Genome Annotation and Comparative Genomics in Fungi

Fungi are important, though often unseen, components of ecosystems, producers of industrial enzymes and chemicals, and important model systems for cellular biology. They are also potent pathogens of plants and animals in agriculture. With relative small genomes (10~100 Mb) genome sequence and assembly can be accomplished with straightforward sequencing library strategies and modest computational hardware. The addition of long sequence reads into the assembly process can improves assemblies especially in cases of varying ploidy and divergent genomes in the case of multi-nucleate fungi. Genome annotation of fungal genomes can be achieved through automated tools including MAKER and EVM incorporating ab intio and evidence based transcript and comparative protein information. Gene prediction training and evidence incorporation can improve the quality of annotations though some manual curation is always needed to finalize gene sets. Projects to sequence at least a thousand Fungi are underway and the use of comparative genomics approaches can assist in validation and potentially correct gene structure annotations. The genome datasets for Fungi will provide rich environment for enzyme and gene family data mining, benchmarking datasets for tools developers, and application of tools for functional prediction, phylogenomics, and other comparative analyses. This presentation will focus on approaches to fungal genome annotation and application of comparative genomics to further validate and improve these results.