@article{guo_fudali_gimeno_digennaro_chang_williamson_bird_nielsen_2017, title={Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping}, volume={206}, ISSN={["1943-2631"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85027059202&partnerID=MN8TOARS}, DOI={10.1534/genetics.117.202531}, abstractNote={AbstractInteractions between species are pervasive among plants, animals, and microbes, and identifying the molecular signals involved is an active area of research..Organisms engage in extensive cross-species molecular dialog, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of 98 isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla. With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites. The effects of parasite genotypes on plant gene expression were often substantial, with up to 90-fold (P = 3.2 × 10−52) changes in expression levels caused by individual parasite loci. Mapped loci included a number of pleiotropic sites, including one 87-kb parasite locus that modulated expression of >60 host genes. The 213 host genes identified were substantially enriched for transcription factors. We distilled higher-order connections between polymorphisms and genes from both species via network inference. To replicate our results and test whether effects were conserved across a broader host range, we performed a confirmatory experiment using M. hapla-infected tomato. This revealed that homologous genes were similarly affected. Finally, to validate the broader utility of cross-species eQTL mapping, we applied the strategy to data from a Salmonella infection study, successfully identifying polymorphisms in the human genome affecting bacterial expression.}, number={4}, journal={Genetics}, author={Guo, Y. and Fudali, S. and Gimeno, J. and DiGennaro, P. and Chang, S. and Williamson, V.M. and Bird, D.M. and Nielsen, D.M.}, year={2017}, pages={2175–2184} }
 @article{guo_pais_weakley_xiang_2013, title={Molecular phylogenetic analysis suggests paraphyly and early diversification of Philadelphus (Hydrangeaceae) in western North America: New insights into affinity with Carpenteria}, volume={51}, ISSN={1674-4918}, url={http://dx.doi.org/10.1111/jse.12041}, DOI={10.1111/jse.12041}, abstractNote={AbstractPhiladelphus (Hydrangeaceae) comprises 60 or fewer species distributed disjunctly in eastern Asia, eastern and western North America to Central America, and southeastern Europe and western Asia. The genus is highly valued in horticulture, but poorly understood regarding taxonomy, species relationships, and biogeographic history. The present study was the first phylogenetic and biogeographic analysis of Philadelphus using both nuclear and chloroplast DNA markers to evaluate classification schemes and to elucidate the biogeographic origin. Our results suggest that Philadelphus is a paraphyletic group with the monotypic genus Carpenteria nested within. Three major lineages were identified in the Philadelphus–Carpenteria clade, each strongly supported by the molecular data. Biogeographic analysis using the Bayes‐DIVA method (implemented in the newly developed RASP) and divergence time dating with BEAST resolved the origin and early diversification of Philadelphus s.l. (including Carpenteria) in western North America (including Mexico) in the Eocene. The lineage diversified and subsequently spread into Asia and other areas in the late Tertiary or Neogene to obtain a worldwide distribution. The study adds an additional example of an “out of western North America” migration in the phylogeographic history of the northern hemisphere.}, number={5}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Guo, Yue-Long and Pais, Andrew and Weakley, Alan S. and Xiang, Qiu-Yun Jenny}, year={2013}, month={Aug}, pages={545–563} }