@article{dye_muga_mwangi_hoyer_ly_rosado_sharpee_mware_wambugu_labadie_et al._2023, title={Cassava begomovirus species diversity changes during plant vegetative cycles}, volume={14}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2023.1163566}, DOI={10.3389/fmicb.2023.1163566}, abstractNote={Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Dye, Anna E. and Muga, Brenda and Mwangi, Jenniffer and Hoyer, J. Steen and Ly, Vanessa and Rosado, Yamilex and Sharpee, William and Mware, Benard and Wambugu, Mary and Labadie, Paul and et al.}, year={2023}, month={May} }
 @misc{leeks_bono_ampolini_souza_hoefler_mattson_dye_diaz-munoz_2023, title={Open questions in the social lives of viruses}, volume={36}, ISSN={["1420-9101"]}, DOI={10.1111/jeb.14203}, abstractNote={Abstract
               Social interactions among viruses occur whenever multiple viral genomes infect the same cells, hosts, or populations of hosts. Viral social interactions range from cooperation to conflict, occur throughout the viral world, and affect every stage of the viral lifecycle. The ubiquity of these social interactions means that they can determine the population dynamics, evolutionary trajectory, and clinical progression of viral infections. At the same time, social interactions in viruses raise new questions for evolutionary theory, providing opportunities to test and extend existing frameworks within social evolution. Many opportunities exist at this interface: Insights into the evolution of viral social interactions have immediate implications for our understanding of the fundamental biology and clinical manifestation of viral diseases. However, these opportunities are currently limited because evolutionary biologists only rarely study social evolution in viruses. Here, we bridge this gap by (1) summarizing the ways in which viruses can interact socially, including consequences for social evolution and evolvability; (2) outlining some open questions raised by viruses that could challenge concepts within social evolution theory; and (3) providing some illustrative examples, data sources, and conceptual questions, for studying the natural history of social viruses.
               Abstract
               Social interactions among viruses are diverse and pervasive, with the potential to affect every stage of the viral lifecycle. Here, we explore some of the challenges and opportunities that these interactions present for evolutionary biology.}, number={11}, journal={JOURNAL OF EVOLUTIONARY BIOLOGY}, author={Leeks, Asher and Bono, Lisa M. and Ampolini, Elizabeth A. and Souza, Lucas S. and Hoefler, Thomas and Mattson, Courtney L. and Dye, Anna E. and Diaz-Munoz, Samuel L.}, year={2023}, month={Nov}, pages={1551–1567} }
 @article{hoyer_wilkins_munshi_wiese_dubey_renard_mortensen_dye_carbone_duffy_et al._2022, title={Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana}, volume={6}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-12-21-0077-R}, abstractNote={ Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the replication-associated ( Rep) gene were readily compensated for by direct reversion or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B), indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Columbia-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks.  [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . }, number={3}, journal={PHYTOBIOMES JOURNAL}, author={Hoyer, J. Steen and Wilkins, Olivia W. and Munshi, Aanandi and Wiese, Emma and Dubey, Divya and Renard, Savannah and Mortensen, Karoline Rosendal Harto and Dye, Anna E. and Carbone, Ignazio and Duffy, Siobain and et al.}, year={2022}, pages={227–235} }
 @article{land_cridland_craige_dye_hildreth_helm_gillaspy_perera_2021, title={A Role for Inositol Pyrophosphates in the Metabolic Adaptations to Low Phosphate in Arabidopsis}, volume={11}, ISSN={["2218-1989"]}, url={http://dx.doi.org/10.3390/metabo11090601}, DOI={10.3390/metabo11090601}, abstractNote={Phosphate is a major plant macronutrient and low phosphate availability severely limits global crop productivity. In Arabidopsis, a key regulator of the transcriptional response to low phosphate, phosphate starvation response 1 (PHR1), is modulated by a class of signaling molecules called inositol pyrophosphates (PP-InsPs). Two closely related diphosphoinositol pentakisphosphate enzymes (AtVIP1 and AtVIP2) are responsible for the synthesis and turnover of InsP8, the most implicated molecule. This study is focused on characterizing Arabidopsis vip1/vip2 double mutants and their response to low phosphate. We present evidence that both local and systemic responses to phosphate limitation are dampened in the vip1/vip2 mutants as compared to wild-type plants. Specifically, we demonstrate that under Pi-limiting conditions, the vip1/vip2 mutants have shorter root hairs and lateral roots, less accumulation of anthocyanin and less accumulation of sulfolipids and galactolipids. However, phosphate starvation response (PSR) gene expression is unaffected. Interestingly, many of these phenotypes are opposite to those exhibited by other mutants with defects in the PP-InsP synthesis pathway. Our results provide insight on the nexus between inositol phosphates and pyrophosphates involved in complex regulatory mechanisms underpinning phosphate homeostasis in plants.}, number={9}, journal={METABOLITES}, publisher={MDPI AG}, author={Land, Eric S. and Cridland, Caitlin A. and Craige, Branch and Dye, Anna and Hildreth, Sherry B. and Helm, Rich F. and Gillaspy, Glenda E. and Perera, Imara Y.}, year={2021}, month={Sep} }
 @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{hoyer_wilkins_munshi_wiese_dubey_renard_mortensen_dye_carbone_duffy_et al._2021, title={Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana}, url={https://doi.org/10.1101/2021.11.29.468282}, DOI={10.1101/2021.11.29.468282}, abstractNote={AbstractCabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the Replication-associated gene (Rep) were readily compensated for by direct reversion and/or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B) indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Col-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks.}, author={Hoyer, J. Steen and Wilkins, Olivia W. and Munshi, Aanandi and Wiese, Emma and Dubey, Divya and Renard, Savannah and Mortensen, Karoline Rosendal Hartø and Dye, Anna E. and Carbone, Ignazio and Duffy, Siobain and et al.}, year={2021}, month={Dec} }