Title: Cyber-infrastructure for Fusarium (CiF): Three integrated platforms supporting strain identification, phylogenetics, comparative genomics, and knowledge sharing Authors
|Park, Bongsoo -|
|Park, Jongsun -|
|Cheong, Kyeong-Chae -|
|Choi, Jaeyoung -|
|Jung, Kyongyong -|
|Lee, Yong-Hwan -|
|Geiser, David -|
|Kang, Seogchan -|
Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 31, 2010
Publication Date: December 20, 2010
Citation: Park, B., Park, J., Cheong, K., Choi, J., Jung, K., Lee, Y., Ward, T.J., O Donnell, K., Geiser, D.M., Kang, S. 2010. Cyber-infrastructure for Fusarium (CiF): Three integrated platforms supporting strain identification, phylogenetics, comparative genomics, and knowledge sharing. Nucleic Acids Research. DOI: 10.1093/nar/gkq1166. Interpretive Summary: A web-based tool was developed to make genetic information on Fusarium available to the scientific community. Fusarium is the most important group of toxin-producing plant pathogens, but the majority of Fusarium species cannot be identified using morphological data alone. Fortunately, extensive molecular phylogenetic studies using DNA sequence data have been conducted and the whole genome sequence of four fusaria has been published. To make this genetic data accessible via the internet, we constructed the Cyber-infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) to support the archiving and utilization of rapidly increasing data and knowledge. The FCP platform functions as an online forum for preserving and sharing knowledge to support education and research. The web-based tools developed in this study will greatly benefit agricultural and medical scientists, mycotoxicologists, and quarantine officials worldwide by making it possible to identify genetically diverse pathogenic and toxigenic fusaria molecularly for the first time.
Technical Abstract: The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber-infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP), and Fusarium Community Platform (FCP). 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 five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from the Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. 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.