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Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire.

Verma S, Gazara RK, Nizam S, Parween S, Chattopadhyay D, Verma PK - Sci Rep (2016)

Bottom Line: A wide range of genes encoding carbohydrate-active enzymes capable for degradation of complex polysaccharides were also identified.Comprehensive analysis predicted a set of 758 secretory proteins including both classical and non-classical secreted proteins.Several of these predicted secretory proteins showed high cysteine content and numerous tandem repeats.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.

ABSTRACT
Constant evolutionary pressure acting on pathogens refines their molecular strategies to attain successful pathogenesis. Recent studies have shown that pathogenicity mechanisms of necrotrophic fungi are far more intricate than earlier evaluated. However, only a few studies have explored necrotrophic fungal pathogens. Ascochyta rabiei is a necrotrophic fungus that causes devastating blight disease of chickpea (Cicer arietinum). Here, we report a 34.6 megabase draft genome assembly of A. rabiei. The genome assembly covered more than 99% of the gene space and 4,259 simple sequence repeats were identified in the assembly. A total of 10,596 high confidence protein-coding genes were predicted which includes a large and diverse inventory of secretory proteins, transporters and primary and secondary metabolism enzymes reflecting the necrotrophic lifestyle of A. rabiei. A wide range of genes encoding carbohydrate-active enzymes capable for degradation of complex polysaccharides were also identified. Comprehensive analysis predicted a set of 758 secretory proteins including both classical and non-classical secreted proteins. Several of these predicted secretory proteins showed high cysteine content and numerous tandem repeats. Together, our analyses would broadly expand our knowledge and offer insights into the pathogenesis and necrotrophic lifestyle of fungal phytopathogens.

No MeSH data available.


Related in: MedlinePlus

Phylogeny of selected Dothideomycetes.Estimated phylogenetic relationship of A. rabiei with other Dothideomycetes based on sequences of four protein-coding genes. Bootstrap based branch supports are shown, calculated according to the approximate Likelihood-Ratio Test, as implemented in RAxML 7.2.
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f3: Phylogeny of selected Dothideomycetes.Estimated phylogenetic relationship of A. rabiei with other Dothideomycetes based on sequences of four protein-coding genes. Bootstrap based branch supports are shown, calculated according to the approximate Likelihood-Ratio Test, as implemented in RAxML 7.2.

Mentions: The predicted proteome of A. rabiei was compared with a few closely related Dothideomycetes, i.e., Cochliobolus heterostrophus, Pyrenophora tritici-repentis and Stagonospora nodorum. OrthoMCL analysis showed that 6,432 (60.7%) of A. rabiei predicted proteins had orthologs in these three fungal species, while 693 (6.5%) predicted proteins were unique (Fig. 2b). Interestingly, 693 unique proteins were predicted to encode 53 glycoside hydrolases (GHs) (Supplementary Fig. S13, Supplementary Table 12). A large number of predicted proteins exhibited very high sequence similarity with those of necrotrophic wheat pathogen S. nodorum (6,701, 63.2%), indicating it as the nearest species among the selected fungi (Supplementary Data 4). Phylogenetic analysis of A. rabiei along with other 21 selected fungal species (20 Dothideomycetes and one Eurotiomycetes outgroup) also suggested that A. rabiei was closely related to S. nodorum (Fig. 3).


Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire.

Verma S, Gazara RK, Nizam S, Parween S, Chattopadhyay D, Verma PK - Sci Rep (2016)

Phylogeny of selected Dothideomycetes.Estimated phylogenetic relationship of A. rabiei with other Dothideomycetes based on sequences of four protein-coding genes. Bootstrap based branch supports are shown, calculated according to the approximate Likelihood-Ratio Test, as implemented in RAxML 7.2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835772&req=5

f3: Phylogeny of selected Dothideomycetes.Estimated phylogenetic relationship of A. rabiei with other Dothideomycetes based on sequences of four protein-coding genes. Bootstrap based branch supports are shown, calculated according to the approximate Likelihood-Ratio Test, as implemented in RAxML 7.2.
Mentions: The predicted proteome of A. rabiei was compared with a few closely related Dothideomycetes, i.e., Cochliobolus heterostrophus, Pyrenophora tritici-repentis and Stagonospora nodorum. OrthoMCL analysis showed that 6,432 (60.7%) of A. rabiei predicted proteins had orthologs in these three fungal species, while 693 (6.5%) predicted proteins were unique (Fig. 2b). Interestingly, 693 unique proteins were predicted to encode 53 glycoside hydrolases (GHs) (Supplementary Fig. S13, Supplementary Table 12). A large number of predicted proteins exhibited very high sequence similarity with those of necrotrophic wheat pathogen S. nodorum (6,701, 63.2%), indicating it as the nearest species among the selected fungi (Supplementary Data 4). Phylogenetic analysis of A. rabiei along with other 21 selected fungal species (20 Dothideomycetes and one Eurotiomycetes outgroup) also suggested that A. rabiei was closely related to S. nodorum (Fig. 3).

Bottom Line: A wide range of genes encoding carbohydrate-active enzymes capable for degradation of complex polysaccharides were also identified.Comprehensive analysis predicted a set of 758 secretory proteins including both classical and non-classical secreted proteins.Several of these predicted secretory proteins showed high cysteine content and numerous tandem repeats.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.

ABSTRACT
Constant evolutionary pressure acting on pathogens refines their molecular strategies to attain successful pathogenesis. Recent studies have shown that pathogenicity mechanisms of necrotrophic fungi are far more intricate than earlier evaluated. However, only a few studies have explored necrotrophic fungal pathogens. Ascochyta rabiei is a necrotrophic fungus that causes devastating blight disease of chickpea (Cicer arietinum). Here, we report a 34.6 megabase draft genome assembly of A. rabiei. The genome assembly covered more than 99% of the gene space and 4,259 simple sequence repeats were identified in the assembly. A total of 10,596 high confidence protein-coding genes were predicted which includes a large and diverse inventory of secretory proteins, transporters and primary and secondary metabolism enzymes reflecting the necrotrophic lifestyle of A. rabiei. A wide range of genes encoding carbohydrate-active enzymes capable for degradation of complex polysaccharides were also identified. Comprehensive analysis predicted a set of 758 secretory proteins including both classical and non-classical secreted proteins. Several of these predicted secretory proteins showed high cysteine content and numerous tandem repeats. Together, our analyses would broadly expand our knowledge and offer insights into the pathogenesis and necrotrophic lifestyle of fungal phytopathogens.

No MeSH data available.


Related in: MedlinePlus