Viral metagenomic-based screening of sugarcane from Florida reveals occurrence of six sugarcane-infecting viruses and high prevalence of Sugarcane yellow leaf virus

Authors: FILLOUX, DENIS - Cirad, France; FERNANDEZ, EMMANUEL - Cirad, France; Comstock, Jack; Mollov, Dimitre; ROUMAGNAC, PHILIPPE - Cirad, France; ROTT, PHILIPPE - University Of Florida

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2018
Publication Date: 5/29/2018
Citation: Filloux, D., Fernandez, E., Comstock, J.C., Mollov, D.S., Roumagnac, P., Rott, P. 2018. Viral metagenomic-based screening of sugarcane from Florida reveals occurrence of six sugarcane-infecting viruses and high prevalence of Sugarcane yellow leaf virus. Plant Disease. https://doi.org/10.1094/PDIS-04-18-0581-RE.
DOI: https://doi.org/10.1094/PDIS-04-18-0581-RE

Interpretive Summary: Viruses, many of which are transmitted by insect vectors, infect sugarcane and cause production losses. The southern part of Florida is the largest sugarcane production area in the U.S. Both scientists, who maintain collections for research and breeding, and growers want to minimize the incidence of virus infections. This research used advanced sequencing techniques to detect sugarcane viruses in Florida fields and in research collections. Among 214 samples that were sequenced, 6 different viruses were detected. The most frequently detected (70% infection rate) was sugarcane yellow leaf virus (SCYLV). We examined the sequences of many of these positives in more detail to understand the variation in the virus population. This led us to propose a revised classification system for SCYLV. The other viruses detected in the sugarcane samples were sugarcane mosaic virus, sugarcane mild mosaic virus, sugarcane baciliform virus, a recently described mastrevirus (sugarcane striate virus) and a potentially new-sugarcane infecting virus. This research benefits both sugarcane scientists and growers with an alternative detection virus method and information about the occurrence of both known and new viruses in Florida.

Technical Abstract: A viral metagenomics study of the sugarcane virome in Florida was performed in 2013/2014 to analyze the occurrence of known and potentially new viruses. Two hundred and fourteen sugarcane leaf samples were collected from commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species from two local germplasm collections. Virion-associated nucleic acids (VANA) metagenomics was used for detection and identification of viruses. VANA sequence reads were obtained for 204 leaf samples and all four previously reported sugarcane viruses occurring in Florida were detected: sugarcane yellow leaf virus (SCYLV, 150 infected samples out of 204), sugarcane mosaic virus (1/204), sugarcane mild mosaic virus (13/204), and sugarcane bacilliform virus (54/204). High prevalence of SCYLV in Florida commercial fields and germplasm collections was confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR). Sequence analyses revealed the presence of SCYLV isolates belonging to two different phylogenetic clades (I and II), including a new genotype of this virus. This viral metagenomics approach also detected a new sugarcane-infecting mastrevirus (recently described and named sugarcane striate virus), and two potentially new viruses; one each in the genera Chrysovirus and Umbravirus.