@article{greenham_sartor_zorich_lou_mockler_mcclung_2020, title={Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns}, volume={9}, ISSN={["2050-084X"]}, DOI={10.7554/eLife.58993}, abstractNote={An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here we describe the circadian transcriptome in the polyploid crop Brassica rapa. Strikingly, almost three-quarters of the expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between B. rapa and Arabidopsis circadian networks to reveal evidence for divergence between B. rapa paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.}, journal={ELIFE}, author={Greenham, Kathleen and Sartor, Ryan C. and Zorich, Stevan and Lou, Ping and Mockler, Todd C. and McClung, C. Robertson}, year={2020}, month={Sep} }
 @article{lou_woody_greenham_vanburen_colle_edger_sartor_zheng_levendoski_lim_et al._2020, title={Genetic and genomic resources to study natural variation in Brassica rapa}, volume={4}, ISSN={["2475-4455"]}, DOI={10.1002/pld3.285}, abstractNote={Abstract}, number={12}, journal={PLANT DIRECT}, author={Lou, Ping and Woody, Scott and Greenham, Kathleen and VanBuren, Robert and Colle, Marivi and Edger, Patrick P. and Sartor, Ryan and Zheng, Yakun and Levendoski, Nathan and Lim, Jan and et al.}, year={2020}, month={Dec} }
 @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{schmitz_tonkonogy_dogan_leblond_whitehead_kim_simpson_sartor_2019, title={Murine Adherent and Invasive E. coli Induces Chronic Inflammation and Immune Responses in the Small and Large Intestines of Monoassociated IL-10(-/-) Mice Independent of Long Polar Fimbriae Adhesin}, volume={25}, ISSN={["1536-4844"]}, DOI={10.1093/ibd/izy386}, abstractNote={BACKGROUND
Adherent and invasive Escherichia coli (AIEC) is preferentially associated with ileal Crohn's disease (CD). The role of AIEC in the development of inflammation and its regional tropism is unresolved. The presence of long polar fimbriae (LPF) in 71% of ileal CD AIEC suggests a role for LPF in the tropism and virulence of AIEC. The aim of our study is to determine if AIEC, with or without LpfA, induces intestinal inflammation in monoassociated IL-10-/- mice.


METHODS
We compared murine AIEC strains NC101 (phylogroup B2, LpfA-) and CUMT8 (phylogroup B1, LpfA+), and isogenic mutant CUMT8 lacking lpfA154, with a non-AIEC (E. coli K12), evaluating histologic inflammation, bacterial colonization, mucosal adherence and invasion, and immune activation.


RESULTS
IL-10-/- mice monoassociated with AIEC (either CUMT8, CUMT8:ΔlpfA, or NC101) but not K12 developed diffuse small intestinal and colonic inflammation. There was no difference in the magnitude and distribution of inflammation in mice colonized with CUMT8:ΔlpfA compared with wild-type CUMT8. Bacterial colonization was similar for all E. coli strains. Fluorescence in situ hybridization revealed mucosal adherence and tissue invasion by AIEC but not K12. Production of the cytokines IL-12/23 p40 by the intestinal tissue and IFN-γ and IL-17 by CD4 T cells correlated with inflammation.


CONCLUSIONS
IL-10-/- mice monoassociated with murine AIEC irrespective of LpfA expression developed chronic inflammation accompanied by IL-12/23 p40 production in the small and large intestines and IFN-γ/IL-17 production by CD4 T cells that model the interplay between enteric pathosymbionts, host susceptibility, and enhanced immune responses in people with IBD.}, number={5}, journal={INFLAMMATORY BOWEL DISEASES}, author={Schmitz, Julia M. and Tonkonogy, Susan L. and Dogan, Belgin and Leblond, Anna and Whitehead, Kristi J. and Kim, Sandra C. and Simpson, Kenneth W. and Sartor, R. Balfour}, year={2019}, month={May}, pages={875–885} }