The genome and genes of Epichloe festucae

Abstract

The ascomycete Epichloë festucae is a model endophyte that 1) switches between mutualistic and antagonistic states, 2) is seed transmissible, 3) has a sexual state amenable to genetic analysis, and 4) is rich in bioprotective alkaloids. This fungus grows systemically and intercellularly throughout the life of its host plant. On each reproductive tiller the fungus either infects benignly and transmits clonally in seeds, or produces its sexual state (stroma) and chokes inflorescence development. The E. festucae genome was estimated at 29 Mb in six chromosomes. The genome sequence was assembled from cloned insert end reads (4.2 x coverage) and preassembled pyrosequencing reads (454-sequencing: 20 x raw, 1.7 x assembled), giving 3967 supercontigs, of which 1004 were larger than 2 kb and covered 92% of the genome. Gene prediction with FGENESH identified ~10,000 putative genes. We also sequenced 25,000 ESTs from each of two normalised libraries — one of choked inflorescences, the other of benignly infected inflorescences — yielding 5077 E. festucae unigenes, annotated by BLAST and InterPro. Sequence data and annotations are stored in a database for visualisation and inspection with the GBrowse browser. The genomic sequences can be queried by BLAST at http://www.genome.ou.edu/blast/ ef_blastall.html. Keywords: bioinformatics, DNA sequence, Epichloë festucae, expressed sequence tags, Festucae pratensis, fungal genomics, Lolium pratense