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Screening the pathogenome – insight on pathogen mechanism from expressed transcripts and genome of Colletotrichum falcatum.

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Title Screening the pathogenome – insight on pathogen mechanism from expressed transcripts and genome of Colletotrichum falcatum.
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Creator C. Naveen Prasanth, R.Viswanathan, P. Malathi and A. Ramesh Sundar
 
Subject C. falcatum, Gene ontology (GO), carbohydrates, KEGG pathway
 
Description Not Available
The present study reports de novo assembling, annotation and characterization of the genome and transcriptome of C. falcatum. High quality reads were filtered assembled using the de novo assembler – primary assembling has been done by Velvet assembler and contig extension/ scaffolding has been done by SSPACE which revealed into total contig length 48,213,341 with a genome size of ~48.2Mb with 9891 annotated genes and 2379 unannotated genes. In transcriptome assembling, CLC work bench v 6.0 revealed that the total contig length is 24,732 with a transcriptome size of ~31 Mb. The reads were assembled into 13,730 transcripts representing 23,136 unique genes. Gene ontology (GO) analysis suggested prevalence of genes associated with biological process categories like metabolism, transport, pigmentation and response to stimulus. Genes associated with molecular function like antioxidant, binding, catalytic activities, electron carrier and enzyme regulator were found in majority. Genes associated with cellular components like cell envelope, extracellular region, macromolecular complex and membrane enclosed organelle were found in abundant. KEGG pathway analyses suggested prevalence of genes encoding carbohydrates, lipids, nucleotides, amino acids, glycans, co-factors, vitamins, terpenoids, polyketides kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants, candidate effectors, transition specific metabolites, proteases and housekeeping genes. A large number of transcripts encoding biotrophy-necrotrophy transition specific and membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by C. falcatum is significantly more as compared to that encoded by several other Colletotrichums infecting different crops. Phylotranscriptomic analysis indicated that C. falcatum is closely related to C. graminicola causing anthracnose in maize and wheat. Global view of syntenic alignments between the genome and transcriptome of C. falcatum leads to linkage group of C. graminicola of about 93% similarity in base pairing and gene clustering, the maximum hit obtained and sharing genes is around 90% with C. graminicola; notably, there is a near absence of homologous sequences among the genomes (Fig 2). Further validation and identification of novel genes is under progress with the help of pathogenomics which will lead us to come up with candidate identification i.e. virulence factors or virulent genes. This is the first attempt to sequence this devastating pathogen in NGS platform and the findings from this study provide a better understanding of the biology of the red rot pathogen and have identified candidate genes/functions required for its pathogenesis.
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Date 2021-08-28T10:08:28Z
2021-08-28T10:08:28Z
2014-06-23
 
Type Proceedings
 
Identifier Not Available
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http://krishi.icar.gov.in/jspui/handle/123456789/60934
 
Language English
 
Relation Not Available;
 
Publisher Society for Sugarcane Research and Development, Coimbatore, India