The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

King, Robert C.; Urban, Martin; Hammond-Kosack, Michael C. U.; Hassani‐Pak, Keywan; Hammond‐Kosack, K. E.

doi:10.1186/s12864-015-1756-1

Cited by 164 publications

(188 citation statements)

References 78 publications

(101 reference statements)

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“…This was due to the presence of the rDNA repeat, located at the end of a chromosome in most species (viz. Figure 1) as was also shown by King et al (2015). The number of rDNA repeats was 110 in JL22, while 80 copies were observed in F. temperatum JL513.…”

Section: Discussionsupporting

confidence: 63%

“…Proper assessment of the role of specific genetic elements such as telomeres, centromeres and repetitive elements will benefit from the availability of a fully assembled genome. To date, the best assembled genomes of Fusarium species are F. graminearum (King et al, 2015); F. fujikuroi (Wiemann et al, 2013) and F. poae (Vanheule et al, 2016). In addition, genome compartmentalization and structural rearrangements within and between chromosomes can only be studied accurately, when a genome is assembled to chromosome-sized contigs.…”

Section: Introductionmentioning

confidence: 99%

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Fusarium in the age of genomics

Waalwijk¹,

Vanheule

Audenaert

et al. 2017

Trop. plant pathol.

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Section: Discussionsupporting

confidence: 63%

Section: Introductionmentioning

confidence: 99%

Fusarium in the age of genomics

Waalwijk¹,

Vanheule

Audenaert

et al. 2017

Trop. plant pathol.

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“…Read mapping and identification of RNA editing sites RNA-seq reads of F. graminearum were aligned to the complete genome of PH-1 (King et al 2015) available in Ensembl Fungi with program HISAT v 0.1.6-beta (Kim et al 2015). RNA editing sites were identified by CLC Genomics Workbench 7.5 (CLC Bio), and a series of stringent filters were implemented to eliminate false positives as described in the Supplemental Methods.…”

Section: Library Construction and Sequencingmentioning

confidence: 99%

Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes

et al. 2016

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Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1 (FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium graminearum, we found that two tandem stop codons, UA1831GUA1834G, in its kinase domain were changed to UG1831GUG1834G by RNA editing in perithecia. To confirm A-to-I editing of PUK1 transcripts, strand-specific RNA-seq data were generated with RNA isolated from conidia, hyphae, and perithecia. PUK1 was almost specifically expressed in perithecia, and 90% of transcripts were edited to UG1831GUG1834G. Genome-wide analysis identified 26,056 perithecium-specific A-to-I editing sites. Unlike those in animals, 70.5% of A-to-I editing sites in F. graminearum occur in coding regions, and more than two-thirds of them result in amino acid changes, including editing of 69 PUK1-like pseudogenes with stop codons in ORFs. PUK1 orthologs and other pseudogenes also displayed stage-specific expression and editing in Neurospora crassa and F. verticillioides. Furthermore, F. graminearum differs from animals in the sequence preference and structure selectivity of A-to-I editing sites. Whereas A's embedded in RNA stems are targeted by ADARs, RNA editing in F. graminearum preferentially targets A's in hairpin loops, which is similar to the anticodon loop of tRNA targeted by adenosine deaminases acting on tRNA (ADATs). Overall, our results showed that A-to-I RNA editing occurs specifically during sexual reproduction and mainly in the coding regions in filamentous ascomycetes, involving adenosine deamination mechanisms distinct from metazoan ADARs.

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“…These CAZymes include a variety of glycoside hydrolases (GHs) as well as 18 putative lytic polysaccharide monooxygenases (LPMOs) [9]. F. graminearum is an efficient degrader of plant biomass, secreting cell wall degrading enzymes, including cellulases, xylanases, pectinases and LPMOs [10,11].…”

Section: Introductionmentioning

confidence: 99%

FgLPMO9A from Fusarium graminearum cleaves xyloglucan independently of the backbone substitution pattern

et al. 2016

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Lytic polysaccharide monooxygenases (LPMOs) are important for the enzymatic conversion of biomass and seem to play a key role in degradation of the plant cell wall. In this study, we characterize an LPMO from the fungal plant pathogen Fusarium graminearum (FgLPMO9A) that catalyzes the mixed C1/C4 oxidative cleavage of cellulose and xyloglucan, but is inactive towards other (1,4)-linked β-glucans. Our findings indicate that FgLPMO9A has unprecedented broad specificity on xyloglucan, cleaving any glycosidic bond in the β-glucan main chain, regardless of xylosyl substitutions. Interestingly, we found that when incubated with a mixture of xyloglucan and cellulose, FgLPMO9A efficiently attacks the xyloglucan, whereas cellulose conversion is inhibited. This suggests that removal of hemicellulose may be the true function of this LPMO during biomass conversion.

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The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

Cited by 164 publications

References 78 publications

Fusarium in the age of genomics

Fusarium in the age of genomics

Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes

FgLPMO9A from Fusarium graminearum cleaves xyloglucan independently of the backbone substitution pattern

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