@article{desai_lawas_valente_leman_grinevich_jagadish_doherty_2021, title={Warm nights disrupt transcriptome rhythms in field-grown rice panicles}, volume={118}, ISSN={["0027-8424"]}, url={https://doi.org/10.1073/pnas.2025899118}, DOI={10.1073/pnas.2025899118}, abstractNote={Significance
          The effects of warmer nighttime temperatures (WNT) on crops are one poorly understood dimension of climate change. WNT result from the asymmetrical increase in nighttime versus daytime temperatures. In rice, WNT reduce grain yield and quality. WNT reduce the amplitude of daily temperature cycles plants use to set their circadian clock. Therefore, we examined how WNT affect the timing of molecular activities. In field-grown plants, WNT alter the daily pattern of the transcriptome. Genes with strong rhythmic expression and those under circadian control are affected most by WNT. Many candidate regulators of the disrupted genes are circadian clock associated, emphasizing the altered timing under WNT. The pathways and mechanisms identified can assist efforts to identify lines tolerant to WNT.}, number={25}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Desai, Jigar S. and Lawas, Lovely Mae F. and Valente, Ashlee M. and Leman, Adam R. and Grinevich, Dmitry O. and Jagadish, S. V. Krishna and Doherty, Colleen J.}, year={2021}, month={Jun} }
 @article{slabaugh_desai_sartor_lawas_krishna jagadish_doherty_2019, title={Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome}, volume={25}, ISSN={["1469-9001"]}, url={https://doi.org/10.1261/rna.070227.118}, DOI={10.1261/rna.070227.118}, abstractNote={RNA-seq analysis has enabled the evaluation of transcriptional changes in many species including nonmodel organisms. However, in most species only a single reference genome is available and RNA-seq reads from highly divergent varieties are typically aligned to this reference. Here, we quantify the impacts of the choice of mapping genome in rice where three high-quality reference genomes are available. We aligned RNA-seq data from a popular productive rice variety to three different reference genomes and found that the identification of differentially expressed genes differed depending on which reference genome was used for mapping. Furthermore, the ability to detect differentially used transcript isoforms was profoundly affected by the choice of reference genome: Only 30% of the differentially used splicing features were detected when reads were mapped to the more commonly used, but more distantly related reference genome. This demonstrated that gene expression and splicing analysis varies considerably depending on the mapping reference genome, and that analysis of individuals that are distantly related to an available reference genome may be improved by acquisition of new genomic reference material. We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs. We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome analysis.}, number={6}, journal={RNA}, publisher={Cold Spring Harbor Laboratory}, author={Slabaugh, Erin and Desai, Jigar S. and Sartor, Ryan C. and Lawas, Lovely Mae F. and Krishna Jagadish, S. V. and Doherty, Colleen J.}, year={2019}, month={Jun}, pages={669–684} }
 @article{desai_slabaugh_liebelt_fredenberg_gray_jagadish_wilkins_doherty_2018, title={Neural Net Classification Combined With Movement Analysis to Evaluate Setaria viridis as a Model System for Time of Day of Anther Appearance}, volume={9}, ISSN={["1664-462X"]}, url={http://dx.doi.org/10.3389/fpls.2018.01585}, DOI={10.3389/fpls.2018.01585}, abstractNote={In many plant species, the time of day at which flowers open to permit pollination is tightly regulated. Proper time of flower opening, or Time of Day of Anther Appearance (TAA), may coordinate flowering opening with pollinator activity or may shift temperature sensitive developmental processes to cooler times of the day. The genetic mechanisms that regulate the timing of this process in cereal crops are unknown. To address this knowledge gap, it is necessary to establish a monocot model system that exhibits variation in TAA. Here, we examine the suitability of Setaria viridis, the model for C4 photosynthesis, for such a role. We developed an imaging system to monitor the temporal regulation of growth, flower opening time, and other physiological characteristics in Setaria. This system enabled us to compare Setaria varieties Ames 32254, Ames 32276, and PI 669942 variation in growth and daily flower opening time. We observed that TAA occurs primarily at night in these three Setaria accessions. However, significant variation between the accessions was observed for both the ratio of flowers that open in the day vs. night and the specific time of day where the rate is maximal. Characterizing this physiological variation is a requisite step toward uncovering the molecular mechanisms regulating TAA. Leveraging the regulation of TAA could provide researchers with a genetic tool to improve crop productivity in new environments.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Desai, Jigar S. and Slabaugh, Erin and Liebelt, Donna J. and Fredenberg, Jacob D. and Gray, Benjamin N. and Jagadish, S. V. Krishna and Wilkins, Olivia and Doherty, Colleen J.}, year={2018}, month={Oct} }
 @article{reyes_flores-vergara_guerra-peraza_rajabu_desai_hiromoto-ruiz_ndunguru_hanley-bowdoin_kjemtrup_ascencio-ibanez_et al._2017, title={A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae}, volume={92}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.13716}, abstractNote={SummaryGeminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus‐resistant genes that derive from alterations in essential host factors. We used a virus‐induced gene silencing (VIGS) vector derived from the geminivirus Cabbage leaf curl virus (CaLCuV) to assess natural variation in virus–host interactions in 190 Arabidopsis accessions. Silencing of CH‐42, encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance. There was a wide range in symptom severity and extent of silencing in different accessions, but two correlations could be made. Lines with severe symptoms uniformly lacked extensive VIGS, and lines that showed attenuated symptoms over time (recovery) showed a concomitant increase in the extent of VIGS. One accession, Pla‐1, lacked both symptoms and silencing, and was immune to wild‐type infectious clones corresponding to CaLCuV or Beet curly top virus (BCTV), which are classified in different genera in the Geminiviridae. It also showed resistance to the agronomically important Tomato yellow leaf curl virus (TYLCV). Quantitative trait locus mapping of a Pla‐1 X Col‐0 F2 population was used to detect a major peak on chromosome 1, which is designated gip‐1 (geminivirus immunity Pla‐1‐1). The recessive nature of resistance to CaLCuV and the lack of obvious candidate genes near the gip‐1 locus suggest that a novel resistance gene(s) confers immunity.}, number={5}, journal={PLANT JOURNAL}, author={Reyes, Maria Ines and Flores-Vergara, Miguel A. and Guerra-Peraza, Orlene and Rajabu, Cyprian and Desai, Jigar and Hiromoto-Ruiz, Yokiko H. and Ndunguru, Joseph and Hanley-Bowdoin, Linda and Kjemtrup, Susanne and Ascencio-Ibanez, Jose T. and et al.}, year={2017}, month={Dec}, pages={796–807} }
 @article{mukherjee_wheaton_counts_ijeomah_desai_kelly_2017, title={VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae}, volume={19}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.13808}, abstractNote={SummaryWhen abruptly exposed to toxic levels of hexavalent uranium, the extremely thermoacidophilic archaeon Metallosphaera prunae, originally isolated from an abandoned uranium mine, ceased to grow, and concomitantly exhibited heightened levels of cytosolic ribonuclease activity that corresponded to substantial degradation of cellular RNA. The M. prunae transcriptome during ‘uranium‐shock’ implicated VapC toxins as possible causative agents of the observed RNA degradation. Identifiable VapC toxins and PIN‐domain proteins encoded in the M. prunae genome were produced and characterized, three of which (VapC4, VapC7, VapC8) substantially degraded M. prunae rRNA in vitro. RNA cleavage specificity for these VapCs mapped to motifs within M. prunae rRNA. Furthermore, based on frequency of cleavage sequences, putative target mRNAs for these VapCs were identified; these were closely associated with translation, transcription, and replication. It is interesting to note that Metallosphaera sedula, a member of the same genus and which has a nearly identical genome sequence but not isolated from a uranium‐rich biotope, showed no evidence of dormancy when exposed to this metal. M. prunae utilizes VapC toxins for post‐transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation.}, number={7}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Mukherjee, Arpan and Wheaton, Garrett H. and Counts, James A. and Ijeomah, Brenda and Desai, Jigar and Kelly, Robert M.}, year={2017}, month={Jul}, pages={2831–2842} }