We discuss a pipeline and the database that assist in the gene annotation for the ascomycete Epichloe festucae (anamorph Neotyphodium).

The Epichloe festucae is a model endophyte that switches between mutualistic and antagonistic states, is seed transmissible, has a sexual state amenable to genetic analysis, and is rich in bioprotective alkaloids. This fungus grows systemically and intercellularly throughout the life of its host plant and represents an interesting model for studying mutualistic and parasitic plant-fungal symbiosis. The Epichloe festucae genome sequence was assembled into 3967 supercontigs from cloned insert end reads and preassembled pyrosequencing reads giving 92% coverage of the genome.

A semi-automated pipeline, including Exonerate, Blast, Interpro, and FGenesh, has been designed and implement to assist with the time consuming computations, annotation process and data management. Gene prediction with FGenesh identified approximatelly 10,000 putative genes. Sequence data and annotations are stored in a database for visualization and inspection with the GBrowse browser.