@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={AbstractArbuscular 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={AbstractCircular 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{charles_edwards_ravishankar_calero_henry_rech_saravitz_you_ade_o'connor_et al._2023, title={Emergent molecular traits of lettuce and tomato grown under wavelength-selective solar cells}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1087707}, abstractNote={The integration of semi-transparent organic solar cells (ST-OSCs) in greenhouses offers new agrivoltaic opportunities to meet the growing demands for sustainable food production. The tailored absorption/transmission spectra of ST-OSCs impacts the power generated as well as crop growth, development and responses to the biotic and abiotic environments. To characterize crop responses to ST-OSCs, we grew lettuce and tomato, traditional greenhouse crops, under three ST-OSC filters that create different light spectra. Lettuce yield and early tomato development are not negatively affected by the modified light environment. Our genomic analysis reveals that lettuce production exhibits beneficial traits involving nutrient content and nitrogen utilization while select ST-OSCs impact regulation of flowering initiation in tomato. These results suggest that ST-OSCs integrated into greenhouses are not only a promising technology for energy-neutral, sustainable and climate-change protected crop production, but can deliver benefits beyond energy considerations.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Charles, Melodi and Edwards, Brianne and Ravishankar, Eshwar and Calero, John and Henry, Reece and Rech, Jeromy and Saravitz, Carole and You, Wei and Ade, Harald and O'Connor, Brendan and et al.}, year={2023}, month={Feb} }
 @article{ravishankar_charles_xiong_henry_swift_rech_calero_cho_booth_kim_et al._2021, title={Balancing crop production and energy harvesting in organic solar-powered greenhouses}, volume={2}, ISSN={["2666-3864"]}, DOI={10.1016/j.xcrp.2021.100381}, abstractNote={Adding semitransparent organic solar cells (ST-OSCs) to a greenhouse structure enables simultaneous plant cultivation and electricity generation, thereby reducing the greenhouse energy demand. However, there is a need to establish the impact of such systems on plant growth and indoor climate and to optimize system tradeoffs. In this work, we consider plant growth under OSCs and system-relevant design. We evaluate the growth of red leaf lettuce under ST-OSC filters and compare the impact of three different OSC active layers that have unique transmittance. We find no significant differences in the fresh weight and chlorophyll content of the lettuce grown under these OSC filters. In addition, OSCs provide an opportunity for further light and thermal management of the greenhouse through device design and optical coatings. The OSCs can thus affect plant growth, power generation, and thermal load of the greenhouse, and this design trade space is reviewed and exemplified.}, number={3}, journal={CELL REPORTS PHYSICAL SCIENCE}, publisher={Elsevier BV}, author={Ravishankar, Eshwar and Charles, Melodi and Xiong, Yuan and Henry, Reece and Swift, Jennifer and Rech, Jeromy and Calero, John and Cho, Sam and Booth, Ronald E. and Kim, Taesoo and et al.}, year={2021}, month={Mar} }
 @article{saville_charles_chavan_muñoz_gómez-alpizar_ristaino_2017, title={Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations}, volume={107}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/PHYTO-02-17-0045-R}, DOI={10.1094/phyto-02-17-0045-r}, abstractNote={ Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas. }, number={12}, journal={Phytopathology}, publisher={Scientific Societies}, author={Saville, Amanda and Charles, Melodi and Chavan, Suchitra and Muñoz, Miguel and Gómez-Alpizar, Luis and Ristaino, Jean Beagle}, year={2017}, month={Dec}, pages={1541–1548} }