Deep Sequencing of Small RNAs from Citrus Affected by Graft-Transmissible Diseases of Unknown Aetiology Leads to Discovery of Two Novel Viruses

Loconsole G., Giampetruzzi A., Saldarelli P., ÖNELGE N., Yokomi R. K., Saponari M.

12th International Citrus Congress - International-Society-of-Citriculture, Valencia, Spain, 18 - 23 November 2012, vol.1065, pp.817-824 identifier identifier

  • Publication Type: Conference Paper / Full Text
  • Volume: 1065
  • Doi Number: 10.17660/actahortic.2015.1065.102
  • City: Valencia
  • Country: Spain
  • Page Numbers: pp.817-824
  • Çukurova University Affiliated: Yes


Diseases of unknown aetiology remain difficult or impossible to diagnose. Illumina next generation sequencing (NGS) technology was used to generate sequence datasets from citrus affected by two such diseases: citrus chlorotic dwarf (CCDD) (whitefly-transmitted) and yellow vein clearing disease (YVCD) (aphid-transmitted). Contigs from small RNAs were assembled and used to screen sequence homologies against the virus database in GenBank. DNA fragments from CCDD-affected plants were used to re-construct a circular single-stranded DNA viral genome with homologies to geminiviruses. The genome size and organization of the provisionally named Citrus chlorotic dwarf-associated virus (CCDaV) was shown to be a highly divergent member of the family Geminiviridae. Similarly, the whole genome sequence of a putative filamentous virus associated with CYVCD-affected lemon plants was reconstructed. The genome structure was found to be typical of flexiviruses and sequence data suggested that CYVCV is a new species in the genus Mandarivirus. PCR-based assays for CCDaV and CYVCV were developed that will be an important diagnostic tool for citrus disease management programs in Turkey and other citrus-producing regions.