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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

Diversity of genes encoding Carbohydrate Active enZymes (CAZymes).The bars represent the number of genes dedicated to CAZymes in the genomes of six fungi. Necrotrophic fungi: A. rabiei, C. heterostrophus and P. tritici-repentis are shown on the left; Biotrophic fungi: Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea are shown on the right. All six CAZyme categories are represented: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs).
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f5: Diversity of genes encoding Carbohydrate Active enZymes (CAZymes).The bars represent the number of genes dedicated to CAZymes in the genomes of six fungi. Necrotrophic fungi: A. rabiei, C. heterostrophus and P. tritici-repentis are shown on the left; Biotrophic fungi: Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea are shown on the right. All six CAZyme categories are represented: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs).

Mentions: Enzymes required for degrading plant cell walls is a crucial factor for pathogen invasion. Not surprisingly, the growth efficiency and aggressiveness of phytopathogens are often associated with their CAZymes. Among the 10,596 unique proteins of A. rabiei, 1,727 (16.3%) showed presence of Pfam protein domain that matched with at least one of the CAZyme families. These putative CAZymes included 58 families of glycoside hydrolases (GHs), 40 families of glycosyl transferases (GTs), 8 families of carbohydrate esterases (CEs), 18 families of carbohydrate-binding modules (CBMs), 9 families of auxiliary activities (AAs) and only 3 families of polysaccharide lyases (PLs) (Supplementary Fig. 15a, Supplementary Table 17). Among all the CAZyme families, the GT family is the most represented, followed by the GH proteins. The most abundant GT classes were strongly geared toward cellulose (GT48), hemicellulose (GT34) and chitin (GT2) degradation (Supplementary Fig. 15b, Supplementary Table 17). The relationship between the number and variety of CAZymes, and fungal nutritional strategy was examined by comparing predicted CAZymes of A. rabiei with those in few other related necrotrophic and biotrophic fungi. Unlike biotrophs, A. rabiei and other necrotrophic fungi had a significantly expanded set of CAZymes (Fig. 5), particularly cellulose and hemicellulose degrading enzymes (Supplementary Figs 16,17). Further study would be required to determine their relevance to plant pathogenicity or other lifestyle characteristics. However, these findings indicated that A. rabiei possessed a battery of CAZymes that would be suitable for the consumption of carbohydrates commonly found in plant hosts and also for the degradation of pectin.


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)

Diversity of genes encoding Carbohydrate Active enZymes (CAZymes).The bars represent the number of genes dedicated to CAZymes in the genomes of six fungi. Necrotrophic fungi: A. rabiei, C. heterostrophus and P. tritici-repentis are shown on the left; Biotrophic fungi: Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea are shown on the right. All six CAZyme categories are represented: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Diversity of genes encoding Carbohydrate Active enZymes (CAZymes).The bars represent the number of genes dedicated to CAZymes in the genomes of six fungi. Necrotrophic fungi: A. rabiei, C. heterostrophus and P. tritici-repentis are shown on the left; Biotrophic fungi: Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea are shown on the right. All six CAZyme categories are represented: carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glucoside hydrolases (GHs), glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs).
Mentions: Enzymes required for degrading plant cell walls is a crucial factor for pathogen invasion. Not surprisingly, the growth efficiency and aggressiveness of phytopathogens are often associated with their CAZymes. Among the 10,596 unique proteins of A. rabiei, 1,727 (16.3%) showed presence of Pfam protein domain that matched with at least one of the CAZyme families. These putative CAZymes included 58 families of glycoside hydrolases (GHs), 40 families of glycosyl transferases (GTs), 8 families of carbohydrate esterases (CEs), 18 families of carbohydrate-binding modules (CBMs), 9 families of auxiliary activities (AAs) and only 3 families of polysaccharide lyases (PLs) (Supplementary Fig. 15a, Supplementary Table 17). Among all the CAZyme families, the GT family is the most represented, followed by the GH proteins. The most abundant GT classes were strongly geared toward cellulose (GT48), hemicellulose (GT34) and chitin (GT2) degradation (Supplementary Fig. 15b, Supplementary Table 17). The relationship between the number and variety of CAZymes, and fungal nutritional strategy was examined by comparing predicted CAZymes of A. rabiei with those in few other related necrotrophic and biotrophic fungi. Unlike biotrophs, A. rabiei and other necrotrophic fungi had a significantly expanded set of CAZymes (Fig. 5), particularly cellulose and hemicellulose degrading enzymes (Supplementary Figs 16,17). Further study would be required to determine their relevance to plant pathogenicity or other lifestyle characteristics. However, these findings indicated that A. rabiei possessed a battery of CAZymes that would be suitable for the consumption of carbohydrates commonly found in plant hosts and also for the degradation of pectin.

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