)、马铃薯黄脉病毒 (PYVV) 和马铃薯拖把病毒 (PMTV)；然而，dsRNA 输入对检测马铃薯病毒 Y (PVY)、马铃薯病毒 X (PVX)、马铃薯病毒 S (PVS) 和甜椒甲内膜病毒 (BPEV) 更为敏感。这些结果表明，在植物病毒组的 HTS 研究中结合不同的 RNA 输入可以更全面地了解真实病毒的多样性。