Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence

Pramesh, D.; Prasannakumar, M. K.; Muniraju, K.M.; Mahesh, H. B.; Pushpa, H D; Manjunatha, C.; Saddamhusen, Alase; Chidanandappa, E.; Yadav, Manoj Kumar; Kumara, Masalavada K; Sharanabasav, H; Rohith, B S; Banerjee, Gaurab; Das, Anupam

doi:10.1007/s13205-020-02336-9

Cited by 14 publications

(8 citation statements)

References 48 publications

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“…The aligned reads were sorted and indexed using Samtools ( Li et al, 2009 ). The aligned reads were utilized in variant calling using Genome Analysis Toolkit (GATK) ( DePristo et al, 2011 ) with optimal practices for germline SNPs and indel calling 10 ( Pramesh et al, 2020 ). At first, the HaplotypeCaller was called without Base Quality Score Recalibration (BQSR), the thus obtained variants were fed to BQSR as know variants, and a recalibration was achieved, while no other modifications were made in the workflow.…”

Section: Methodsmentioning

confidence: 99%

Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood

Usha

Middha²,

Babu

et al. 2022

Front. Genet.

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The wonder fruit pomegranate (Punica granatum, family Lythraceae) is one of India’s economically important fruit crops that can grow in different agro-climatic conditions ranging from tropical to temperate regions. This study reports high-quality de novo draft hybrid genome assembly of diploid Punica cultivar “Bhagwa” and identifies its genomic features. This cultivar is most common among the farmers due to its high sustainability, glossy red color, soft seed, and nutraceutical properties with high market value. The draft genome assembly is about 361.76 Mb (N50 = 40 Mb), ∼9.0 Mb more than the genome size estimated by flow cytometry. The genome is 90.9% complete, and only 26.68% of the genome is occupied by transposable elements and has a relative abundance of 369.93 SSRs/Mb of the genome. A total of 30,803 proteins and their putative functions were predicted. Comparative whole-genome analysis revealed Eucalyptus grandis as the nearest neighbor. KEGG-KASS annotations indicated an abundance of genes involved in the biosynthesis of flavonoids, phenylpropanoids, and secondary metabolites, which are responsible for various medicinal properties of pomegranate, including anticancer, antihyperglycemic, antioxidant, and anti-inflammatory activities. The genome and gene annotations provide new insights into the pharmacological properties of the secondary metabolites synthesized in pomegranate. They will also serve as a valuable resource in mining biosynthetic pathways for key metabolites, novel genes, and variations associated with disease resistance, which can facilitate the breeding of new varieties with high yield and superior quality.

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Section: Methodsmentioning

confidence: 99%

Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood

Usha

Middha²,

Babu

et al. 2022

Front. Genet.

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“…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.…”

Section: Phenotype Characters Of Rfs Fungus Albino Strain Ln02mentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Xue,

Zhao,

et al. 2023

IJMS

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Rice false smut (RFS) caused by Villosiclava virens (anamorph: Ustilaginoidea virens) has become one of the most destructive fungal diseases to decrease the yield and quality of rice grains. An albino strain LN02 was isolated from the white RFS balls collected in the Liaoning Province of China in 2019. The strain LN02 was considered as a natural albino mutant of V. virens by analyzing its phenotypes, internal transcribed spacer (ITS) conserved sequence, and biosynthesis gene clusters (BGCs) for secondary metabolites. The total assembled genome of strain LN02 was 38.81 Mb, which was comprised of seven nuclear chromosomes and one mitochondrial genome with an N50 value of 6,326,845 bp and 9339 protein-encoding genes. In addition, the genome of strain LN02 encoded 19 gene clusters for biosynthesis of secondary metabolites mainly including polyketides, terpenoids and non-ribosomal peptides (NRPs). Four sorbicillinoid metabolites were isolated from the cultures of strain LN02. It was found that the polyketide synthase (PKS)-encoding gene uspks1 for ustilaginoidin biosynthesis in strain LN02 was inactivated due to the deletion of four bases in the promoter sequence of uvpks1. The normal uvpks1 complementary mutant of strain LN02 could restore the ability to synthesize ustilaginoidins. It demonstrated that deficiency of ustilaginoidin biosynthesis is the cause of albinism for RFS albino strain LN02, and V. virens should be a non-melanin-producing fungus. This study further confirmed strain LN02 as a white phenotype mutant of V. virens. The albino strain LN02 will have a great potential in the development and application of secondary metabolites. The physiological and ecological functions of ustilaginoidins in RFS fungus are needed for further investigation.

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“…BUSCO (v4.1.4) (Seppey et al, 2019) was used to analyze the completeness of the genome assembly, and results showed that 98.80% of genes were represented, indicating a high-quality assembly of the JS60-2 genome. The JS60-2 genome is the first gap-free U. virens genome, and the contig N 50 has been improved in comparison to previous U. virens genomes (Zhang et al, 2021;Pramesh et al, 2020;Kumagai et al, 2016). We obtained 10.5 Gb of RNA-seq data from mycelia cultured under light condition, mycelia cultured under dark condition and chlamydospore balls on inoculated rice spikelets.…”

Section: Genome Announcementmentioning

confidence: 99%

Gap-free nuclear and mitochondrial genomes ofUstilaginoidea virensstrain JS60-2, a fungal pathogen causing rice false smut

Wang

Yang

et al. 2022

Preprint

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Rice false smut (RFS), caused by Ustilaginoidea virens, has become a major disease in recent years, and mycotoxins produced by U. virens often threaten food safety. To study fungal pathogenesis and identify potential targets for developing new fungicides, gap-free nuclear and complete mitochondrial genomes of U. virens JS60-2 were sequenced and assembled. Using the second and third generation sequencing data, we assembled a 38.02-Mb genome that consists of seven contigs with the contig N50 being 6.32-Mb. In total, 8,486 protein-coding genes were annotated in the genome, including 21 secondary metabolism gene clusters. We also assembled the complete mitochondrial genome, which is 102,498 bp, with 28% GC content. The JS60-2 genomes assembled in this study will facilitate research on U. virens and contribute to RFS control.

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Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence

Cited by 14 publications

References 48 publications

Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood

Hybrid Assembly and Annotation of the Genome of the Indian Punica granatum, a Superfood

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

Gap-free nuclear and mitochondrial genomes ofUstilaginoidea virensstrain JS60-2, a fungal pathogen causing rice false smut

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