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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #283258

Title: Deep sequencing of citrus affected by graft-transmissible diseases of unknown etiology leads to discovery of two novel viruses.

item LOCONSOLE, G - University Of Bari
item GIAMPETRUZZI, A - University Of Bari
item SALDARELLI, P - National Research Council - Italy
item Yokomi, Raymond - Ray
item ONELGE, N - Cukurova University
item SAPONARI, MARIA - National Research Council - Italy

Submitted to: International Citrus Congress Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 9/5/2012
Publication Date: 11/18/2012
Citation: Loconsole, G., Giampetruzzi, A., Saldarelli, P., Yokomi, R.K., Onelge, N., Saponari, M. 2012. Deep sequencing of citrus affected by graft-transmissible diseases of unknown etiology leads to discovery of two novel viruses. International Citrus Congress Proceedings. S14011, p. 237.

Interpretive Summary:

Technical Abstract: Citrus is susceptible to graft-transmissible disease agents and to a number of arthropod-transmitted pathogens. Citrus cultivars vary greatly in susceptibility or tolerance to these pathogens. Furthermore, pathogenicity amongst pathogen strains also varies. Established tests for known disease agents are used by certification and disease management programs. However, diseases with unknown etiology remain difficult or impossible to diagnose. Illumina next generation sequencing (NGS) technology was used to generate sequence datasets from citrus affected by two diseases of unknown etiology: citrus chlorotic dwarf (CCDD) (whitefly-transmitted) and yellow vein clearing disease (YVCD) (aphid-transmitted). CCDD is the most serious citrus disease in Turkey; YVCD is a graft-transmissible disorder observed in lemon and sour orange in Pakistan and India and later in Turkey (2000) and China (2010). Contigs from small interfering RNAs were assembled and used to screen sequence homologies against the virus database in GenBank. DNA fragments from CCDD-infected plants were used to re-construct a circular single-stranded DNA viral genome with homologies encoded by geminiviruses. The genome size and organization of the provisionally named Citrus chlorotic dwarf-associated virus (CCDaV) was determined indicating that it was a highly divergent member of the family Geminiviridae. Similarly, the whole genome of a putative filamentous virus associated with a CYCV-affected lemon was reconstructed. The genome structure was typical of flexiviruses and led to new serological, biological and molecular investigations on the provisionally named Citrus yellow vein clearing virus (CYVCV). These data suggested that CYVCV is a new species in the genus Mandarivirus. PCR-based assays for CCDaV and CYVCD were developed to serve as important new diagnostic tools for citrus disease management programs in Turkey and other citrus-producing regions.