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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

The k-mer distribution, repetitive sequences and repeat-induced point mutations in repetitive sequences of A. rabiei.(a) K-mer depth distribution plot of whole-genome Illumina reads. Paired-end reads of 64-mer were mapped to the genome using ABySS. A peak was identified at 178. (b) The percentage distribution of different types of repetitive elements in the A. rabiei genome. (c) The frequencies of all four types of di-nucleotide RIP mutations in different families of repeat elements are shown.
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f1: The k-mer distribution, repetitive sequences and repeat-induced point mutations in repetitive sequences of A. rabiei.(a) K-mer depth distribution plot of whole-genome Illumina reads. Paired-end reads of 64-mer were mapped to the genome using ABySS. A peak was identified at 178. (b) The percentage distribution of different types of repetitive elements in the A. rabiei genome. (c) The frequencies of all four types of di-nucleotide RIP mutations in different families of repeat elements are shown.

Mentions: We used the genome of an Indian isolate of A. rabiei (ITCC No. 4638) for sequencing. This isolate was identified as mating type 2 (MAT1–2) using MAT locus-specific primers (Supplementary Fig. 1). Four paired-end libraries with average insert sizes ranging from 200 bp to 500 bp and a mate-pair library of 5 kb average insert size were sequenced using Illumina HiSeq1000 platform to generate 100 bp X 2 short sequence reads. Filtered high quality paired-end reads amounting to approximately 100 Gb sequencing data (Supplementary Tables 1,2) were assembled using ABySS5, resulting in a total assembly size of 34.6 Mb that is in accordance to estimated genome size of 23–34 Mb of 112 distinct A. rabiei isolates67. High coverage of 178X was achieved as estimated by k-mer analysis of read count versus k-mer coverage (Fig. 1a) and consisted of 338 scaffolds (Table 1), with N50 scaffold size of approximately 154.8 kb (Supplementary Table 2).


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)

The k-mer distribution, repetitive sequences and repeat-induced point mutations in repetitive sequences of A. rabiei.(a) K-mer depth distribution plot of whole-genome Illumina reads. Paired-end reads of 64-mer were mapped to the genome using ABySS. A peak was identified at 178. (b) The percentage distribution of different types of repetitive elements in the A. rabiei genome. (c) The frequencies of all four types of di-nucleotide RIP mutations in different families of repeat elements are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: The k-mer distribution, repetitive sequences and repeat-induced point mutations in repetitive sequences of A. rabiei.(a) K-mer depth distribution plot of whole-genome Illumina reads. Paired-end reads of 64-mer were mapped to the genome using ABySS. A peak was identified at 178. (b) The percentage distribution of different types of repetitive elements in the A. rabiei genome. (c) The frequencies of all four types of di-nucleotide RIP mutations in different families of repeat elements are shown.
Mentions: We used the genome of an Indian isolate of A. rabiei (ITCC No. 4638) for sequencing. This isolate was identified as mating type 2 (MAT1–2) using MAT locus-specific primers (Supplementary Fig. 1). Four paired-end libraries with average insert sizes ranging from 200 bp to 500 bp and a mate-pair library of 5 kb average insert size were sequenced using Illumina HiSeq1000 platform to generate 100 bp X 2 short sequence reads. Filtered high quality paired-end reads amounting to approximately 100 Gb sequencing data (Supplementary Tables 1,2) were assembled using ABySS5, resulting in a total assembly size of 34.6 Mb that is in accordance to estimated genome size of 23–34 Mb of 112 distinct A. rabiei isolates67. High coverage of 178X was achieved as estimated by k-mer analysis of read count versus k-mer coverage (Fig. 1a) and consisted of 338 scaffolds (Table 1), with N50 scaffold size of approximately 154.8 kb (Supplementary Table 2).

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