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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

Functional annotation of the A. rabiei effector candidates.(a) Percentage distribution of the proteins with distinct enzymatic functions. (b) Summary of the six CAZyme categories: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs). (c) Distinct summaries of each of the CAZyme categories representing the most abundant CAZyme classes. The prediction of CAZymes from A. rabiei effector candidates and their classification were performed using tools from the Carbohydrate-Active EnZymes (CAZyme) database. (d) Percentage distribution of different types of peptidases present in A. rabiei secretome.
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f6: Functional annotation of the A. rabiei effector candidates.(a) Percentage distribution of the proteins with distinct enzymatic functions. (b) Summary of the six CAZyme categories: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs). (c) Distinct summaries of each of the CAZyme categories representing the most abundant CAZyme classes. The prediction of CAZymes from A. rabiei effector candidates and their classification were performed using tools from the Carbohydrate-Active EnZymes (CAZyme) database. (d) Percentage distribution of different types of peptidases present in A. rabiei secretome.

Mentions: In addition, 201 effector candidates (26.5% of the total secretome) were annotated with the CAZyme database (Fig. 6a,b, Supplementary Table 19). The repertoire of secreted CAZymes consisted of 36 families of GHs, 2 families of GTs, 5 families of CEs, 3 families of PLs and 6 families each of CBMs and AAs. The 36 families of GHs comprising of 95 CAZymes was the most common (47%) in the total secreted CAZymes (Fig. 6a), followed by 6 families of AAs that contributed 19% to the overall secreted CAZymes. These analyses suggested existence of a clear dual preference in A. rabiei secreted CAZymes. Very high prevalence of GHs, CEs and AAs, which are required for degradation of the structures of plant cells was observed. In contrast, CBMs that functions in modification of the fungal cell wall for growth or protection from host-defenses were also in abundance. The most prevalent GHs CAZyme class was GH28 and GH43 which represented polygalacturonase and xylanase, respectively (Fig. 6c, Supplementary Table 19). Polygalacturonase and xylanase degrades polygalacturonan and hemicellulose, respectively, present in the plant cell walls to convert plant material into usable nutrients. The most abundant classes of CBMs were CBM50, CBM1 and CBM13 that consists of LysM domain containing proteins. The LysM domain-containing fungal effectors have been shown to inhibit plant chitinases28. Moreover, they bind to chitin to prevent elicitation of pathogen associated molecular pattern (PAMP) triggered immunity (PTI) and, thereby, prevent induction of host defense29. A. rabiei secretome also contained distinct peptidases, lipases, peroxidases and oxidoreductases (Fig. 6a,d). Therefore, these analyses suggested that the secretome of A. rabiei consists of proteins of diverse nature, which might function in facilitating proper colonization of the fungus, degradation of the host plant matter to acquire nutrients and inactivation of the host defenses.


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)

Functional annotation of the A. rabiei effector candidates.(a) Percentage distribution of the proteins with distinct enzymatic functions. (b) Summary of the six CAZyme categories: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs). (c) Distinct summaries of each of the CAZyme categories representing the most abundant CAZyme classes. The prediction of CAZymes from A. rabiei effector candidates and their classification were performed using tools from the Carbohydrate-Active EnZymes (CAZyme) database. (d) Percentage distribution of different types of peptidases present in A. rabiei secretome.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f6: Functional annotation of the A. rabiei effector candidates.(a) Percentage distribution of the proteins with distinct enzymatic functions. (b) Summary of the six CAZyme categories: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs). (c) Distinct summaries of each of the CAZyme categories representing the most abundant CAZyme classes. The prediction of CAZymes from A. rabiei effector candidates and their classification were performed using tools from the Carbohydrate-Active EnZymes (CAZyme) database. (d) Percentage distribution of different types of peptidases present in A. rabiei secretome.
Mentions: In addition, 201 effector candidates (26.5% of the total secretome) were annotated with the CAZyme database (Fig. 6a,b, Supplementary Table 19). The repertoire of secreted CAZymes consisted of 36 families of GHs, 2 families of GTs, 5 families of CEs, 3 families of PLs and 6 families each of CBMs and AAs. The 36 families of GHs comprising of 95 CAZymes was the most common (47%) in the total secreted CAZymes (Fig. 6a), followed by 6 families of AAs that contributed 19% to the overall secreted CAZymes. These analyses suggested existence of a clear dual preference in A. rabiei secreted CAZymes. Very high prevalence of GHs, CEs and AAs, which are required for degradation of the structures of plant cells was observed. In contrast, CBMs that functions in modification of the fungal cell wall for growth or protection from host-defenses were also in abundance. The most prevalent GHs CAZyme class was GH28 and GH43 which represented polygalacturonase and xylanase, respectively (Fig. 6c, Supplementary Table 19). Polygalacturonase and xylanase degrades polygalacturonan and hemicellulose, respectively, present in the plant cell walls to convert plant material into usable nutrients. The most abundant classes of CBMs were CBM50, CBM1 and CBM13 that consists of LysM domain containing proteins. The LysM domain-containing fungal effectors have been shown to inhibit plant chitinases28. Moreover, they bind to chitin to prevent elicitation of pathogen associated molecular pattern (PAMP) triggered immunity (PTI) and, thereby, prevent induction of host defense29. A. rabiei secretome also contained distinct peptidases, lipases, peroxidases and oxidoreductases (Fig. 6a,d). Therefore, these analyses suggested that the secretome of A. rabiei consists of proteins of diverse nature, which might function in facilitating proper colonization of the fungus, degradation of the host plant matter to acquire nutrients and inactivation of the host defenses.

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