RNA‐mediated gene silencing in the cereal fungal pathogen <i>Cochliobolus sativus</i>

Leng, Yueqiang; Wu, Chengxiang; Liu, Zhaohui; Friesen, Timothy L.; Rasmussen, J. B.; Zhong, Shaobin

doi:10.1111/j.1364-3703.2010.00666.x

Cited by 28 publications

(19 citation statements)

References 43 publications

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“…Fungal transformation and molecular characterization of gene knockout mutants were conducted according to the methods of [120]. The split marker system [121] was used for gene deletion.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

et al. 2013

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The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

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“…Fungal transformation and molecular characterization of gene knockout mutants were conducted according to the methods of [120]. The split marker system [121] was used for gene deletion.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

et al. 2013

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“…RT-PCR analysis was done according to the method described by Leng et al [51]. Briefly, total RNA was extracted from each of the samples as collected for RNA-seq using the SV Total RNA Isolation Kit (Promega, Madison, WI) and purified by treatment with DNase I (NEB, Ipswich, MA) according to the manufacturers’ manuals.…”

Section: Methodsmentioning

confidence: 99%

RNA-Seq Revealed Differences in Transcriptomes between 3ADON and 15ADON Populations of Fusarium graminearum In Vitro and In Planta

et al. 2016

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Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) in barley and wheat in North America. The fungus not only causes yield loss of the crops but also produces harmful trichothecene mycotoxins [Deoxynivalenol (DON) and its derivatives-3-acetyldeoxynivalenol (3ADON) and 15-acetyldeoxynivalenol (15ADON), and nivalenol (NIV)] that contaminate grains. Previous studies showed a dramatic increase of 3ADON-producing isolates with higher aggressiveness and DON production than the 15ADON-producing isolates in North America. However, the genetic and molecular basis of differences between the two types of isolates is unclear. In this study, we compared transcriptomes of the 3ADON and 15ADON isolates in vitro (in culture media) and in planta (during infection on the susceptible wheat cultivar ‘Briggs’) using RNA-sequencing. The in vitro gene expression comparison identified 479 up-regulated and 801 down-regulated genes in the 3ADON isolates; the up-regulated genes were mainly involved in C-compound and carbohydrate metabolism (18.6%), polysaccharide metabolism (7.7%) or were of unknown functions (57.6%). The in planta gene expression analysis revealed that 185, 89, and 62 genes were up-regulated in the 3ADON population at 48, 96, and 144 hours after inoculation (HAI), respectively. The up-regulated genes were significantly enriched in functions for cellular import, C-compound and carbohydrate metabolism, allantoin and allantoate transport at 48 HAI, for detoxification and virulence at 96 HAI, and for metabolism of acetic acid derivatives, detoxification, and cellular import at 144 HAI. Comparative analyses of in planta versus in vitro gene expression further revealed 2,159, 1,981 and 2,095 genes up-regulated in the 3ADON isolates, and 2,415, 2,059 and 1,777 genes up-regulated in the 15ADON isolates at the three time points after inoculation. Collectively, our data provides a foundation for further understanding of molecular mechanisms involved in aggressiveness and DON production of the two chemotype isolates of F. graminearum.

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“…Recently, RNA interference (RNAi) has emerged as a powerful tool for gene targeting in fungi [26][27][28]. Conventional RNAi machinery components, including the RNA-dependent RNA polymerase, Argonaut proteins and Dicers are conserved in some fungi, e.g., Cryptococcus neoformans [29], Bipolaris oryzae [30], Aspergillus and Fusarium Species [31] and Cochliobolus sativus [32]. However, its application in C. globosum has not been reported.…”

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confidence: 99%

A PKS gene, pks-1, is involved in chaetoglobosin biosynthesis, pigmentation and sporulation in Chaetomium globosum

Hao

Lou

et al. 2012

Sci. China Life Sci.

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Chaetomium globosum is one of the most common fungi in nature. It is best known for producing chaetoglobosins; however, the molecular basis of chaetoglobosin biosynthesis is poorly understood in this fungus. In this study, we utilized RNA interference (RNAi) to characterize a polyketide synthase gene, pks-1, in C. globosum that is involved in the production of chaetoglobosin A. When pks-1 was knocked down by RNAi, the production of chaetoglobosin A dramatically decreased. Knock-down mutants also displayed a pigment-deficient phenotype. These results suggest that the two polyketides, melanin and chaetoglobosin, are likely to share common biosynthetic steps. Most importantly, we found that pks-1 also plays a critical role in sporulation. The silenced mutants of pks-1 lost the ability to produce spores. We propose that polyketides may modulate cellular development via an unidentified action. We also suggest that C. globosum pks-1 is unique because of its triple role in melanin formation, chaetoglobosin biosynthesis and sporulation. This work may shed light on chaetoglobosin biosynthesis and indicates a relationship between secondary metabolism and fungal morphogenesis.

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RNA‐mediated gene silencing in the cereal fungal pathogen Cochliobolus sativus

Cited by 28 publications

References 43 publications

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

RNA-Seq Revealed Differences in Transcriptomes between 3ADON and 15ADON Populations of Fusarium graminearum In Vitro and In Planta

A PKS gene, pks-1, is involved in chaetoglobosin biosynthesis, pigmentation and sporulation in Chaetomium globosum

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