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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

Comparison of orthologous genes between necrotrophic and biotrophic fungi.Venn diagram showing the distribution of unique and shared orthologous gene families between and among the three necrotrophic and three biotrophic ascomycete fungi based on gene family cluster analysis. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis, Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea were identified using OrthoMCL. Comparison revealed 1,458 genes are orthologous in the selected three necrotrophic fungi. Additionally, 112 orthologous genes are present among the selected three biotrophic fungi.
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f4: Comparison of orthologous genes between necrotrophic and biotrophic fungi.Venn diagram showing the distribution of unique and shared orthologous gene families between and among the three necrotrophic and three biotrophic ascomycete fungi based on gene family cluster analysis. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis, Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea were identified using OrthoMCL. Comparison revealed 1,458 genes are orthologous in the selected three necrotrophic fungi. Additionally, 112 orthologous genes are present among the selected three biotrophic fungi.

Mentions: Comparative analysis was carried out between a set of necrotrophic (A. rabiei, C. heterostrophus and P. tritici-repentis) and biotrophic fungi (Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea). OrthoMCL analysis showed that 1,458 and 112 proteins were orthologous among the necrotrophic and biotrophic fungi, respectively (Fig. 4). Annotation of 1,458 orthologous proteins showed that most of them were transporters and enzymes (Supplementary Data 7) whereas, 112 orthologous proteins were mostly related to cell fusion, morphogenesis, voltage gated calcium channels and DNA damage repair (Supplementary Data 8). Interestingly, 1,458 orthologous proteins among necrotrophs had 296 CAZymes (20%) whereas 112 orthologous proteins among biootrophs had only 13 CAZymes (11%) (Supplementary Table 13,14).


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)

Comparison of orthologous genes between necrotrophic and biotrophic fungi.Venn diagram showing the distribution of unique and shared orthologous gene families between and among the three necrotrophic and three biotrophic ascomycete fungi based on gene family cluster analysis. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis, Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea were identified using OrthoMCL. Comparison revealed 1,458 genes are orthologous in the selected three necrotrophic fungi. Additionally, 112 orthologous genes are present among the selected three biotrophic fungi.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Comparison of orthologous genes between necrotrophic and biotrophic fungi.Venn diagram showing the distribution of unique and shared orthologous gene families between and among the three necrotrophic and three biotrophic ascomycete fungi based on gene family cluster analysis. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis, Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea were identified using OrthoMCL. Comparison revealed 1,458 genes are orthologous in the selected three necrotrophic fungi. Additionally, 112 orthologous genes are present among the selected three biotrophic fungi.
Mentions: Comparative analysis was carried out between a set of necrotrophic (A. rabiei, C. heterostrophus and P. tritici-repentis) and biotrophic fungi (Blumeria graminis f.sp. tritici, Blumeria graminis f.sp. hordei and Claviceps purpurea). OrthoMCL analysis showed that 1,458 and 112 proteins were orthologous among the necrotrophic and biotrophic fungi, respectively (Fig. 4). Annotation of 1,458 orthologous proteins showed that most of them were transporters and enzymes (Supplementary Data 7) whereas, 112 orthologous proteins were mostly related to cell fusion, morphogenesis, voltage gated calcium channels and DNA damage repair (Supplementary Data 8). Interestingly, 1,458 orthologous proteins among necrotrophs had 296 CAZymes (20%) whereas 112 orthologous proteins among biootrophs had only 13 CAZymes (11%) (Supplementary Table 13,14).

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