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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

Circular map displaying genomic features of the A. rabiei genome and a comparison of orthologous genes.(a) Schematic representation of genomic characteristics of A. rabiei pseudo-genome (Mb scale). Circle a: pseudo-genome of 34.6 Mb. Circle b: positions of the protein coding genes. Circle c: positions of exons of the respective protein coding genes in circle b. Circle d: positions of introns of the respective protein coding genes in circle b. Circle e: distribution of the putative secretory proteins. Circle f: distribution of repetitive sequences in the A. rabiei genome. Circle g: histogram shows the tRNA density as represented by the number of tRNAs in 100-kb non-overlapping windows. The peak of the histogram correlates with the tRNA density. The diagram was plotted using Circos. (b) Venn diagram showing unique and shared orthologous gene families between and among the four closely related Dothideomycetes fungi. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis and S. nodorum were identified using OrthoMCL. Comparison of the four species revealed 693 gene families unique to A. rabiei. However, A. rabiei shares 151, 110 and 269 gene families with C. heterostrophus, P. tritici-repentis and S. nodorum, respectively. Moreover, 6,432 gene families are orthologous in all the four fungi.
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f2: Circular map displaying genomic features of the A. rabiei genome and a comparison of orthologous genes.(a) Schematic representation of genomic characteristics of A. rabiei pseudo-genome (Mb scale). Circle a: pseudo-genome of 34.6 Mb. Circle b: positions of the protein coding genes. Circle c: positions of exons of the respective protein coding genes in circle b. Circle d: positions of introns of the respective protein coding genes in circle b. Circle e: distribution of the putative secretory proteins. Circle f: distribution of repetitive sequences in the A. rabiei genome. Circle g: histogram shows the tRNA density as represented by the number of tRNAs in 100-kb non-overlapping windows. The peak of the histogram correlates with the tRNA density. The diagram was plotted using Circos. (b) Venn diagram showing unique and shared orthologous gene families between and among the four closely related Dothideomycetes fungi. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis and S. nodorum were identified using OrthoMCL. Comparison of the four species revealed 693 gene families unique to A. rabiei. However, A. rabiei shares 151, 110 and 269 gene families with C. heterostrophus, P. tritici-repentis and S. nodorum, respectively. Moreover, 6,432 gene families are orthologous in all the four fungi.

Mentions: RepeatScout11 was used to identify 155 repetitive families of repetitive sequences in the A. rabiei genome. These 155 families represent approximately 9.94% of the total genome (Figs 1b and 2a). Classification of the transposable elements (TEs) was performed using TEclass12. Of 155 repetitive families, 38 families were of DNA transposons, 72 families of LTRs, 1 family of LINEs and 6 families of SINEs. Thirty-eight families did not show homology to any of the existing class of TEs and hence, categorized as unclassified (Supplementary Table 5). All the repeat sequence families were further annotated manually by TBLASTX search against the fungal RepBase library13. Overall, 155 families of TEs accounted for 4,477 elements covering 3,445,339 bp (Supplementary Tables 5 and 6). DNA transposons (Class I TEs) and retrotransposons (Class II TEs) were abundant in A. rabiei and covered 335,061 bp and 2,610,681 bp, respectively (Supplementary Fig. 6, Supplementary Table 6). The majority of these are LTR retrotransposons/Gypsy followed by Copia LTR retrotransposons.


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)

Circular map displaying genomic features of the A. rabiei genome and a comparison of orthologous genes.(a) Schematic representation of genomic characteristics of A. rabiei pseudo-genome (Mb scale). Circle a: pseudo-genome of 34.6 Mb. Circle b: positions of the protein coding genes. Circle c: positions of exons of the respective protein coding genes in circle b. Circle d: positions of introns of the respective protein coding genes in circle b. Circle e: distribution of the putative secretory proteins. Circle f: distribution of repetitive sequences in the A. rabiei genome. Circle g: histogram shows the tRNA density as represented by the number of tRNAs in 100-kb non-overlapping windows. The peak of the histogram correlates with the tRNA density. The diagram was plotted using Circos. (b) Venn diagram showing unique and shared orthologous gene families between and among the four closely related Dothideomycetes fungi. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis and S. nodorum were identified using OrthoMCL. Comparison of the four species revealed 693 gene families unique to A. rabiei. However, A. rabiei shares 151, 110 and 269 gene families with C. heterostrophus, P. tritici-repentis and S. nodorum, respectively. Moreover, 6,432 gene families are orthologous in all the four fungi.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Circular map displaying genomic features of the A. rabiei genome and a comparison of orthologous genes.(a) Schematic representation of genomic characteristics of A. rabiei pseudo-genome (Mb scale). Circle a: pseudo-genome of 34.6 Mb. Circle b: positions of the protein coding genes. Circle c: positions of exons of the respective protein coding genes in circle b. Circle d: positions of introns of the respective protein coding genes in circle b. Circle e: distribution of the putative secretory proteins. Circle f: distribution of repetitive sequences in the A. rabiei genome. Circle g: histogram shows the tRNA density as represented by the number of tRNAs in 100-kb non-overlapping windows. The peak of the histogram correlates with the tRNA density. The diagram was plotted using Circos. (b) Venn diagram showing unique and shared orthologous gene families between and among the four closely related Dothideomycetes fungi. The orthologous gene families among A. rabiei, C. heterostrophus, P. tritici-repentis and S. nodorum were identified using OrthoMCL. Comparison of the four species revealed 693 gene families unique to A. rabiei. However, A. rabiei shares 151, 110 and 269 gene families with C. heterostrophus, P. tritici-repentis and S. nodorum, respectively. Moreover, 6,432 gene families are orthologous in all the four fungi.
Mentions: RepeatScout11 was used to identify 155 repetitive families of repetitive sequences in the A. rabiei genome. These 155 families represent approximately 9.94% of the total genome (Figs 1b and 2a). Classification of the transposable elements (TEs) was performed using TEclass12. Of 155 repetitive families, 38 families were of DNA transposons, 72 families of LTRs, 1 family of LINEs and 6 families of SINEs. Thirty-eight families did not show homology to any of the existing class of TEs and hence, categorized as unclassified (Supplementary Table 5). All the repeat sequence families were further annotated manually by TBLASTX search against the fungal RepBase library13. Overall, 155 families of TEs accounted for 4,477 elements covering 3,445,339 bp (Supplementary Tables 5 and 6). DNA transposons (Class I TEs) and retrotransposons (Class II TEs) were abundant in A. rabiei and covered 335,061 bp and 2,610,681 bp, respectively (Supplementary Fig. 6, Supplementary Table 6). The majority of these are LTR retrotransposons/Gypsy followed by Copia LTR retrotransposons.

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