@article{aimone_giauque_hawkes_2023, title={Fungal Symbionts Generate Water-Saver and Water-Spender Plant Drought Strategies via Diverse Effects on Host Gene Expression}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-01-22-0006-FI}, abstractNote={ Foliar fungal endophytes are known to alter plant physiology but the mechanisms by which they do so remain poorly understood. We focused on how plant gene expression was altered by six fungal strains that generated “water-saver” and “water-spender” drought physiologies in a C4 grass, Panicum hallii. Water-saver physiologies have lower plant water loss, improved wilt resistance, and higher survival compared with water-spender strategies. We expected that fungi within each functional group would have similar effects on P. hallii, and this was largely true for plant physiology but not for plant gene expression. When we focused only on genes that were differentially expressed relative to fungus-free controls, we found surprisingly little overlap in plant differentially expressed genes or gene regulatory pathways across the fungal treatments, including within and between the water-saver and water-spender strategies. Nevertheless, using lasso regression, we identified a small subset of genes that predicted 39 and 53% of the variation in plant wilt resistance and water loss, respectively. These results suggest that fungal effects on plant transcription may identify how they extend the plant phenotype, and the comparison across multiple fungi allows us to differentiate broadly fungal-responsive plant genes versus those plant genes that respond only to single fungal taxa. The genes identified here could be targeted for future study to understand their function and, ultimately, represent candidates for precision breeding efforts to increase plant drought tolerance. }, journal={PHYTOBIOMES JOURNAL}, author={Aimone, Catherine D. and Giauque, Hannah and Hawkes, Christine V.}, year={2023}, month={Mar} }
 @article{aimone_hoyer_dye_deppong_duffy_carbone_hanley-bowdoin_2022, title={An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing}, volume={300}, ISSN={["1879-0984"]}, url={http://dx.doi.org/10.1016/j.jviromet.2021.114405}, DOI={10.1016/j.jviromet.2021.114405}, abstractNote={The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.}, journal={JOURNAL OF VIROLOGICAL METHODS}, publisher={Elsevier BV}, author={Aimone, Catherine D. and Hoyer, J. Steen and Dye, Anna E. and Deppong, David O. and Duffy, Siobain and Carbone, Ignazio and Hanley-Bowdoin, Linda}, year={2022}, month={Feb} }
 @article{aimone_de leon_dallas_ndunguru_ascencio-ibanez_hanley-bowdoin_2021, title={A New Type of Satellite Associated with Cassava Mosaic Begomoviruses}, volume={95}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00432-21}, abstractNote={Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase.}, number={21}, journal={JOURNAL OF VIROLOGY}, author={Aimone, Catherine D. and De Leon, Leandro and Dallas, Mary M. and Ndunguru, Joseph and Ascencio-Ibanez, Jose T. and Hanley-Bowdoin, Linda}, year={2021}, month={Nov} }
 @article{aimone_lavington_hoyer_deppong_mickelson-young_jacobson_kennedy_carbone_hanley-bowdoin_duffy_2021, title={Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation}, volume={102}, ISSN={0022-1317 1465-2099}, url={http://dx.doi.org/10.1099/jgv.0.001622}, DOI={10.1099/jgv.0.001622}, abstractNote={Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5′ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.}, number={7}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Aimone, Catherine D. and Lavington, Erik and Hoyer, J. Steen and Deppong, David O. and Mickelson-Young, Leigh and Jacobson, Alana and Kennedy, George G. and Carbone, Ignazio and Hanley-Bowdoin, Linda and Duffy, Siobain}, year={2021}, month={Jul} }
 @article{hoyer_fondong_dallas_aimone_deppong_duffy_hanley-bowdoin_2020, title={Deeply Sequenced Infectious Clones of Key Cassava Begomovirus Isolates from Cameroon}, volume={9}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00802-20}, abstractNote={We deeply sequenced two pairs of widely used infectious clones (4 plasmids) of the bipartite begomoviruses African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV). The ACMV clones were quite divergent from published sequences. Raw reads, consensus plasmid sequences, and the infectious clones themselves are all publicly available.}, number={46}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Hoyer, J. Steen and Fondong, Vincent N. and Dallas, Mary M. and Aimone, Catherine Doyle and Deppong, David O. and Duffy, Siobain and Hanley-Bowdoin, Linda}, year={2020}, month={Nov} }
 @article{ndunguru_de leon_doyle_sseruwagi_plata_legg_thompson_tohme_aveling_ascencio-ibanez_et al._2016, title={Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease}, volume={90}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02834-15}, abstractNote={ABSTRACT}, number={8}, journal={JOURNAL OF VIROLOGY}, author={Ndunguru, Joseph and De Leon, Leandro and Doyle, Catherine D. and Sseruwagi, Peter and Plata, German and Legg, James P. and Thompson, Graham and Tohme, Joe and Aveling, Theresa and Ascencio-Ibanez, Jose T. and et al.}, year={2016}, month={Apr}, pages={4160–4173} }