- Adjunct Professor in the Program of Biological Sciences, Northwestern University
- Senior 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
- Genome and gene-family evolution
- Phylogenomics and bioinformatics
- Reconstructing rapid species radiations
- Evolution of parasitism and novel life histories
- Horizontal gene transfer
Lab Website: https://wickettlab.github.io/
Research in my lab group focuses on how genome-level processes (e.g. gene duplication, horizontal gene transfer, introgression) and natural selection have shaped the morphological, molecular, and phylogenetic diversity of plants. Projects in the lab span a broad diversity of photosynthetic organisms, including bryophytes, flowering plants, diatoms, parasitic plants, and more. To explore the relationship between the diversification of genes, genomes, and species, we frequently work with modern methods of DNA sequencing (high-throughput or "next generation" sequencing) and their application to non-model organisms. Much of what we do with these DNA sequence data involves phylogenomic analyses, both in terms of species histories and gene histories. Ongoing work includes the evolution of floral scent in evening primroses (Onagraceae), breeding system evolution and phylogeny of the Hawaiian Islands endemic genus Schiedea (Caryophyllaceae), phylogenomics of pleurocarpous mosses, and horizontal gene transfer and genomics of diatoms.
Current Projects in the Lab:
Unlocking the evolutionary history of Schiedea (Caryophyllaceae): rapid radiation of an endemic plant genus in the Hawaiian Islands
The primary aim of this project is to reconstruct breeding system evolution in Schiedea through an integrated program of field, laboratory, and genomic studies. Nuclear genome sequencing, targeted sequence capture, and GBS are being used to reconstruct a highly resolved phylogeny of Schiedea, identify sources of phylogenetic conflict, and investigate patterns of historical introgression. The phylogenetic hypotheses developed will be used to interpret the evolution of breeding systems including transitions from hermaphroditism to dioecy, shifts from biotic to abiotic pollination, and traits associated with pollination biology (including scent and nectar production). This project is in collaboration with Ann Sakai and Steve Weller (UC Irvine), Mike Moore (Oberlin), Warren Wagner (NTBG, Smithsonian), Krissa Skogen (CBG), and Lauren Weisenberger (USFWS). (NSF Award DEB-1752785)
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). My primary roles in this project are to reconstruct phylogenies at multiple taxonomic levels using hundreds of nuclear genes, and to sequence the nuclear genomes of three species of Onagracae for use in Genome Wide Association studies (GWAS) to uncover alleles associated with scent polymorphisms. 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)
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 have used transcriptome sequencing and target enrichment (HybSeq) to reconstruct the phylogeny of pleurocarps using hundreds of genes for hundreds of species. Transcriptome sequences of over 100 mosses were also generated to determine the distribution of gene or genome duplication 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). (NSF Award DEB-1239992)
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 uses massively parallel sequencing technologies to sequence the complete genomes of several diatom species and comprehensively sequence the transcribed genes (i.e., the transcriptomes) from over 200 diatoms and their nearest relatives. In addition to phylogenetic reconstruction, we are using these data to infer the relative timing and importance of whole genome duplications and horizontal gene transfers from associated bacteria throughout the evolutionary history of diatoms. 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 worked 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.
I am also collaborating with the Royal Botanic Gardens, Kew on the Plant and Fungal Tree of Life Project (Click HERE for more information). We recently developed a set of probe sequences that can be used to enrich 353 nuclear genes for flowering plant systematics (open access pubication available HERE and kit available HERE) to help the PAFTOL project towards its goal of generating DNA sequence data for at least one representative of all genera of angiosperms.
CL Ribeiro, D Conde, KM Balmant, C Dervinis, MG Johnson, AP McGrath, P Szewczyk, F Unda, CA Finegan, HW Schmidt, B Miles, DR Drost, E Novaes, CA Gonzalez-Benecke, GF Peter, JG Burleigh, TA Martin, SD Mansfied, G Chang, NJ Wickett, M Kirst. 2020. The uncharacterized gene EVE contributes to vessel element dimensions in Populus. PNAS 117(9):5059-5066.
Wong, GK, DE Soltis, JH Leebens-Mack, NJ Wickett, MS Barker, Y Van de Peer, SW Graham, M Melkonian. 2020. Sequencing and analyzing the transcriptomes of a thousand species across the tree of life for green plants. Annual Review of Plant Biology 71:741-765.
Gardner, EM, MG Johnson, JT Pereira, ASA Puad, Sahromi, D Arifiani, NJ Wickett, NJC Zerega. 2020. Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). In press Systematic Biology.
One Thousand Plant Transcriptomes Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574:679-685.
Carpenter EJ, N Matasci, S Ayyampalayam, S Wu, J Sun, J Yu, F Rocha J Vieira, C Bowler, RG Dorrell, MA Gitzendanner, L Li, W Du, KK Ullrich, NJ Wickett, TJ Barkmann, MS Barker, JH Leebens-Mack, GKS Wong. 2019. Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP). GigaScience 8(10):giz126.
Dodsworth S, L Pokorny, MG Johnson, JT Kim, O Maurin, NJ Wickett, F Forest, WJ Baker. 2019. Hyb-Seq for Flowering Plant Systematics. Trends in Plant Science 24(10):887-891.
Medina, R, MG Johnson, Y Liu, NJ Wickett, AJ Shaw, B Goffinet. 2019. Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma. Journal of Systematics and Evolution 57(4):404-417.
Johnson, MG, L Pokorny, S Dodsworth, LR Botigué, RS Cowan, A Devault, WL Eiserhardt, N Epitawalage, F Forest, JT Kim, JH Leebens-Mack, IJ Leitch, O Maurin, DE Soltis, PS Soltis, GKS Wong, WJ Baker, NJ Wickett. 2019. A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering. Systematic Biology 68(4):594-606.
Bruzzese, DJ, DL Wagner, T Harrison, T Jogesh, RP Overson, NJ Wickett, RA Raguso, KA Skogen. 2019. Phylogeny, host use, and diversification in the moth family Momphidae (Lepidoptera: Gelechioidea). PLoS ONE 14(6):e0207833.
Liu, Y, MG Johnson, CJ Cox, R Medina, N Devos, A Vanderpoorten, L Hedenäs, NE Bell, JR Shevock, B Aguero, D Quandt, NJ Wickett, AJ Shaw, B Goffinet. 2019. Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications 10:1485.
Villaverde, T, L Pokorny, S Olsson, M Rincón, MG Johnson, EM Gardner, NJ Wickett, J Molero, R Riina, I Sanmartín. 2018. Bridging the micro and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. New Phytologist 220:636–650.
Guillory, WX, A Onyshchenko, EC Ruck, MB Parks, T Nakov, NJ Wickett, AJ Alverson. 2018. Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta). Genome Biology and Evolution 6:1504–1515.
Laricchia, KM, MG Johnson, D Ragone, EW Williams, NJC Zerega, NJ Wickett. 2018. A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.). American Journal of Botany 105(5):915–926.
Parks, MB, T Nakov, EC Ruck, NJ Wickett, AJ Alverson. 2018. Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta). American Journal of Botany 105(3):330–347.
Kates, HR, MG Johnson, EM Gardner, NJC Zerega, NJ Wickett. 2018. Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus. Americal Journal of Botany 105(3):404–416.
Parks, MB, NJ Wickett, AJ Alverson. 2018. Signal, uncertainty, and conflict in phylogenomic data for a diverse lineage of microbial eukaryotes (diatoms, Bacillariophyta). Molecular Biology and Evolution 35(1):80–93.
Medina, R, JG Johnson, Y Liu, N Wilding, TA Hedderson, NJ Wickett, B Goffinet. 2018. Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm a rapid radiation in the moss family Funariaceae. Molecular Phylogenetics and Evolution 120:240–247.
Briscoe, LRE, NJC Zerega, HT Lumbsch, M Stech, E Kraichak, MJ Von Konrat, JJ Engel, NJ Wickett. 2017. Molecular, morphological, and biogeographic perspectives on the classification of Acrobolboideae (Acrobolbaceae, Marchantiophyta). Phytotaxa 319(1):056–070.
Carvalho-Silva, M, M Stech, LH Soares-Silva, WR Buck, NJ Wickett, Y Liu, PEAS Camara. 2017. A molecular phylogeny of the Sematophyllaceae s.l. (Hypnales) based on plastid, mitochondrial, and nuclear markers, and its taxonomic implications. Taxon 66(4):811–831.
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. PNAS 111(14):E4859–E4868.
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. PNAS 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 7(5):941–954.
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.