- Adjunct Assistant Professor in the Program of Biological Sciences, Northwestern University
- Associate Editor, Applications in Plant Sciences
- Committee on Evolutionary Biology, University of Chicago
- Research Associate, The Field Museum
American Bryological and Lichenological Society
American Society of Plant Taxonomists
Botanical Society of America
- Evolution of land plants
- Bryophyte (mosses, liverworts, hornworts) diversification
- Evolution of parasitism and novel life histories
- Phylogenomics and bioinformatics
- Genome and gene-family evolution
- Horizontal gene transfer
I am broadly interested in the origin of new genetic material through both endogenous (e.g. gene or whole genome duplication) and exogenous (e.g. horizontal gene transfer) processes, and the role of these processes in adaptation and diversification in plants. In particular, I am interested in understanding how changes at the genome scale have led to the evolution and diversification of bryophytes (mosses, liverworts, and hornworts), but I am excited by how these questions can be applied to all photosynthetic organisms. In addition to bryophytes, I am currently involved in projects focused on flowering plants (Onagraceae, the Evening Primrose family), land plants (embryophytes), and diatoms (a group of phytoplankton).
My research makes use of high-throughput (“next generation”) DNA sequencing and bioinformatics to uncover patterns and processes that underlay the acquisition of novel genes or traits. Fundamental shifts in life history or habitat may have been, at least in part, driven by processes such as horizontal gene transfer (e.g. the integration of fungal genes into the plant genome) or polyploidy, the latter of which creates thousands of new genes. In order to understand this information at a genomic scale, partial or complete genome sequences are necessary. By leveraging the high volume of data produced by recently developed, high-throughput sequencing technologies, the sequencing of a large fraction of a plant's genome is becoming increasingly accessible, particularly for understudied or non-model organisms (like moss!).
At present, I am working on three NSF-funded projects:
Assembling the Pleurocarp (Moss) Tree of Life: Resolving the Rapid Radiation Using Genomics and Transcriptomics
Pleurocarpous mosses (traditionally defined as having short, lateral reproductive branches), Hypnanae, comprise the most speciose lineage of mosses, a result of an explosive radiation during the Jurassic, at a time when flowering plants began to dominate many terrestrial environments. Repeated, multi-directional habitat transitions occurred as this group evolved (e.g. terrestrial to epiphytic), leading to the loss of morphological synapomorphies that may be used to circumscribe groups. Furthermore, phylogenetic analyses based on targeted gene sequencing have been unable to resolve many relationships, including those along the backbone, within the pleurocarps. To address this lack of resolution, we will use transcriptome sequencing and gene enrichment through solution-based hybridization to sequence organellar genomes, and hundreds of low-copy nuclear genes for phylogenetic analyses. Additionally, the transcriptome sequences of over 100 mosses will be used to determine the distribution of polyploidy events throughout the evolutionary history of mosses, and to characterize how these events may be related to diversification and habitat shifts. This project is in collaboration with Bernard Goffinet (University of Connecticut) and Jon Shaw (Duke University), who will be leading the sequence-capture effort. Here at the Chicago Botanic Garden, we will be sequencing transcriptomes and developing the bioinformatics infrastructure to sort genes into gene families for downstream phylogenetic analyses. (NSF Award DEB-1239992)
Landscapes of Linalool: Scent Mediated Diversification of Flowers and Moths Across Western North America
This project, funded through the NSF Dimensions of Biodiversity program, focuses on how chemically-mediated interactions between flowering plants, pollinators, and enemies affect diversification at the population, species, and higher taxonomic levels. Onagraceae (evening primrose family) is one of the most species-rich families of night-blooming plants in North America. Many Onagraceae, particularly species in tribe Onagreae, produce floral scent that likely dictates the primary biotic drivers impacting plant fitness, including legitimate pollinators (hawkmoths, bees) and floral and seed predators (Mompha moths). The same floral characteristics (color, shape, scent) that attract pollinators are also suspected to attract floral antagonists to host plants. Mompha is one such moth genus that specializes on Onagraceae. A thorough survey of these micromoths associated with Onagreae in western North America will result in a more accurate assessment of diversity in this group. My primary roles in this project are to 1) characterize genetic diversity in focal species of Onagraceae using high-throughput GBS (Genotyping by Sequencing) approaches, 2) sequence the nuclear genomes of three species of Onagracae for use in Genome Wide Association studies (GWAS) to uncover the genetic basis of scent differentiation, and 3) develop markers for liquid-phase sequence capture of low-copy nuclear genes for phylogenetic analyses in Onagraceae and Mompha. This project is a multi-institutional collaboration between the Chicago Botanic Garden (Krissa Skogen, Jeremie Fant, Norm Wickett), Cornell (Rob Raguso), and Amherst College (Rachel Levin) that involves collaborators from several other institutions. (NSF Award DEB-1342873)
Evaluating the contributions of horizontally transferred bacterial genes and endogenous duplication events to the diversification of diatoms
The goal of this project is to identify the primary genomic drivers of the phylogenetic and functional diversification of diatoms, a hyperdiverse lineage of photosynthetic microalgae. With estimates ranging from 100,000 to 10,000,000 species, diatoms are one of the most diverse lineages in the eukaryotic tree of life. This project will use massively parallel sequencing technologies to sequence the complete genomes of five diatom species and comprehensively sequence the transcribed genes (i.e., the transcriptomes) from 200 diatoms and their nearest relatives. These data will be used to reconstruct the diatom phylogeny and resolve, for the first time, the radiation of the raphid pennate clade. Unlike most other eukaryotes, diatom genomes have been inordinately shaped by cross-kingdom horizontal gene transfer, with foreign bacterial genes comprising as many as 7.5% of the genes in some species. The pattern and timing of these transfers will be reconstructed on the phylogeny to determine whether bacterial gene acquisitions coincide with major species diversifications or the origins of important functional traits. Towards this end, considerable effort will be made to sample across the morphologically, functionally, and ecologically diverse raphid pennate clade, which has experienced major recent influxes of bacterial genes. Extensive outgroup sampling will allow circumscription of the set of diatom-specific bacterial genes and reveal which, if any, of them were acquired shortly after the split between diatoms and their sister lineage, providing insights into the origins of "defining" synapomorphic diatom traits. Diatom genomes are also characterized by species-specific single-copy genes, ancient gene duplicates, and differential gene-family expansions and contractions, indicating that endogenous processes are an important source of novel genetic material as well. Transcriptome data will be used to pinpoint gene- and whole-genome duplications on the phylogeny to determine how they correlate with the origins of major groups and novel traits. This is a collaborative project between the University of Arkansas (Andrew Alverson) and the Chicago Botanic Garden (Norm Wickett). (From the Project Summary; NSF Award DEB-1353152)
In addition to these primary projects, I have recently been working closely with the 1KP (One Thousand Plants) project. My involvement in this project is largely focused on the circumscription of gene families and downstream phylogenetic analyses. In particular, I am interested in how these data can be used to better resolve the backbone phylogeny of land plants, with an emphasis on the branching order of the three lineages of bryophytes (mosses, liverworts, hornworts). To learn more about this project, please visit onekp.com.
Johnson, MG, EM Gardner, Y Liu, R Medina, B Goffinet, AJ Shaw, NJC Zerega, NJ Wickett. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7): 1600016.
Gardner, EM, MG Johnson, D Ragone, NJ Wickett, NJC Zerega. 2016. Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery. Applications in Plant Sciences 4(7): 1600017.
Johnson, MG, C Malley, B Goffinet, AJ Shaw, NJ Wickett. 2016. A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). Molecular Phylogenetics and Evolution 98: 29-40.
Honaas, LA, EK Wafula, NJ Wickett, JP Der, Y Zhang, PP Edger, NS Altman, JC Pires, JH Leebens-Mack, CW dePamphilis. 2016. Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome. PLoS ONE 11(1): e0146062.
Das, M, M Fernández-Aparicio, Z Yang, K Huang, NJ Wickett, S Alford, EK Wafula, CW dePamphilis, H Bouwmeester, MP Timko, JI Yoder, JH Westwood. 2015. Parasitic plants Striga and Phelipanche dependent upon exogenous strigolactones for germination have retained genes for strigolactone biosynthesis. American Journal of Plant Sciences 6(8): 1151-1166.
Wilson, A, NJ Wickett, P Grabowski, J Fant, J Borevitz, G Mueller. 2015. Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor with either a reference genome or simple denovo analysis. Mycologia 107(1): 217-226.
Wickett, NJ, S Mirarab, N Nguyen, T Warnow, E Carpenter, N Matasci, S Ayyampalayam, M Barker, JG Burleigh, MA Gitzendanner, BR Ruhfel, E Wafula, JP Der, SW Graham, S Mathews, M Melkonian, DE Soltis, PS Soltis, NW Miles, CJ Rothfels, L Pokorny, AJ Shaw, L DeGironimo, DW Stevenson, B Surek, JC Villarreal, B Roure, H Philippe, CW dePamphilis, T Chen, MK Deyholos, RS Baucom, TM Kutchan, MM Augustin, J Wang, Y Zhang, Z Tian, Z Yan, X Wu, X Sun, G Ka-Shu Wong, J Leebens-Mack. 2014. A phylotranscriptomics analysis of the origin and diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America doi:10.1073/pnas.1323926111.
Matasci, N, LH Hung, Z Yan, EJ Carpenter, NJ Wickett, S Mirarab, N Nguyen, T Warnow, S Ayyampalayam, M Barker, JG Burleigh, MA Gitzendanner, E Wafula, JP Der, CW dePamphilis, B Roure, H Philippe, BR Ruhfel, NW Miles, SW Graham, S Mathews, B Surek, M Melkonian, DE Soltis, PS Soltis, C Rothfels, L Pokorny, AJ Shaw, L DeGironimo, DW Stevenson, JC Villarreal, T Chen, TM Kutchan, M Rolf, RS Baucom, MK Deyholos, R Samudrala, Z Tian, X Wu, X Sun, Y Zhang, J Wang, J Leebens-Mack, G Ka-Shu Wong. 2014. Data access for the 1000 Plants (1KP) pilot. Gigascience 3:17.
Kessenich, CR, EC Ruck, AM Schurko, NJ Wickett, AJ Alverson. 2014. Transcriptomic insights into the life history of bolidophytes, the sister lineage to diatoms. Journal of Phycology 50(6): 977-983.
Wicke, S, KF Müller, CW dePamphilis, D Quandt, NJ Wickett, Y Zhang, SS Renner, GM Schneeweiss. 2013. Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family. The Plant Cell 25(10): 3711-3725.
Villarreal, JC, LL Forrest, NJ Wickett, B Goffinet. 2013. The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): Phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain. American Journal of Botany 100(3): 467-477.
Zhang, Y, M Fernandez-Aparicio, EK Wafula, M Das, Y Jiao, NJ Wickett, LA Honaas, PE Ralph, MF Wojciechowski, MP Timko, JI Yoder, JH Westwood, CW dePamphilis. 2013. Evolution of a horizontally acquired legume gene, albumin 1, I the parasitic plant Phelipanche aegyptiaca and related species. BMC Evolutionary Biology 13:48.
Bliss, BJ, S Wanke, A Barakat, S Ayyampalayam, NJ Wickett, PK Wall, Y Jiao, L Landherr, PE Ralph, Y Hu, C Heinhuis, J Leebens-Mack, K Arumuganathan, SW Clifton, SN Maximova, H Ma, CW dePamphilis. 2013. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. BMC Plant Biology 13:13.
Honaas, LA, EK Wafula, Z Yang, JP Der, NJ Wickett, NS Altman, CG Taylor, JI Yoder, MP Timko, JH Westwood, CW dePamphilis. 2013. Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biology 13:9.
Merckx, VSFT, JV Freudenstein, J Kissling, MJM Christenhusz, RE Stotler, B Crandall-Stotler, NJ Wickett, PJ Rudall, HM de Kamer, PJM Maas. 2013. Taxonomy and Classification In Merckx, V (Ed.) Mycoheterotrophy: The Biology of Plants Living on Fungi. Springer, 356pp.
Fernández-Aparicio, M, K Huang, EK Wafula, LA Honaas, NJ Wickett, MP Timko, CW dePamphilis, JI Yoder, JH Westwood. 2013. Application of qRT-PCR and RNA-Seq analysis for the identification of housekeeping genes useful fo normalization of gene expression values during Striga hermonthica development. Molecular Biology Reports 40(4): 3395-3407.
Jiao, Y, J Leebens-Mack, S Ayyampalayam, JE Bowers, MR McKain, J McNeal, M Rolf, DR Ruzicka, E Wafula, NJ Wickett, X Wu, Y Zhang, J Wang, Y Zhang, EJ Carpenter, MK Deyholos, TM Kutchan, AS Chanderbali, PS Soltis, DW Stevenson, R McCombie, JC Pires, G Wong, DE Soltis, CW dePamphilis. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13: R3.
McKain, MR, NJ Wickett, Y Zhang, S Ayyampalayam, WR McCombie, MW Chase, JC Pires, CW dePamphilis, J Leebens-Mack. 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany 99(2): 397-406.
Bandaranayake, PCG, A Tomilov, NB Tomilova, QA Ngo, NJ Wickett, CW dePamphilis, JI Yoder. 2012. The TvPirin gene is necessary for haustorium development in the parasitic plant Triphysaria versicolor. Plant Physiology 158(2): 1046-1053.
Westwood, JW, CW dePamphilis, M Das, M Fernandez-Aparicio, LA Honaas, MP Timko, NJ Wickett, JI Yoder. 2012. The Parasitic Plant Genome Project: New tools for understanding the biology of Orobanche and Striga. Weed Science 60(2): 295-306.
Wickett, NJ, LA Honaas, EK Wafula, M Das, K Huang, B Wu, L Landherr, MP Timko, J Yoder, JH Westwood, CW dePamphilis. 2011. Transcriptomes of the parasitic plant family Orobanchaceae reveal surprising conservation of chlorophyll synthesis. Current Biology 21(24): 2098-2104.
Wickett NJ, LL Forrest, JM Budke, B Shaw & B Goffinet. 2011. Frequent pseudogenization and loss of the plastid-encoded, sulfate transport gene cysA throughout the evolution of liverworts. American Journal of Botany 98(8): 1263-1275.
Hsu CY, JP Adams, H Kim, K No, C Ma, SH Strauss, J Drnevich, L Vandervelde, JD Ellis, BM Rice, NJ Wickett, LE Gunter, GA Tuskan, AM Brunner, GP Page, A Barakat, JE Carlson, CW dePamphilis, DS Luthe & C Yuceer. In Press. FT Duplication Coordinates Reproductive and Vegetative Growth. Proceedings of the National Academy of Sciences of the United States of America 108(26): 10756-10761.
Jiao Y, NJ Wickett, S Ayyampalayam, A Chanderbali, L Landherr, PE Ralph, LP Tomsho, Y Hu, H Liang, PS Soltis, DE Soltis, SW Clifton, SE Schlarbaum, SC Schuster, H Ma, J Leebens-Mack & CW dePamphilis. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
Der JP, MS Barker, NJ Wickett, CW dePamphilis & PG Wolf. 2011. De novo Characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics 99:12.
Forrest LL, NJ Wickett, CJ Cox & B Goffinet. 2011. Deep sequencing of Ptilidium pulcherrimum suggests evolutionary stasis in liverwort chloroplast structure. Plant Ecology and Evolution 144(1): 29-43.
Liang H, S Ayyampalayam, NJ Wickett, A Barakat, Y Xu, L Landherr, P Ralph, T Xu, SE Schlarbaum, H Ma, JH Leebens-Mack & CW dePamphilis. 2011. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. Tree Genetics and Genomes DOI: 10.1007/s11295-011-0386-2.
Preußing M, S Olsson, A Schäfer-Verwimp, NJ Wickett, S Wicke, D Quandt & M Nebel. 2010. New insights in the evolution of the liverwort family Aneuraceae (Metzgeriales, Marchantiophyta) with an emphasis on the genus Lobatiriccardia. Taxon 59(5): 1424-1440.
Cox CJ, B Goffinet, NJ Wickett, SB Boles & AJ Shaw. 2010. Moss diversity: a molecular phylogenetic analysis of genera. Phytotaxa 9:175-195.
Wickett NJ, Y Fan, PO Lewis & B Goffinet. 2008. Distribution and evolution of pseudogenes, gene losses and a gene rearrangement in pthe plastid genome of the non-photosynthetic liverwort, Aneura mirabilis (Metzgeriales, Jungermanniopsida). Journal of Molecular Evolution 67: 111-122.
Wickett NJ, Y Zhang, SK Hansen, JM Roper, JV Kuehl, SA Plock, PG Wolf, CW dePamphilis, JL Boore & B Goffinet. 2008. Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis. Molecular Biology and Evolution 25(2): 393-401.
Wickett, NJ, & B Goffinet. 2008. Origin and relationships of the myco-heterotrophic liverwort Cryptothallus mirabilis Malmb. (Metzgeriales, Marchantiophyta). Botanical Journal of the Linnean Society 156: 1-12.
Goffinet B, NJ Wickett, O Werner, RM Ros, AJ Shaw & CJ Cox. 2007. Distribution and phylogenetic significance of the 71 kb inversion in the chloroplast genome in the Funariidae (Bryophyta). Annals of Botany 99: 747-753.
Goffinet, B, NJ Wickett, AJ Shaw, & CJ Cox. 2005. Phylogenetic significance of the RpoA loss in the chloroplast genome of mosses. Taxon 54 (2): 353-360.
Goffinet B, AJ Shaw, CJ Cox, NJ Wickett & S Boles. 2004. Phylogenetic inferences in the Orthotrichoideae (Orthotrichaceae: Bryophyta) based on variation in four loci from all genomes. Monographs in Systematic Botany from the Missouri Botanical Garden 98:270-289.