Abstract:

In order to systematically investigate the occurrence and infection status of grapevine viruses and viroids in Northern Xinjiang. LncRNA sequencing technology was used to obtain virus and viroid sequences from four mixed and six individual young grape leaf samples. Eleven plant viruses belonging to 7 viral families and 9 genera，along with 3 viroids from 1 viroid family and 2 genera were identified. This study provides the first molecular evidence confirming the presence of grapevine fabavirus（GFabV），grapevine geminivirus A（GGVA），grapevine rupestris vein feathering virus（GRVFV）and cucumber mosaic virus（CMV）in Xinjiang’s viticultural areas. Subsequent RT-PCR testing of 117 samples from five major grape cultivars in the primary viticultural regions of Shihezi and Changji，revealed grapevine berry inner necrosis virus（GINV）as the most prevalent virus（73.5%）infection rate and Hop stunt viroid（HSVd） as the dominant viroid（88.9% infection rate）. Viral infection profiles exhibited significant variation across grapevine cultivars，with distinct dominant virus species observed in each cultivar. Among them，the table grape cultivar‘Thompson Seedless’demonstrated the most comprehensive infection virus，harboring all 11 virus and 3 viroid species identified in this investigation. Notably，mixed infections were widespread in the grape samples, with 95.7% of samples showing co-infection by viruses and viroids. High prevalence of complex infections was observed，with 60 samples harboring co-infections by more than five distinct viral pathogens，and the most common mixed infection type was GINV + grapevine pinot gris virus（GPGV）+ grapevine rupestris stem pitting associated virus（GRSPaV）+ HSVd，accounting for 35%. The presence of the newly identified GPoV-1 in both table and wine grapes cultivars from Shihezi vineyards but was not detected in wine grapes collected from Changji. Phylogenetic analysis of full-length or near full-length viral sequences revealed that GINV，GRSPaV，GPGV and grapevine yellow speckle viroid 1（GYSVd-1）had multiple isolates. Notably，GINV and GPGV exhibited geographic correlations. In contrast，other viral isolates displayed high sequence divergence，with scattered distribution and no geographic correlation. Single nucleotide polymorphism and insertion-deletion analyses revealed that all viruses and viroids exhibited high genetic variability. In Xinjiang vineyards，viroids exhibited a significant preference for Indel，while viral genomes showed a predominant tendency toward single-nucleotide variations.

Key words: grape, high-throughput sequencing, RT-PCR, phylogenetic analysis, sequence variation analysis