Biological and molecular characterization of hop stunt viroid variants from pistachio trees in Iran

Abstract

Hop stunt viroid (HSVd) infects a large number of woody plants such as grapevine, citrus, plum, peach, fig, mulberry, pear, pistachio and almond. Kerman Province is the most important pistachio‐growing region in Iran. During 2015–2016, pistachio orchards were surveyed in Kerman for the detection of HSVd. A total of 106 symptomatic and asymptomatic leaf samples from pistachio trees were collected and assayed for HSVd by reverse transcription polymerase chain reaction (RT‐PCR) and dot‐blot hybridization methods. The genomes of 11 HSVd isolates were PCR amplified, cloned, sequenced and compared with those available in GenBank. The full‐length genomes of Iranian variants range from 297 to 302 nucleotides, which are comparable to those of previously known HSVd variants. Phylogenetic analyses showed that four HSVd pistachio variants from Anar region were classified together with five Tunisian HSVd pistachio variants and formed a sub‐cluster within the HSVd‐hop isolates group, whereas two variants from Shahr‐e‐Babak region were grouped with known HSVd‐citrus variants. The other remaining five variants were clustered into the recombinant isolates group (P‐H/cit3). Phylogenetically, we discuss that the presence of HSVds in pistachio trees has a long history in Iran, and Tunisian HSVd pistachio variants probably originated from Iran. The infectivity of two HSVd pistachio variants was further verified by mechanical inoculation on some Cucurbitaceae plant species. The viroid was also transmitted to three healthy pistachio rootstocks by bud grafting. This is the first report on HSVd in pistachio trees in Iran.

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

“…The identity between Russian isolates was at the level of 94.3-100%, while the identity with isolates from the GenBank was from 99.6% to 100% (Supplementary Table S2). Phylogenetic analysis showed that 39 isolates clustered near isolates of the Hop group (Supplementary Figure S15a-f), the host plants for most of which were Vitis Vinifera [147]. A total of 11 isolates clustered with representative sequences from the Plum-Hop/cit3 group, host plants for most of which were stone fruits.…”

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

“…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 ...…”

Pospiviroides de importância para hortaliças e ornamentais: panorama dos aspectos fitopatológicos e dos riscos para os sistemas agrícolas brasileiros

“…e uma gama ampla de hospedeiras incluindo frutíferas lenhosas das famílias Anacardiaceae (pistache) (MADDAHIAN et al 2019), Moraceae (amoreira e figueira), Rosaceae (ameixeira, amendoeira, cerejeira, damasco, macieira, pereira e pessegueiro), Rutaceae (Citrus spp.) (HATAYA et al 2017;VAMENANI et al 2019) e Vitaceae (videira) (SANO et al 1985;EIRAS et al 2006b).…”