High-Quality Genome Resource of Ustilaginoidea virens (UV2_4G), Causal Agent of an Emerging False Smut Disease in Rice

Abstract

Ustilaginoidea virens is the fungal pathogen causing an emerging false smut disease which affects crop yield as well as deteriorates quality of the grains by producing mycotoxins. High quality genome of U. virens isolate UV2_4G was sequenced using Nanopore and Illumina HiSeq 2000 sequencing platforms. The total assembled genome of Indian isolate UV2_4G was 35.9 Mb, which comprised of 89 scaffolds with N50 700296 bp. A total of 358697 variants were identified in the genome, out of which 355173 were SNPs and 3524 were INDELS. Further, 7390 SSRs belonging to different repeat type were also identified in the genome. Out of 7444 proteins predicted, 7206 were functionally annotated. A total of 1307 CAZymes, 501 signal peptides, 1876 effectors and 2709 genes involved in host-pathogen interactions were identified. Comparative analysis revealed isolate UV2_4G is distinct with 31 unique clusters and placed distantly in phylogenetic analysis. Taken together, this high-quality genome assembly and sequence annotation resource can give an improved insight for characterizing the biological and pathogenic mechanisms of Ustilaginoidea virens.

A Genome-Wide Comparison of Rice False Smut Fungus Villosiclava virens Albino Strain LN02 Reveals the Genetic Diversity of Secondary Metabolites and the Cause of Albinism

“…Though strain LN02 could produce conidia, the concentration of conidia in strain LN02 was significantly lower than that in strain P1 (Figure 2C). The complete genome sequencing of normal RFS fungus has been reported by a few research groups, with some strains including UV8b [14], IPU010 [15], UV_Gvt [16], UV-FJ-1 [17], JS60-2 [18], and UV2_4G [19]. Unfortunately, there is no detailed report on the genome of albino RFS fungus.…”

“…About 9339 protein-encoding genes were identified in strain LN02 by gene prediction using GeneMark-ES. However, the genomes of strains UV8b, IPU010, UV_Gvt, UV-FJ-1, JS60-2, and UV2_4G harbored 8426, 6451, 6627, 7164, 8468, and 7444 proteinencoding genes, respectively [14][15][16][17][18][19]. The comparative genomics of different RFS fungal genomes are shown in Table S2.…”

“…The complete genome sequencing of normal RFS fungus has been reported by a few research groups, with some strains including UV8b [14], IPU010 [15], UV_Gvt [16], UV-FJ-1 [17], JS60-2 [18], and UV2_4G [19]. Unfortunately, there is no detailed report on the genome of albino RFS fungus.…”

Activation of Ustilaginoidin Biosynthesis Gene uvpks1 in Villosiclava virens Albino Strain LN02 Influences Development, Stress Responses, and Inhibition of Rice Seed Germination

“…Rice false smut (RFS), caused by Villosiclava virens (anamorph: Ustilaginoidea virens), is a destructive rice disease in rice-producing areas worldwide. Moreover, the RFS pathogen (V. virens) can produce mycotoxins to decrease the yield and quality of grains [1][2][3][4]. White rice false smut was first reported in Japan in 1991 [5].…”