Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay

Autoři: Shih-hua Tan aff001;  Fatima Osman aff002;  Sohrab Bodaghi aff001;  Tyler Dang aff001;  Greg Greer aff001;  Amy Huang aff001;  Sarah Hammado aff001;  Shurooq Abu-Hajar aff001;  Roya Campos aff001;  Georgios Vidalakis aff001
Působiště autorů: Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America aff001;  Department of Plant Pathology, University of California, Davis, California, United States of America aff002
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223958


Citrus tatter leaf virus (CTLV) threatens citrus production worldwide because it induces bud-union crease on the commercially important Citrange (Poncirus trifoliata × Citrus sinensis) rootstocks. However, little is known about its genomic diversity and how such diversity may influence virus detection. In this study, full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside, were characterized using next generation sequencing. Genome structure and sequence for all CTLV isolates were similar to Apple stem grooving virus (ASGV), the type species of Capillovirus genus of the Betaflexiviridae family. Phylogenetic analysis highlighted CTLV’s point of origin in Asia, the virus spillover to different plant species and the bottleneck event of its introduction in the United States of America (USA). A reverse transcription quantitative polymerase chain reaction assay was designed at the most conserved genome area between the coat protein and the 3’-untranslated region (UTR), as identified by the full genome analysis. The assay was validated with different parameters (e.g. specificity, sensitivity, transferability and robustness) using multiple CTLV isolates from various citrus growing regions and it was compared with other published assays. This study proposes that in the era of powerful affordable sequencing platforms the presented approach of systematic full-genome sequence analysis of multiple virus isolates, and not only a small genome area of a small number of isolates, becomes a guideline for the design and validation of molecular virus detection assays, especially for use in high value germplasm programs.

Klíčová slova:

Apples – Citrus – DNA sequence analysis – Genome analysis – Nucleotide sequencing – Polymerase chain reaction – Sequence analysis – Viral genomics


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2019 Číslo 10