Project description:We report here an update of the Botrytis cinerea strains B05.10 and T4 genomes, as well as an automated preliminary gene structure annotation. High-coverage de novo assemblies and reference-based alignments led to a correction of wrong base calls, elimination of sequence gaps, and improved joining of contigs. The new assemblies have substantially lower numbers of scaffolds and a concomitant increase in the N(50).The list of protein-coding genes was generated using the evidence-driven gene predictor Augustus, with expressed sequence tag evidence and RNA-Seq data as input.
Project description:Comparison of Botrytis cinerea wild-type B.05.10 and T4 strains using label-free nUPLC-MSE and 2-DE approaches. B. cinerea strain mycelium were grown in synthetic minimal medium-modified Czapeck-Dox. Protein extracts were obtained from pulverized mycelium using TCA-phenol method. Acquired spectra were internally calibrated with peptides from trypsin 180 autolysis (M+H+=842.509,M+H+=2211.104) with an m/z precision of ±20 ppm. A combined search (PMF and MS/MS) was performed with GPS ExplorerTM software v3.5 (Applied Biosystems) over non-redundant NCBI databases using the MASCOT search engine. The database search utilized the following parameters: taxonomy restrictions to Fungi (06.17.2011), one missed cleavage sites, 100 ppm mass tolerance in MS and 0.5 Da for MS/MS data, cysteine carbamidomethylation as a fixed modification, and methionine oxidation as a variable modification. The confidence in the peptide mass fingerprinting matches (p<0.05) was based on the MOWSE score.
