Ph.D., University of Connecticut, 2007
Teaching and Research Affiliations
My research makes use of high-throughput (next generation) DNA sequencing and bioinformatics to gain insight into how genome and gene-family diversification is related to the evolution of morphological, ecological, and molecular novelty in plants. In particular, I am interested in understanding how changes at the genome scale have led to the evolution and diversification of parasitic plants and bryophytes (mosses, liverworts, and hornworts). By leveraging the high volume of data produced by recently developed, short-read sequencing technologies, the sequencing of a large fraction of a plant's genome is becoming increasingly accessible. Recently, I have focused on sequencing cDNA (complementary DNA produced from extracted mRNA) for only those genes that encode proteins, and that are expressed in the plant tissues selected for sequencing, i.e. the transcriptome. The use of transcriptome sequencing enables comparisons across long evolutionary time scales and, when multiple life history stages are sampled, can reflect the up- or down-regulation of genes, which may provide insight into the role of certain genes or gene families in specific developmental and metabolic processes.
Assembling the Pleurocarp (Moss) Tree of Life. Pleurocarpous mosses are traditionally defined as having short, lateral reproductive branches. Pleurocarps, 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, 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. A recently funded project by the NSF Assembling the Tree of Life program will use transcriptome sequencing and gene enrichment through solution-based hybridization to sequence organellar genomes, and over one thousand low-copy nuclear genes for phylogenetic analyses of the pleurocarps. 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 CBG, we will be sequencing transcriptomes and developing the bioinformatics infrastructure to sort genes into gene families for downstream phylogenetic analyses.
At present, I am continuing to analyze transcriptome data from my postdoctoral research as part of the Parasitic Plant Genome Project and as part of the computational and phylogenomics team of the 1000 Plants Initiative through the iPlant Collaborative. With the Parasitic Plant Genome Project, we have sequenced transcriptomes for a series of life history stages (germinating seed through flowering shoot) from three plants from the family Orobanchaceae that vary in their degree of parasitism: Triphysaria versicolor, a facultative parasite; Striga hermonthica, an obligate parasite with some photosynthetic ability; and Phelipanche aegyptiaca, an obligate holoparasite that does not photosynthesize. We are using this comparative evolutionary framework to identify genes, gene-families, and functional categories of genes that likely play a role in the evolution of parasitism and a parasite-specific organ involved in host attachment, the haustorium. With the 1000 Plants Initiative, I continue to be involved in using transcriptome data to reconstruct the relationships of land plants and their algal relatives using tens of thousands of genes for phylogenetic analyses.
Currently, I am beginning to apply genome and transcriptome level data to better understand the molecular processes involved in the formation of ecosystems, specifically the tallgrass prairie. I and my colleagues at the Chicago Botanic Garden anticipate that these data will allow us to investigate whether particular functional categories of genes may have played a significant role in adaptation to the early tallgrass prairie environment. Additionally, I will be using comparative genomics and transcriptomics to better understand how changes at the genome scale may have led to adaptation and the diversification of early land plants.
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.