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The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism.

Lysøe E, Harris LJ, Walkowiak S, Subramaniam R, Divon HH, Riiser ES, Llorens C, Gabaldón T, Kistler HC, Jonkers W, Kolseth AK, Nielsen KF, Thrane U, Frandsen RJ - PLoS ONE (2014)

Bottom Line: In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species.Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology.We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Health and Plant Protection, Bioforsk - Norwegian Institute of Agricultural and Environmental Research, Ås, Norway.

ABSTRACT
Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6-43.1 MB, with 13217-13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

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Architecture of the gibberellic acid (GA) gene clusters from F. fujikuroi MP-A, F. avenaceum and Sphaceloma manihoticola.The gene cluster and surrounding genes are identical in the three F. avenaceum strains and only Fa05001 is shown (FaLH03 cluster: FAVG2_04186 - FAVG2_04192 and FaLH27 cluster: FAVG3_04219 - FAVG3_04224). The mVista trace shows the similarity over a 100 bp sliding windows (Shuffle-LAGAN plot) between the F. avenaceum and F. fujikuroi clusters, bottom line  = 50% and second line  = 75% identity. Genes: gss2  =  geranylgeranyldiphosphate synthase, cps/ks  =  copalyldiphosphate/ent-kaurene synthase, P450-4  =  ent-kaurene oxidase, P450-1  =  GA14 synthase, P450-2  =  C20-oxidase, P450-3  =  13-hydroxylase and DES  =  desaturase. Note that the intergenic regions are unknown for the S. manihoticola GA cluster, while the size of these regions is not to drawn to size.
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pone-0112703-g007: Architecture of the gibberellic acid (GA) gene clusters from F. fujikuroi MP-A, F. avenaceum and Sphaceloma manihoticola.The gene cluster and surrounding genes are identical in the three F. avenaceum strains and only Fa05001 is shown (FaLH03 cluster: FAVG2_04186 - FAVG2_04192 and FaLH27 cluster: FAVG3_04219 - FAVG3_04224). The mVista trace shows the similarity over a 100 bp sliding windows (Shuffle-LAGAN plot) between the F. avenaceum and F. fujikuroi clusters, bottom line  = 50% and second line  = 75% identity. Genes: gss2  =  geranylgeranyldiphosphate synthase, cps/ks  =  copalyldiphosphate/ent-kaurene synthase, P450-4  =  ent-kaurene oxidase, P450-1  =  GA14 synthase, P450-2  =  C20-oxidase, P450-3  =  13-hydroxylase and DES  =  desaturase. Note that the intergenic regions are unknown for the S. manihoticola GA cluster, while the size of these regions is not to drawn to size.

Mentions: One of the four Type II terpene synthase encoding genes (TS_II_01: FAVG1_10701, FAVG2_04190 and FAVG3_04223) shared by all three F. avenaceum strains was found to be orthologous to the gibberellic acid (GA) copalyldiphosphate/ent-kaurene synthase (cps/ks) from F. fujikuroi (Table S9 in File S1). Previously, the ability to synthesize the GA group of diterpenoid plant growth hormones in fungi has only been found in F. fujikuroi mating population A, Fusarium proliferatum, Sphaceloma manihoticola and Phaeosphaeria sp. strain L487 [70]–[74]. Biosynthesis of GA was first thoroughly characterized in F. fujikuroi and depends on the coordinated activity of seven enzymes, encoded by the GA gene cluster, that convert dimethylallyl diphosphate (DMAPP) to various types of gibberellic acids, with the main end-products being GA1 and GA3[70]. S. manihoticola's GA biosynthesis ends at the intermediate GA4 due to the lack two of genes (DES and P450-3), compared to F. fujikuroi, responsible for converting GA4 to GA7, GA3 and GA1[73]. Analysis of the genes surrounding the F. avenaceum CPS/KS encoding gene showed that six of the seven genes from the F. fujikuroi GA gene cluster are also found in all three F. avenaceum genomes, with only P450-3 (C13-oxidase) missing (Figure 7). The architecture of the GA cluster in F. avenaceum is highly similar to the F. fujikuroi cluster, and a single inversion in five of the six genes can explain the relocation of the desaturase (des) encoding gene. The inversion could potentially have involved the P450-3 gene and resulted in the disruption of its coding sequence, however the shuffle-LAGAN analysis (Figure 7) and dot plot showed that this has not been the case. The missing gene is not found elsewhere in the genome based on a tblastn search. The presence of six of the seven GA biosynthesis genes suggest that F. avenaceum has the potential to produce all the GA's up to G4 and G7, but lack the ability to convert these into the GA1 and GA3. None of the three F. avenaceum isolates have been reported to produce this plant growth hormone.


The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism.

Lysøe E, Harris LJ, Walkowiak S, Subramaniam R, Divon HH, Riiser ES, Llorens C, Gabaldón T, Kistler HC, Jonkers W, Kolseth AK, Nielsen KF, Thrane U, Frandsen RJ - PLoS ONE (2014)

Architecture of the gibberellic acid (GA) gene clusters from F. fujikuroi MP-A, F. avenaceum and Sphaceloma manihoticola.The gene cluster and surrounding genes are identical in the three F. avenaceum strains and only Fa05001 is shown (FaLH03 cluster: FAVG2_04186 - FAVG2_04192 and FaLH27 cluster: FAVG3_04219 - FAVG3_04224). The mVista trace shows the similarity over a 100 bp sliding windows (Shuffle-LAGAN plot) between the F. avenaceum and F. fujikuroi clusters, bottom line  = 50% and second line  = 75% identity. Genes: gss2  =  geranylgeranyldiphosphate synthase, cps/ks  =  copalyldiphosphate/ent-kaurene synthase, P450-4  =  ent-kaurene oxidase, P450-1  =  GA14 synthase, P450-2  =  C20-oxidase, P450-3  =  13-hydroxylase and DES  =  desaturase. Note that the intergenic regions are unknown for the S. manihoticola GA cluster, while the size of these regions is not to drawn to size.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4237347&req=5

pone-0112703-g007: Architecture of the gibberellic acid (GA) gene clusters from F. fujikuroi MP-A, F. avenaceum and Sphaceloma manihoticola.The gene cluster and surrounding genes are identical in the three F. avenaceum strains and only Fa05001 is shown (FaLH03 cluster: FAVG2_04186 - FAVG2_04192 and FaLH27 cluster: FAVG3_04219 - FAVG3_04224). The mVista trace shows the similarity over a 100 bp sliding windows (Shuffle-LAGAN plot) between the F. avenaceum and F. fujikuroi clusters, bottom line  = 50% and second line  = 75% identity. Genes: gss2  =  geranylgeranyldiphosphate synthase, cps/ks  =  copalyldiphosphate/ent-kaurene synthase, P450-4  =  ent-kaurene oxidase, P450-1  =  GA14 synthase, P450-2  =  C20-oxidase, P450-3  =  13-hydroxylase and DES  =  desaturase. Note that the intergenic regions are unknown for the S. manihoticola GA cluster, while the size of these regions is not to drawn to size.
Mentions: One of the four Type II terpene synthase encoding genes (TS_II_01: FAVG1_10701, FAVG2_04190 and FAVG3_04223) shared by all three F. avenaceum strains was found to be orthologous to the gibberellic acid (GA) copalyldiphosphate/ent-kaurene synthase (cps/ks) from F. fujikuroi (Table S9 in File S1). Previously, the ability to synthesize the GA group of diterpenoid plant growth hormones in fungi has only been found in F. fujikuroi mating population A, Fusarium proliferatum, Sphaceloma manihoticola and Phaeosphaeria sp. strain L487 [70]–[74]. Biosynthesis of GA was first thoroughly characterized in F. fujikuroi and depends on the coordinated activity of seven enzymes, encoded by the GA gene cluster, that convert dimethylallyl diphosphate (DMAPP) to various types of gibberellic acids, with the main end-products being GA1 and GA3[70]. S. manihoticola's GA biosynthesis ends at the intermediate GA4 due to the lack two of genes (DES and P450-3), compared to F. fujikuroi, responsible for converting GA4 to GA7, GA3 and GA1[73]. Analysis of the genes surrounding the F. avenaceum CPS/KS encoding gene showed that six of the seven genes from the F. fujikuroi GA gene cluster are also found in all three F. avenaceum genomes, with only P450-3 (C13-oxidase) missing (Figure 7). The architecture of the GA cluster in F. avenaceum is highly similar to the F. fujikuroi cluster, and a single inversion in five of the six genes can explain the relocation of the desaturase (des) encoding gene. The inversion could potentially have involved the P450-3 gene and resulted in the disruption of its coding sequence, however the shuffle-LAGAN analysis (Figure 7) and dot plot showed that this has not been the case. The missing gene is not found elsewhere in the genome based on a tblastn search. The presence of six of the seven GA biosynthesis genes suggest that F. avenaceum has the potential to produce all the GA's up to G4 and G7, but lack the ability to convert these into the GA1 and GA3. None of the three F. avenaceum isolates have been reported to produce this plant growth hormone.

Bottom Line: In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species.Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology.We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Health and Plant Protection, Bioforsk - Norwegian Institute of Agricultural and Environmental Research, Ås, Norway.

ABSTRACT
Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6-43.1 MB, with 13217-13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

Show MeSH
Related in: MedlinePlus