Introduction to the Fusarium Comparative Genomics Platform (FCGP)
Rapidly accumulating genome sequence data from diverse Fusarium species with different traits offers tremendous opportunities for understanding the molecular and evolutionary mechanisms underpinning functional diversification at a genome level (Coleman et al., 2009; Cuomo et al., 2007; Ma et al., 2010). The FCGP was developed to facilitate the realization of such opportunities. Currently, the genomes of four Fusarium species, including F. graminearum (two strains), F. oxysporum, F. verticillioides, and F. solani, have been published (Coleman et al., 2009; Cuomo et al., 2007; Ma et al., 2010) with more species and isolates currently being sequenced or annotated. The first three species were sequenced by the Broad Institute, while the Department of Energy Joint Genome Institute sequenced F. solani.
The SNU Genome Browser (SNUGB) (Jung et al., 2008) supports visualization and utilization of genome sequences and features both within and across species. All sequence data and contig information are displayed through the Contig Browser. Annotation information in a chosen region, such as transcripts, ORFs, tRNAs/rRNAs, exon/intron structure, SignalP, PSort and InterPro domains, can be displayed in multiple formats. In addition, the Chromosome Viewer shows the chromosomal locations of the phylogenetic markers stored in Fusarium-ID. The FCGP also presents computed characteristics of multiple gene families and functional groups using the Fungal Transcription Factor Database (FTFD) (Park et al., 2008b), the Fungal Cytochrome P450 Database (FCPD) (Park et al., 2008a), and the Fungal Secretome Database (FSD) (Choi et al., 2010). Currently available data include 3,095 transcription factors (TFs), 579 cytochrome P450s, and 11,905 putative secretory proteins, and provide an overview of these proteins within and across species. A BLAST server for each dataset is available for quick search. Moreover, genes that appear unique to each species, as well as those that are present in subsets of the four species, were identified through BLASTMatrix2, a modified BLAST program that searches gene(s) homologous to a query in multiple species simultaneously.
In addition to depositing newly released Fusarium genome sequences, characteristics of additional protein groups, such as ABC transporters and carbohydrate degrading enzymes, will be added once the corresponding fungal kingdom-wide databases are established. Available expressed sequence tags from Fusarium species will also be archived and linked to the corresponding genomes. In combination with the phylogenetic framework and accessioned cultures available through Fusarium-ID, the FCGP will help users study the evolution of Fusarium genes, gene networks, and whole genomes.
*Correspondence concerning FCGP should be sent to: Seogchan Kang (814-863-3846)
References cited
- Choi, J., Park, J., Kim, D., Jung, K., Kang, S., and Lee, Y.-H. (2010). Fungal Secretome Database: Integrated platform for annotation of fungal secretomes. BMC Genomics 11, 105.
- Coleman, J.J., Rounsley, S.D., Rodriguez-Carres, M., Kuo, A., Wasmann, C.C., Grimwood, J., Schmutz, J., Taga, M., White, G.J., Zhou, S., et al. (2009). The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. PLoS Genet 5, e1000618.
- Cuomo, C.A., Guldener, U., Xu, J.-R., Trail, F., Turgeon, B.G., Di Pietro, A., Walton, J.D., Ma, L.-J., Baker, S.E., Rep, M., et al. (2007). The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization. Science 317, 1400-1402.
- Jung, K., Park, J., Choi, J., Park, B., Ahn, K., Choi, J., Kim, S., Choi, D., Kang, S., and Lee, Y.-H. (2008). SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. BMC Bioinformatics 9, 586.
- 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.
- Park, J., Choi, J., Ahn, K., Park, B., Park, J., Kang, S., and Lee, Y.-H. (2008a). Fungal cytochrome P450 database. BMC Bioinformatics 9, 402.
- Park, J., Park, J., Jang, S., Kim, S., Kong, S., Choi, J., Ahn, K., Kim, J., Lee, S., Kim, S., et al. (2008b). FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics 24, 1024-1025.