Molecular characterization of grapevine yellow speckle viroid-2 (GYSVd-2)

Abstract

Grapevine yellow speckle viroid-2 (GYSVd-2) is a viroid found only in grapevines in China and Australia. Here, we report the molecular characterization of GYSVd-2 isolated from three grapevine varieties in China. A total of 90 cDNA clones were sequenced including 30 cDNA clones obtained from each of the Black Olympia, Zaoyu, and Thomson Seedless isolates. Sequencing analysis identified 20, 18, and 12 different sequence variants from the 3 isolates, respectively. Furthermore, each of the isolates included one predominant sequence variant. Compared to the Australian variant of GYSVd-2 (Accession number: NC_003612), the Black Olympia variant was identical and the Zaoyu variant contained one substitution. In contrast, the Thomson Seedless isolate significantly varied from the Australian variant with three substitutions, two insertions, and four deletions. In silico structure analysis predicted that the variations were clustered in the terminal left, the pathogenicity, and the variable region of the predicted secondary structure of GYSVd-2.

Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses

“…Currently, the viroids GYSVd-1, GYSVd-2 and AGVd are assigned to the genus Apscaviroid, while HSVd is assigned to the genus Hostuviroid [73]. HSVd and GYSVd-1 are widely distributed in vineyards worldwide [74,75], whereas the distribution of AGVd and GYSVd-2 is limited [76,77]. In Russia, all four viroids have been detected in vineyards and collection plantations in the Krasnodar Krai [30,54].…”

“…The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/v14122623/s1, Figure S1 S1: Basic information of selected grape samples and viral infection; Table S2: Complete sequences of viruses and viroids uploaded into GenBank with their identifier; Table S3: List of the RT-PCR primers used for virus detection [30,54,60,76,[88][89][90][91][92][93][94][95][96][97][98][99]; Table S4: List of sequences after Sanger sequencing submitted to the GenBank; Table S5: List of the RT-qPCR primers used for virus detection and calibration curve parameters for simplex RT-qPCR [100,101]; Table S6: List of representative umbraviruses and umbra-like viruses; Table S7: List of representative badnaviruses, caulimoviruses, unclassified caulimoviruses and ruflodivirus; Table S8: Initial data of complete or almost complete genomes for phylogenetic analysis; Table S9: Representative virus isolates used for group definition [30,61,[102][103][104][105]; Table S10: Number of reads and contigs obtained for each library after sequencing by Illumina NovaSeq 6000 Sequencing System; Table S11: Bioinformatics analysis and its validation; Table S12: Bioinformatics analysis, mapping of preprocessed reads to closest genome; Table S13: Viruses detected in GV-Sat positive samples; Table ...…”

High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia

“…The following are available online at https://www.mdpi.com/article/10 .3390/v13122432/s1. Supplementary Figures: Figure S1 S1: Basic information about the sampled vineyards; Table S2: Primers used for validation of the HTS results [28,29,39,47,61,117,[137][138][139][140][141][142][143][144][145][146][147][148][149][150][151]; Table S3: Primers used for the phylogenetic analysis [21,29,47,57,61,110,142,144,145,147,149,[152][153][154][155][156][157]; Table S4: Amplified sequences of viruses uploaded into GenBank with their identifiers; Table S5: Initial statistics for the sequencing results; Table S6: Summary of the two bioinformatic approaches used in the study for the sRNA HTS analysis according to libraries and viruses; Table S7: Supplementary information on th...…”

Diversity of viroids infecting grapevines in South Africa

“…The rod-shaped secondary structure of the viroid has been shown to serve as functional motifs which interact with cellular factors of the host to accomplish various aspects of replication and disease induction (48). These GSYVd-2 viroids were obtained from a variety of hosts including different table and wine grape species and cultivars, and lack of variation between isolates suggests that they are not under diversifying selection (45). Only GYSVd-1 and − 2 result in disease in grapevine (33), symptoms were not surveyed during this study due to the presence of grapevine leaf roll-associated viruses and vitiviruses in the majority of the 229 accessions.…”