Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing

• Published in: Plant disease Vol. 102; no. 7; p. 1419
• Main Authors: Al Rwahnih, Maher, Rowhani, Adib, Westrick, Nathaniel, Stevens, Kristian, Diaz-Lara, Alfredo, Trouillas, Florent P, Preece, John, Kallsen, Craig, Farrar, Kristen, Golino, Deborah
• Format: Journal Article
• Language: English
• Published: United States 01.07.2018
• ISSN: 0191-2917
• DOI: 10.1094/pdis-12-17-1988-re

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of sequence information from 60 trees identified a novel virus, provisionally named "Pistachio ampelovirus A" (PAVA), in the NCGR that showed low amino acid sequence identity (approximately 42%) compared with members of the genus Ampelovirus (family Closteroviridae). A putative viroid, provisionally named "Citrus bark cracking viroid-pistachio" (CBCVd-pis), was also found in the NCGR and showed approximately 87% similarity to Citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 hybrid rootstock seedlings (P. atlantica × P. integerrima). A field survey of 123 trees from commercial orchards found no incidence of PAVA but five (4%) samples were infected with CBCVd-pis. Of 675 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (25.4%) were positive for CBCVd-pis by reverse-transcription polymerase chain reaction. Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families. These findings require further study and confirmation. This study establishes the occurrence of viral and viroid populations infecting pistachio trees.