Introduction to the Cyber-infrastructure for Fusarium (CiF)
The genus Fusarium poses a multifaceted threat to global crop production and animal/human health. Due to its practical importance, the genus has been extensively studied at levels ranging from genetic mechanisms underlying important traits, such as toxin production and pathogenicity, to global biodiversity and evolution (Balmas et al., 2010; Desjardins, 2006; Ma et al., 2010; O'Donnell et al., 2004; O'Donnell et al., 2010; Summerell et al., 2001). The goal of CiF is to support research and education on the fungal genus Fusarium by archiving data, materials, and knowledge from diverse areas of Fusarium research, including genomics, phylogenetics, population genetics, and epidemiology in a format that can be easily accessed and updated. The CiF consists of three platforms (Fig. 1). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives genomes from Fusarium species and supports genome browsing and analysis. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education. More information can be founded on the home page of each platform. Via systematically archiving datasets from multiple areas of research on Fusarium, the CiF aims to efficiently leverage new knowledge and support problem solving.
Figure 1. System structure of the Cyber-infrastructure of Fusarium (CiF) The three main components of CiF, Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP), and Fusarium Community Platform (FCP), are illustrated. Several databases specialized for fungal genome sequences or gene families and functional groups, including Fungal Transcription Factor Database (FTFD), Fungal Cytochrome P450 Database (FCPD), Fungal Secretome Database (FSD), and Comparative Fungal Genomics Platform (CFGP), feed data to FCGP. Data analysis and visualization tools from CFGP, the Seoul National University Genome Browser (SNUGB), and the Phytophthora Database (PD) support data visualization and analysis in Fusarium-ID and FCGP.
References Cited
- Balmas, V., Migheli, Q., Scherm, B., Garau, P., O'Donnell, K., Ceccherelli, G., Kang, S., and Geiser, D.M. (2010). Multilocus phylogenetics show high levels of endemic fusaria inhabiting Sardinian soils (Tyrrhenian Islands). Mycologia 102, 803-812.
- Desjardins, A.E. (2006). Fusarium Mycotoxins: Chemistry, Genetics & Biology (St. Paul, MN, APS Press).
- Ma, L.-J., van der Does, H.C., Borkovich, K.A., Coleman, J.J., Daboussi, M.-J., Di Pietro, A., Dufresne, M., Freitag, M., Grabherr, M., Henrissat, B., et al. (2010). Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367-373.
- O'Donnell, K., Ward, T.J., Geiser, D.M., Kistler, H.C., and Aoki, T. (2004). Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade. Fungal Genet. Biol. 41, 600-623.
- O'Donnell, K., Sutton, D.A., Rinaldi, M.G., Sarver, B.A.J., Balajee, S.A., Schroers, H.-J., Summerbell, R.C., Robert, V.A.R.G., Crous, P.W., Zhang, N., et al. (2010). An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections. J Clin Microbiol 48, 3708-3718.
- Summerell, B.A., Leslie, J.F., Backhouse, D., Bryden, W.L., and Burgess, L.W., eds. (2001). Fusarium: Paul E. Nelson Memorial Symposium (St. Paul, MN, APS Press).