Toward de novo genome assembly of phyrenochaeta lycopersici, a tomato fungal pathogen
Aragona, M.; Ferrarini, A.; Valente, M.T.; Orrù, L.; Minio, A.; Valè, G.; Cattivelli, L.; Delledonne, M.; Infantino, A..
Abstract XVIII Convegno Nazionale Società Italiana di Patoplogia Vegetale, Sassari, 24-26 settembre 2012, presentazione orale
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Pyrenochaeta lycopersici (Gerlach and Schneider 1964) is a soil-living ascomycete, the causal agent of an important disease of tomato and other Solanaceous crops worldwide, named Corky Root Rot (CRR); up to 40–70% yield loss has been reported for certain years. The fungus attacks the root system of plant: infected roots develop necrotic lesions that spread along the entire root system. A first draft of genome assembly of P. lycopersici was obtained from short sequence reads using a paired-end Illumina platform. The total assembly, obtained with Velvet, was 56 Mb with a N50 of 70 kb. An in silico prediction using GeneMarkES led us to identify about 15,000 genes with an average length of 1,500-1,700 bases. In addition to the fungal genome sequencing, RNAs obtained from tomato roots after 8 days post infection (dpi) with a P. lycopersici isolate and RNAs from mycelium grown in absence of contact with the host plant, have been sequenced. Analysis of RNA-seq data with Cufflinks identified more than 15,000 putative transcripts, 80% of which overlap with the in silico predictions. Putative transcripts have been functionally annotated using the fungal protein database of UniProt. These results, although preliminary, show that de novo assembly of a large size genome as that of a filamentous fungus may be successfully obtained by paired-end sequencing and the resulting data can be used for investigating both the fungal lifestyle during pathogenesis and for comparative studies with other important fungal pathogens.