@article{pais_ristaino_whetten_xiang_2024, title={Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in <i>Cornus florida</i> (Cornaceae)}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1282188}, abstractNote={IntroductionUnderstanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted.  The flowering dogwood tree (Cornus florida L.), an ecologically important species in North America, is threatened by powdery mildew and dogwood anthracnose diseases, and knowledge of the microbial diversity harbored within genetically and environmental distinct populations of this species remains largely unknown.MethodsWe conducted a metagenomics study utilizing the sequences of RAD-tag/genotype-by-sequence libraries from leaf tissues of C. florida to examine such host-fungus interactions across the dogwood's US range. We performed various combinations of alignments to both host and pathogen genomes to obtain filtered sets sequences for metagenomics analysis. Taxonomic assignments were determined on each filtered set of sequences, followed by estimation of microbial diversity and correlation to environment and host-genetic variation.ResultsOur data showed that microbial community composition significantly differed between visually healthy and diseased sites. Several microbial taxa known to interact with dogwood were identified from these sequences. We found no correlation between microbial diversity and relative abundances of sequences aligning to draft genomes of either pathogen causing powdery mildew or dogwood anthracnose. We found a significant relationship between differences of fungal communities and geographic distances of plant populations, suggesting roles of environments in shaping fungal communities in leaf tissues.  Significant correlations between the genetic differentiation of plant samples and fungal community dissimilarity (beta diversity) were also observed in certain sets of our analyses—suggesting the possibility of a relationship between microbial community composition and plant genetic distance. This relationship persisted in significance even after controlling for significant effects of geographic-bioclimatic variation of microbial diversity.DiscussionOur results suggest that both genetics and the environment play a significant role in shaping foliar fungal communities. Our findings underscore the power of leveraging hidden microbial sequences within datasets originally collected for plant genetic studies to understand plant-pathogen interactions.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Pais, Andrew and Ristaino, Jean and Whetten, Ross and Xiang, Qiu-Yun}, year={2024}, month={Jan} }
 @article{pais_li_xiang_2018, title={Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida
 L.}, volume={8}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.4090}, DOI={10.1002/ece3.4090}, abstractNote={AbstractUnderstanding intraspecific relationships between genetic and functional diversity is a major goal in the field of evolutionary biology and is important for conserving biodiversity. Linking intraspecific molecular patterns of plants to ecological pressures and trait variation remains difficult due to environment‐driven plasticity. Next‐generation sequencing, untargeted liquid chromatography–mass spectrometry (LC‐MS) profiling, and interdisciplinary approaches integrating population genomics, metabolomics, and community ecology permit novel strategies to tackle this problem. We analyzed six natural populations of the disease‐threatened Cornus florida L. from distinct ecological regions using genotype‐by‐sequencing markers and LC‐MS‐based untargeted metabolite profiling. We tested the hypothesis that higher genetic diversity in C. florida yielded higher chemical diversity and less disease susceptibility (screening hypothesis), and we also determined whether genetically similar subpopulations were similar in chemical composition. Most importantly, we identified metabolites that were associated with candidate loci or were predictive biomarkers of healthy or diseased plants after controlling for environment. Subpopulation clustering patterns based on genetic or chemical distances were largely congruent. While differences in genetic diversity were small among subpopulations, we did observe notable similarities in patterns between subpopulation averages of rarefied‐allelic and chemical richness. More specifically, we found that the most abundant compound of a correlated group of putative terpenoid glycosides and derivatives was correlated with tree health when considering chemodiversity. Random forest biomarker and genomewide association tests suggested that this putative iridoid glucoside and other closely associated chemical features were correlated to SNPs under selection.}, number={11}, journal={Ecology and Evolution}, publisher={Wiley}, author={Pais, Andrew L. and Li, Xu and Xiang, Qiu-Yun (Jenny)}, year={2018}, month={May}, pages={5619–5636} }
 @article{zhou_ji_obata_pais_dong_peet_xiang_2018, title={Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling}, volume={126}, ISSN={1055-7903}, url={http://dx.doi.org/10.1016/j.ympev.2018.04.001}, DOI={10.1016/j.ympev.2018.04.001}, abstractNote={Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.}, journal={Molecular Phylogenetics and Evolution}, publisher={Elsevier BV}, author={Zhou, Wenbin and Ji, Xiang and Obata, Shihori and Pais, Andrew and Dong, Yibo and Peet, Robert and Xiang, Qiu-Yun (Jenny)}, year={2018}, month={Sep}, pages={1–16} }
 @article{pais_whetten_xiang_2016, title={Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing}, volume={7}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.2623}, DOI={10.1002/ece3.2623}, abstractNote={AbstractDiscovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next‐generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees (Cornus florida L.) using genotyping by sequencing (GBS). This species is ecologically important to eastern US forests but is severely threatened by fungal diseases. We analyzed subpopulations in divergent ecological habitats within North Carolina to uncover loci under local selection and associated with environmental–functional traits or disease infection. At this scale, we tested the effect of incorporating additional sequencing before scaling for a broader examination of the entire range. To test for biases of GBS, we sequenced two similarly sampled libraries independently from six populations of three ecological habitats. We obtained environmental–functional traits for each subpopulation to identify associations with genotypes via latent factor mixed modeling (LFMM) and gradient forests analysis. To test whether heterogeneity of abiotic pressures resulted in genetic differentiation indicative of local adaptation, we evaluated Fst per locus while accounting for genetic differentiation between coastal subpopulations and Piedmont‐Mountain subpopulations. Of the 54 candidate loci with sufficient evidence of being under selection among both libraries, 28–39 were Arlequin–BayeScan Fst outliers. For LFMM, 45 candidates were associated with climate (of 54), 30 were associated with soil properties, and four were associated with plant health. Reanalysis of combined libraries showed that 42 candidate loci still showed evidence of being under selection. We conclude environment‐driven selection on specific loci has resulted in local adaptation in response to potassium deficiencies, temperature, precipitation, and (to a marginal extent) disease. High allele turnover along ecological gradients further supports the adaptive significance of loci speculated to be under selection.}, number={1}, journal={Ecology and Evolution}, publisher={Wiley}, author={Pais, Andrew L. and Whetten, Ross W. and Xiang, Qiu-Yun Jenny}, year={2016}, month={Dec}, pages={441–465} }
 @article{qi_yu_liu_pais_ranney_whetten_xiang_2015, title={Phylogenomics of polyploidy Fothergilla (Hamamelidaceae) by RAD-tag based GBS—Insights into species origin and effects of software pipelines}, volume={53}, ISSN={16744918}, url={http://doi.wiley.com/10.1111/jse.12176}, DOI={10.1111/jse.12176}, abstractNote={AbstractFothergilla (Hamamelidaceae) consists of Fothergilla gardenii (4x) from the coastal plains of the southeastern USA, F. major (6x) from the piedmont and mountains of the same region, and a few allopatric diploid populations of unknown taxonomic status. The objective of this study was to explore the relationships of the polyploid species with the diploid plants. Genotyping by sequencing (GBS) was applied to generate genome‐wide molecular markers for phylogenetic and genetic structure analyses of 36 accessions of Fothergilla. Sanger sequencing of three plastid and one nuclear regions provided data for comparison with GBS‐based results. Phylogenetic outcomes were compared using data from different sequencing runs and different software workflows. The different data sets showed substantial differences in inferred phylogenies, but all supported a genetically distinct 6x F. major and two lineages of the diploid populations closely associated with the 4x F. gardenii. We hypothesize that the 4x F. gardenii originated through hybridization between the Gulf coastal 2x and an extinct (or undiscovered) 2x lineage, followed by backcrosses to the Atlantic coastal 2x before chromosome doubling, and the 6x F. major also originated from the “extinct” 2x lineage. Alternative scenarios are possible but are not as well supported. The origins and divergence of the polyploid species likely occurred during the Pleistocene cycles of glaciation, although fossil evidence indicates the genus might have existed for a much longer time with a wider past distribution. Our study demonstrates the power of combining GBS data with Sanger sequencing in reconstructing the evolutionary network of polyploid lineages.}, number={5}, journal={Journal of Systematics and Evolution}, publisher={Wiley}, author={Qi, Zhe-Chen and Yu, Yi and Liu, Xiang and Pais, Andrew and Ranney, Thomas and Whetten, Ross and Xiang, Qiu-Yun Jenny}, year={2015}, month={Sep}, pages={432–447} }
 @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} }