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:

Roy Avijit1ORCID,Grinstead Sam1ORCID,Leon Martínez Guillermo2,Pinzón Juan Carlos Campos2,Nunziata Schyler O.3,Padmanabhan Chellappan3ORCID,Hammond John4ORCID

Affiliation:

1. Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA

2. AGROSAVIA, Centro de Investigación La Libertad, Km.17 vía Pto. Lopez, Villavicencio, Meta, Colombia

3. Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA

4. Floral and Nursery Plants Research Unit, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA

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.

Funder

USDA-ARS

USDA-APHIS PPQ Citrus Health Response Program

Publisher

MDPI AG

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