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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

A. rabiei effector orthologs and summary of the cysteine-rich effector proteins.(a) Both classically and non-classically secreted A. rabiei putative effector candidates are shown. The number of effector candidates with and without orthologs in closely related Dothideomycetes, i.e., C. heterostrophus, P. tritici-repentis, and S. nodorum are shown. (b) The unannotated secretory proteins or those that could not be assigned any enzymatic function were analyzed for the presence of a high number of cysteine residues (≥ 6). The x-axis shows the total number of cysteine residues present in a protein sequence, and the y-axis denotes the number of proteins harboring these cysteine residues.
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f7: A. rabiei effector orthologs and summary of the cysteine-rich effector proteins.(a) Both classically and non-classically secreted A. rabiei putative effector candidates are shown. The number of effector candidates with and without orthologs in closely related Dothideomycetes, i.e., C. heterostrophus, P. tritici-repentis, and S. nodorum are shown. (b) The unannotated secretory proteins or those that could not be assigned any enzymatic function were analyzed for the presence of a high number of cysteine residues (≥ 6). The x-axis shows the total number of cysteine residues present in a protein sequence, and the y-axis denotes the number of proteins harboring these cysteine residues.

Mentions: In order to determine conservation of A. rabiei putative effectors, 323 putative effectors (lacking CAZymes and known domain proteins) were searched for the presence of orthologs in closely related C. heterostrophus, P. tritici-repentis, and S. nodorum (Query coverage ≥50%, identity ≥40%). Out of 323, only 148 putative effectors had their orthologs in at least one of the three fungi whereas, 175 putative effectors were unique to A. rabiei suggesting that effectors are less conserved in nature (Fig. 7a, Supplementary Data 13). Moreover, particularly non-classically secreted effectors were found less conserved as compared to classically secreted effectors.


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)

A. rabiei effector orthologs and summary of the cysteine-rich effector proteins.(a) Both classically and non-classically secreted A. rabiei putative effector candidates are shown. The number of effector candidates with and without orthologs in closely related Dothideomycetes, i.e., C. heterostrophus, P. tritici-repentis, and S. nodorum are shown. (b) The unannotated secretory proteins or those that could not be assigned any enzymatic function were analyzed for the presence of a high number of cysteine residues (≥ 6). The x-axis shows the total number of cysteine residues present in a protein sequence, and the y-axis denotes the number of proteins harboring these cysteine residues.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7: A. rabiei effector orthologs and summary of the cysteine-rich effector proteins.(a) Both classically and non-classically secreted A. rabiei putative effector candidates are shown. The number of effector candidates with and without orthologs in closely related Dothideomycetes, i.e., C. heterostrophus, P. tritici-repentis, and S. nodorum are shown. (b) The unannotated secretory proteins or those that could not be assigned any enzymatic function were analyzed for the presence of a high number of cysteine residues (≥ 6). The x-axis shows the total number of cysteine residues present in a protein sequence, and the y-axis denotes the number of proteins harboring these cysteine residues.
Mentions: In order to determine conservation of A. rabiei putative effectors, 323 putative effectors (lacking CAZymes and known domain proteins) were searched for the presence of orthologs in closely related C. heterostrophus, P. tritici-repentis, and S. nodorum (Query coverage ≥50%, identity ≥40%). Out of 323, only 148 putative effectors had their orthologs in at least one of the three fungi whereas, 175 putative effectors were unique to A. rabiei suggesting that effectors are less conserved in nature (Fig. 7a, Supplementary Data 13). Moreover, particularly non-classically secreted effectors were found less conserved as compared to classically secreted effectors.

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