@article{hornstein_charles_franklin_edwards_vintila_kleiner_sederoff_2024, title={<i>IPD3</i>, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host <i>Arabidopsis</i> when restored long after its evolutionary loss}, volume={114}, ISSN={["1573-5028"]}, url={https://doi.org/10.1007/s11103-024-01422-3}, DOI={10.1007/s11103-024-01422-3}, abstractNote={Abstract Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana . To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3 , a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis , and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4 . Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.}, number={2}, journal={PLANT MOLECULAR BIOLOGY}, author={Hornstein, Eli D. and Charles, Melodi and Franklin, Megan and Edwards, Brianne and Vintila, Simina and Kleiner, Manuel and Sederoff, Heike}, year={2024}, month={Apr} }
 @article{budnick_franklin_utley_edwards_charles_hornstein_sederoff_2024, title={Long- and short-read sequencing methods discover distinct circular RNA pools in <i>Lotus japonicus</i>}, volume={1}, ISSN={["1940-3372"]}, url={https://doi.org/10.1002/tpg2.20429}, DOI={10.1002/tpg2.20429}, abstractNote={Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5' site to an upstream 3' end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.}, journal={PLANT GENOME}, author={Budnick, Asa and Franklin, Megan J. and Utley, Delecia and Edwards, Brianne and Charles, Melodi and Hornstein, Eli D. and Sederoff, Heike}, year={2024}, month={Jan} }
 @article{hornstein_sederoff_2023, title={Back to the Future: Re-Engineering the Evolutionarily Lost Arbuscular Mycorrhiza Host Trait to Improve Climate Resilience for Agriculture}, volume={9}, ISSN={["1549-7836"]}, url={https://doi.org/10.1080/07352689.2023.2256093}, DOI={10.1080/07352689.2023.2256093}, abstractNote={The coming century in agriculture will be marked by increasing exposure of crops to abiotic stress and disease due to climate change. The plant traits with the strongest potential to mitigate these stresses are complex, and are increasingly recognized to involve interaction with the microbiome. Through symbiosis with soil fungi, plants form arbuscular mycorrhizae (AM) that can alleviate nutrient, water, and temperature stress, and can confer pathogen resistance and increased yield. The portfolio of advantages offered by AM overlaps with the benefits of agriculturally useful plant traits that have been the subject of decades of intensive biotechnological efforts, such as C4 photosynthesis and rhizobial nitrogen fixation. In this article we illustrate the prospective benefits of genetic engineering to produce AM in nonmycorrhizal plants and modify AM in already-mycorrhizal crops. We highlight recent advances which have clarified the key genetic and metabolic components of AM symbiosis, and show that many of these components are involved in other plant biological processes and have already been subject to extensive genetic engineering in nonsymbiotic contexts. We provide a theoretical research roadmap to accomplish engineering of AM into the nonmycorrhizal model Arabidopsis including specific molecular genetic approaches. We conclude that AM is potentially more tractable than other complex plant traits, and that a concerted research initiative for biotechnological manipulation of AM could fill unique needs for agricultural resilience. Finally, we note that engineering of AM provides a potential back door into manipulation of other essential plant traits, including carbon storage, and beneficial microbiome assembly.}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, author={Hornstein, Eli D. and Sederoff, Heike}, year={2023}, month={Sep} }
 @article{edwards_hornstein_wilson_sederoff_2022, title={High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes}, volume={23}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-022-08918-6}, abstractNote={Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes.This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.}, number={1}, journal={BMC GENOMICS}, author={Edwards, Brianne and Hornstein, Eli D. and Wilson, Nathan J. and Sederoff, Heike}, year={2022}, month={Oct} }
 @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} }