@article{laosuntisuk_vennapusa_somayanda_leman_jagadish_doherty_2024, title={A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses}, volume={1}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.16654}, DOI={10.1111/tpj.16654}, abstractNote={SUMMARY RNA‐Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA‐Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike‐ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike‐ins as a normalization control produces differences in RNA‐Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike‐ins with 3' RNA‐Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.}, journal={PLANT JOURNAL}, author={Laosuntisuk, Kanjana and Vennapusa, Amaranatha and Somayanda, Impa M. and Leman, Adam R. and Jagadish, S. V. Krishna and Doherty, Colleen J.}, year={2024}, month={Jan} }
 @article{yow_laosuntisuk_young_doherty_gillitt_perkins-veazie_jenny xiang_iorizzo_2023, title={Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-45722-y}, abstractNote={Abstract Pineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Laosuntisuk, Kanjana and Young, Roberto A. and Doherty, Colleen J. and Gillitt, Nicholas and Perkins-Veazie, Penelope and Jenny Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Nov} }
 @misc{laosuntisuk_elorriaga_doherty_2023, title={The Game of Timing: Circadian Rhythms Intersect with Changing Environments}, volume={74}, ISSN={["1545-2123"]}, DOI={10.1146/annurev-arplant-070522-065329}, abstractNote={Recurring patterns are an integral part of life on Earth. Through evolution or breeding, plants have acquired systems that coordinate with the cyclic patterns driven by Earth's movement through space. The biosystem responses to these physical rhythms result in biological cycles of daily and seasonal activity that feed back into the physical cycles. Signaling networks to coordinate growth and molecular activities with these persistent cycles have been integrated into plant biochemistry. The plant circadian clock is the coordinator of this complex, multiscale, temporal schedule. However, we have detailed knowledge of the circadian clock components and functions in only a few species under controlled conditions. We are just beginning to understand how the clock functions in real-world conditions. This review examines what we know about the circadian clock in diverse plant species, the challenges with extrapolating data from controlled environments, and the need to anticipate how plants will respond to climate change. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, journal={ANNUAL REVIEW OF PLANT BIOLOGY}, author={Laosuntisuk, Kanjana and Elorriaga, Estefania and Doherty, Colleen J.}, year={2023}, pages={511–538} }
 @misc{laosuntisuk_doherty_2022, title={The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures}, volume={50}, ISSN={["1470-8752"]}, url={https://doi.org/10.1042/BST20190572}, DOI={10.1042/BST20190572}, abstractNote={Increasing temperatures impact plant biochemistry, but the effects can be highly variable. Both external and internal factors modulate how plants respond to rising temperatures. One such factor is the time of day or season the temperature increase occurs. This timing significantly affects plant responses to higher temperatures altering the signaling networks and affecting tolerance levels. Increasing overlaps between circadian signaling and high temperature responses have been identified that could explain this sensitivity to the timing of heat stress. ELF3, a circadian clock component, functions as a thermosensor. ELF3 regulates thermoresponsive hypocotyl elongation in part through its cellular localization. The temperature sensitivity of ELF3 depends on the length of a polyglutamine region, explaining how plant temperature responses vary between species. However, the intersection between the circadian system and increased temperature stress responses is pervasive and extends beyond this overlap in thermosensing. Here, we review the network responses to increased temperatures, heat stress, and the impacts on the mechanisms of gene expression from transcription to translation, highlighting the intersections between the elevated temperature and heat stress response pathways and circadian signaling, focusing on the role of ELF3 as a thermosensor.}, number={3}, journal={BIOCHEMICAL SOCIETY TRANSACTIONS}, publisher={Portland Press Ltd.}, author={Laosuntisuk, Kanjana and Doherty, Colleen J.}, year={2022}, month={Jun}, pages={1151–1165} }