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Genetic diversity of 100+ Aspergillus species - the aspMine analysis resource. T. C. Vesth1, J. L. Nybo (1), S. THEOBALD (1), R. P. DE VRIES (4), I. V. GRIGORIEV (3), S. E. BAKER2, M. R. ANDERSEN (1)
1) Department of Bioingineering, Technical University of Denmark, Lyngby, Denmark; 2) Joint Bioenergy Institute, Berkeley, CA, USA, Berkeley, CA, USA; 3) Joint Genome Institute, Walnut Creek, CA, USA, Walnut Creek, CA, USA; 4) Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, the Netherlands, Utrecht, The Netherlands.
The filamentous fungal species of the Aspergillus genus are of broad interest to the scientific community including applied, medical and basic research. These fungi are prolific producers of native and heterologous proteins, organic acids, and secondary metabolites (including bioactives and toxins such as ochratoxin A). Because of these abilities, they represent a substantial economic interests in pharmaceutical, biotechnology, and bioenergy applications. In a project collaboration with the US Joint Genome Institute and JBEI we are de novo sequencing 300 different species of Aspergillus and establishing an online analysis platform for the scientific community, aspMine. The goal of this project is to develop a targeted tool to expand and improve our knowledge and expertise about this versatile group of fungi. At time of writing, 200 genomes are in various stages of sequencing and a bioinformatic pipeline has been established to analyze and store the data. This project covers a wide range of biologically interesting ideas surrounding the concept of speciation, such as genetic diversity, primary and secondary metabolism and proteome diversity. Complementary to the tools offered by FungiDB and JGI, the aspMine analysis resource offers tools for tracking genes and functions across species, allowing for investigation of shared genes and clusters across the genus as well as species- and clade-specific genes. The online platform also offers comparative analysis of secondary metabolism gene clusters with focus on synteny and functional conservation across species. The aspMine is implemented as a number of web applications created in R shiny, a graphical interface for analysis. The different tools are collected on a webpage which also includes method descriptions and relevant literature. The webpage is available from the beginning of 2016 and will be continually expanded. It is our goal to provide a comprehensive analysis platform for the community for comparative analysis of Aspergillus species.