Direct Metatranscriptomic Survey of the Sunflower Microbiome and Virome

Abstract

Sunflowers (Helianthus annuus L.) are susceptible to multiple diseases in field production. In this study, we collected diseased sunflower leaves in fields located in South Dakota, USA, for virome investigation. The leaves showed visible symptoms on the foliage, indicating phomopsis and rust infections. To identify the viruses potentially associated with the disease diagnosed, symptomatic leaves were obtained from diseased plants. Total RNA was extracted corresponding to each disease diagnosed to generate libraries for paired-end high throughput sequencing. Short sequencing reads were assembled de novo and the contigs with similarities to viruses were identified by aligning against a custom protein database. We report the discovery of two novel mitoviruses, four novel partitiviruses, one novel victorivirus, and nine novel totiviruses based on similarities to RNA-dependent RNA polymerases and capsid proteins. Contigs similar to bean yellow mosaic virus and Sclerotinia sclerotiorum hypovirulence-associated DNA virus were also detected. To the best of our knowledge, this is the first report of direct metatranscriptomics discovery of viruses associated with fungal infections of sunflowers bypassing culturing. These newly discovered viruses represent a natural genetic resource from which we can further develop potential biopesticide to control sunflower diseases.

Long-Term Anthropogenic Management and Associated Loss of Plant Diversity Deeply Impact Virome Richness and Composition of Poaceae Communities

“…Before the advent of metagenomics, the ICTV criterion of 50% amino acid identity was sufficient, because the limited number of known species was sufficiently distinct (e.g., only 30% identity between Saccharomyces cerevisiae virus L-A and Saccharomyces cerevisiae virus L-BC in the 717-amino-acid (aa) region of highest similarity) ( 49 ). However, the numerous Totivirus species identified here and in other metagenomics studies ( 36 , 50 ) presented less clear tendencies that could eventually suggest reconsideration of demarcation criteria for the genus (e.g., harmonizing rules with victoriviruses that also belong to the Totiviridae family and present a demarcation threshold of 60% aa identity).…”

Clinical Efficacy of Huangkui Capsule plus Methylprednisolone in the Treatment of Nephropathy and the Effect on Urinary Protein and Serum Inflammatory Factors in Patients

“…Wang et al confirmed that Huangkui capsules can inhibit glomerular immunity of the organism to abate the inflammatory response, and it also inhibits platelet aggregation to mitigate the impairment of kidney function. In addition, the Huangkui capsule also has the effect of scavenging oxygen free radicals, reducing urine protein, blood urea nitrogen, and muscle libido [ 16 , 17 ].…”

Long term anthropic management and associated loss of plant diversity deeply impact virome richness and composition ofPoaceaecommunities

“…However, the numerous Totivirus species identified here and in other metagenomics studies (34,48) presented less clear tendencies that could eventually suggest to reconsider demarcation criteria for the genus (e.g. harmonizing rules with victoriviruses that also belong to the Totiviridae family and present a demarcation threshold of 60% aa identity).…”