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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #408451
Research Project: Discovery, Characterization, and Diagnostics of Endemic and Exotic Citrus Pathogens Using High Throughput Sequencing (HTS)

Location: Molecular Plant Pathology Laboratory

Title: Meta-transcriptomic analysis uncovers the presence of four novel viruses and multiple known virus genera in a single Hibiscus rosa-sinensis plant in Colombia

Author
item Roy, Avijit
item Grinstead, Sam
item LEON, GUILLERMO - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item JUAN CARLOS, CAMPOS - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item NUNZIATA, SCHYLER - Animal And Plant Health Inspection Service (APHIS)
item PADMANABHAN, CHELLAPPAN - Animal And Plant Health Inspection Service (APHIS)
item Hammond, John

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2024
Publication Date: 2/7/2024
Citation: Roy, A., Grinstead, S.C., Leon, G.M., Juan Carlos, C.P., Nunziata, S., Padmanabhan, C., Hammond, J. 2024. Meta-transcriptomic analysis uncovers the presence of four novel viruses and multiple known virus genera in a single Hibiscus rosa-sinensis plant in Colombia. Viruses. 16:267. https://doi.org/10.3390/v16020267.
DOI: https://doi.org/10.3390/v16020267

Interpretive Summary: During surveys of CiLVs in the citrus growing regions in Colombia, several hibiscus samples were collected for virus testing as hibiscus is a well-known host for viruses associated with citrus leprosis disease syndrome. Hibiscus leaf samples in Risaralda, Colombia, showing black spots on upper and lower sides was selected for virome analysis using High-throughput metagenomic sequencing. Bioinformatic and phylogenetic analysis revealed the presence of four novel Carlavirus, one Potexvirus species along with known Betacarmovirus, Nepovirus, Tobamovirus and three cileviruses in mixed infection. This is first time any carla-, nepo- and potexvirus infection has been identified in hibiscus.

Technical Abstract: Hibiscus is not native to Colombia but well suited to its arid soil and dry climates. A single hibiscus plant from Risaralda, showing black spots on upper and lower sides of its leaves, was collected for virome analysis using meta-transcriptomic high-throughput sequencing technology. Bioinformatic analysis identified 12.5% of the total reads in the Ribo-Zero cDNA library which mapped to viral genomes. BLAST searches revealed the presence of carlavirus, potexvirus, and of known members of the genera Betacarmovirus, Cilevirus, Nepovirus, and Tobamovirus in the sample; confirmed by RT-PCR with virus-specific primers followed by amplicon sequencing. Furthermore, in silico analysis suggested the possibility of a novel soymovirus, and a new hibiscus strain of citrus leprosis virus C2 in the mixed infection. Both RNA dependent RNA polymerase and coat protein gene sequences of the potex and carla viruses shared less than 72% nucleotide and 80% amino acid identities with any alphaflexi- and betaflexi-virus sequences available in GenBank, identifying three novel carlavirus and one potexvirus species in the Hibiscus rosa-sinensis plant. The detection of physalis vein necrosis nepovirus and passion fruit green spot cilevirus in hibiscus are also new reports from Colombia. Overall, the meta-transcriptome analysis identified the complex virome associated with the black spot symptoms on hibiscus leaves and demonstrated the diversity of virus genera tolerated in the mixed infection of a single H. rosa-sinensis plant.