Cyber-infrastructure for knowledge preservation and sharing: Rapid increases in various types of data present complex challenges to data preservation and sharing. “Due to the need for studying and controlling diverse diseases threatening agricultural and environmental systems with limited resources, the importance of working closely together and pooling resources and knowledge is much greater in plant pathology than most other disciplines” (Kang, Mol. Plant Pathology 15:315). However, efforts to preserve accumulated knowledge and data in a format that can effectively coordinate and support future research and problem solving were limited. Kang and groups of collaborators built and have curated numerous online platforms to address this critical community need. These platforms can be classified into two groups based on the type and utility of archived data.
The first group supports pathogen identification, monitoring and molecular diagnosis, as well as new species discovery, and includes Phytophthora Database (http://www.phytophthoradb.org), Cyberinfrastructure for Fusarium (http://www.fusariumdb.org) and VertShield (http://www.verticilliumdb.org/). Phytophthora Database archives phylogenetically informative sequence data and phenotypic characters of 123 formally described Phytophthora species and 23 provisional species as references. It offers multiple tools, including GIS tools for visualizing geographic origins of characterized strains. Cyberinfrastructure for Fusarium consists of comparative genomics platform, Fusarium-ID, and communication tools, which were designed to support comparative analysis of Fusarium genomes, multigene-based Fusarium identification, and community-networking, respectively. Both platforms log ~1,300 unique visits each per month from many countries. VertShield provides a morphological identification key, PCR-based diagnostic tools, protocols and phylogenetically informative sequences to help identify Verticillium species. Besides supporting pathogen detection and identification and new species discovery, these platforms also contributed to protecting key culture collections. Culture collections are irreplaceable resources that connect “discoveries of the present with established knowledge of the past” (Kang et al., Phytopathology 96:920-925). Unfortunately, their survival is threatened on multiple fronts. Most data archived in the three platforms mentioned above were derived from vouchered cultures, thus enhancing the value and use of analyzed culture collections by increasing their visibility to user communities.
The second group of online platforms supports comparative genomics of fungi. Rapidly accumulating genome sequences of diverse fungi presented novel opportunities in exploring the functional and evolutionary mechanisms underpinning critical processes through comparative functional and evolutionary genomic analyses at multiple taxon levels. However, because most researchers are not trained to manage a huge amount of data, user-friendly informatics platforms for comprehensive data mining are essential. Kang supported his long-term collaborator Yong-Hwan Lee at Seoul National University in constructing a series of fungal comparative genomics platforms. The first platform, entitled Comparative Fungal Genomics Platform (http://cfgp.snu.ac.kr/), was developed to archive fungal genome sequences scattered across multiple databases into a single database. This platform currently archives 549 genomes from 392 species, including some from other kingdoms as references, and offer diverse data analysis and visualization tools. Data archived in Comparative Fungal Genomics Platform enabled the development of multiple platforms specialized for comparative and functional genomics of specific gene families or functional groups. Three platforms Kang has contributed to include Fungal Cytochrome P450 Database (http://p450.riceblast.snu.ac.kr/), Fungal Transcription Factor Database (http://ftfd.snu.ac.kr/), and Fungal Secretome Database (http://fsd.snu.ac.kr/). He is currently leading the development of Fungal Calcium Signaling Database (http://fcsd.ifungi.org/) and Fungal Terpene Biosynthesis Database.
Development of innovative research tools: Kang developed several tool kits to support molecular and cellular analyses of fungal interaction with plants and the environment. One of them is a collection of vectors/protocols for Agrobacterium tumefaciens-mediated transformation and gene manipulation of fungi. Resulting vectors have been distributed to several hundred labs around the world, enabling transformation and genetic manipulation of diverse groups of fungi. The first paper reporting this protocol has been cited >550 times. Novel imaging tools also enabled time lapse monitoring of fungal root pathogenesis without physically disrupting the rhizosphere, studies on gene function-surface property relationship during plant-fungal interactions, and visualization of spatial and temporal changes of cytoplasmic calcium ions (Ca2+) caused by external stimuli, which are known as the Ca2+ signature, in fungi. Fluorescent protein-based Ca2+ imaging enabled studies on how fungi translate external stimuli into Ca2+ signatures and how Ca2+ signatures control growth, infection and/or mycotoxin production.
Enhanced preparedness against invasive pathogens: Kang has worked with the Pennsylvania Department of Agriculture (PDA) for ~14 years to enhance state’s preparedness for and response to several groups of invasive exotic pathogens. This collaboration has resulted in new molecular diagnostic tools, discovery of exotic pathogen species, and better understanding of historical patterns of pathogen occurrence in Pennsylvania. In addition, since 2010, Kang and PDA have annually performed molecular diagnosis of Phytophthora ramorum in stream bait samples collected from 7-15 eastern states. This project, funded by the US Forest Service, has guided risk assessment of forest ecosystems from P. ramorum and has resulted in >2,000 Phytophthora cultures. These cultures are being characterized for species identity and genetic diversity, which will help understand spatial and temporal patterns of Phytophthora communities in streams and surrounding forest ecosystems.
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