Viromics Reveals the Viral Diversity in Cultivated and Wild Kiwifruit

China, the center of origin of kiwifruit, has the largest kiwifruit cultivation and production area worldwide, and Shaanxi Province is the major kiwifruit-growing region in China. However, our knowledge of kiwifruit viruses is largely skewed toward their pathology in cultivated orchards, and little is known about viral diversity in wild kiwifruit. To determine the viral diversity in cultivated and wild kiwifruit, 32 cultivated kiwifruit samples from Shaanxi Province and 30 wild kiwifruit samples from the Qinling Mountains were collected and subjected to high-throughput sequencing in this study. Eleven known viruses were found among the 32 cultivated kiwifruit samples, and 8 known viruses and 2 new viruses were found among the 30 wild kiwifruit samples. One of the two new viruses, Actinidia yellowing virus 3 (AcYV3), a member of the genus Idaeovirus, may be associated with severe yellowing of kiwifruit leaves. In addition, more than 50 nearly full-length genome sequences of known viruses were obtained. The detection rates, recombination, and molecular variation of these viruses were further analyzed. The results obtained in this study provide valuable information for understanding the virome of cultivated and wild kiwifruit.