@article{coomber_saville_carbone_ristaino_2023, title={An open-access T-BAS phylogeny for emerging Phytophthora species}, volume={18}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0283540}, DOI={10.1371/journal.pone.0283540}, abstractNote={Phytophthora species cause severe diseases on food, forest, and ornamental crops. Since the genus was described in 1875, it has expanded to comprise over 190 formally described species. There is a need for an open access bioinformatic tool that centralizes diverse streams of sequence data and metadata to facilitate research and identification of Phytophthora species. We used the Tree-Based Alignment Selector Toolkit (T-BAS) to develop a phylogeny of 192 formally described species and 33 informal taxa in the genus Phytophthora using sequences of eight nuclear genes. The phylogenetic tree was inferred using the RAxML maximum likelihood method. A search engine was also developed to identify genotypes of P. infestans based on genetic distance to known lineages. The T-BAS tool provides a visualization framework allowing users to place unknown isolates on a curated phylogeny of all Phytophthora species. Critically, this resource can be updated in real-time to keep pace with new species descriptions. The tool contains metadata such as clade, host species, substrate, sexual characteristics, distribution, and reference literature, which can be visualized on the tree and downloaded for other uses. This phylogenetic resource will allow data sharing among research groups and the database will enable the global Phytophthora community to upload sequences and determine the phylogenetic placement of an isolate within the larger phylogeny and to download sequence data and metadata. The database will be curated by a community of Phytophthora researchers and housed on the T-BAS web portal in the Center for Integrated Fungal Research at NC State. The T-BAS web tool can be leveraged to create similar metadata enhanced phylogenies for diverse populations of pathogens.}, number={4}, journal={PLOS ONE}, author={Coomber, Allison and Saville, Amanda and Carbone, Ignazio and Ristaino, Jean Beagle}, editor={Blair, Jaime E.Editor}, year={2023}, month={Apr} }
 @article{george_hornstein_clower_coomber_dillard_mugwanya_pezzini_rozowski_2022, title={Lessons for a SECURE Future: Evaluating Diversity in Crop Biotechnology Across Regulatory Regimes}, volume={10}, ISSN={["2296-4185"]}, url={http://dx.doi.org/10.3389/fbioe.2022.886765}, DOI={10.3389/fbioe.2022.886765}, abstractNote={Regulation of next-generation crops in the United States under the newly implemented “SECURE” rule promises to diversify innovation in agricultural biotechnology. Specifically, SECURE promises to expand the number of products eligible for regulatory exemption, which proponents theorize will increase the variety of traits, genes, organisms, and developers involved in developing crop biotechnology. However, few data-driven studies have looked back at the history of crop biotechnology to understand how specific regulatory pathways have affected diversity in crop biotechnology and how those patterns might change over time. In this article, we draw upon 30 years of regulatory submission data to 1) understand historical diversification trends across the landscape and history of past crop biotechnology regulatory pathways and 2) forecast how the new SECURE regulations might affect future diversification trends. Our goal is to apply an empirical approach to exploring the relationship between regulation and diversity in crop biotechnology and provide a basis for future data-driven analysis of regulatory outcomes. Based on our analysis, we suggest that diversity in crop biotechnology does not follow a single trajectory dictated by the shifts in regulation, and outcomes of SECURE might be more varied and restrictive despite the revamped exemption categories. In addition, the concept of confidential business information and its relationship to past and future biotechnology regulation is reviewed in light of our analysis.}, journal={FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY}, publisher={Frontiers Media SA}, author={George, Dalton R. and Hornstein, Eli D. and Clower, Carrie A. and Coomber, Allison L. and Dillard, DeShae and Mugwanya, Nassib and Pezzini, Daniela T. and Rozowski, Casey}, year={2022}, month={May} }