Pan-genomic Insights into Indian Isolates of Ustilaginoidea virens, the False Smut Pathogen of Rice
Rice false smut (RFS) caused by the fungus Ustilaginoidea virens has recently emerged as a highly destructive grain disease in rice cultivation areas around the globe. In the rice field, this disease can be detected on the panicle after the grain-filling stage. RFS not only causes significant yield losses but also produces mycotoxins, posing serious health risks to both humans and animals. In India, the yield losses in different states have been estimated to vary between 0.2% and 49% depending on the disease intensity and rice variety. The high severity of the disease in field conditions can be attributed to the extensive cultivation of high-yield cultivars and hybrids, excessive use of chemical fertilizers, and an apparent shift in regional and global climatic patterns. Currently, the genome sequences of three U. virens isolates, UV-8b, IPU010, and UV-Gvt, originated from China, Japan, and India, respectively, are publicly available on the assembly database of NCBI. The genome sizes of these U. virens isolates range from 26.97 to 38.06 Mb. Recently, in our lab, a high quality genome of U. virens isolate UV2_4G was sequenced using Nanopore and Illumina HiSeq 2000 sequencing platforms.A pan-genome contains all the gene information across all the strains of a species. In this study, eight isolates of U. virens (MB-3, Uv103, Uv212, Uv302, Uv410, Uv412, Uv417, and Uv419) isolated from different geographical locations in India were selected for pan-genome and comparative genome analysis, which shall be used for population structure assessment, diversity analysis, and identification of important functional genes.