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ARS Home » Pacific West Area » Davis, California » Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes » Research » Publications at this Location » Publication #349109
Title: Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing

Author
item AL RWAHNIH, MAHER - University Of California
item ADIB, ROWHANI - University Of California
item STEVENS, KRISTIAN - University Of California
item DIAZ-LARA, ALFREDO - University Of California
item TROUILLAS, FLORENT - University Of California
item Preece, John
item KALLSEN, CRAIG - University Of California - Cooperative Extension Service
item FARRAR, KRISTEN - University Of California
item GOLINO, DEBORAH - University Of California

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2018
Publication Date: 7/1/2018
Citation: Al Rwahnih, M., Adib, R., Stevens, K., Diaz-Lara, A., Trouillas, F.P., Preece, J.E., Kallsen, C., Farrar, K., Golino, D. 2018. Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing. Plant Disease. 102(7):1419-1425. https://doi.org/10.1094/PDIS-12-17-1988-RE.
DOI: https://doi.org/10.1094/PDIS-12-17-1988-RE

Interpretive Summary: 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 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identified a novel virus, provisionally named “pistachio ampelovirus A” (PAVA), in the NCGR that showed low amino acid sequence homology (~42%) to members of 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 the species citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families which requires further study and confirmation. Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 seedlings. A field survey of 123 trees from commercial orchards found no incidence of PAVA, but five (4%) samples were infected with CBCVd-pis. Of 690 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (24.9%) were positive for CBCVd-pis by RT-PCR. Results of the study establish the natural occurrence of viral and viroid populations infecting pistachio trees.

Technical Abstract: 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 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identified a novel virus, provisionally named “pistachio ampelovirus A” (PAVA), in the NCGR that showed low amino acid sequence homology (~42%) to members of 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 the species citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families which requires further study and confirmation. Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 seedlings. A field survey of 123 trees from commercial orchards found no incidence of PAVA, but five (4%) samples were infected with CBCVd-pis. Of 690 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (24.9%) were positive for CBCVd-pis by RT-PCR. Results of the study establish the natural occurrence of viral and viroid populations infecting pistachio trees.