2022-2024
Zuntini, AR, T Carruthers, O Maurin et al. 2024. Phylogenomics and the rise of the angiosperms. Nature (2024).
Overson, RP, MG Johnson, LL Bechen, SP Kinosian, NA Douglas, JB Fant, PC Hoch, RA Levin, MJ Moore, RA Raguso, WL Wagner, KA Skogen, NJ Wickett. 2023. A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci. BMC Ecology and Evolution 23:66.
McCourt, RM, LA Lewis, PK Strother, CF Delwiche, NJ Wickett, J de Vries, JL Bowman. 2023. Green Land: Multiple perspectives on green algal evolution and the earliest land plants. American Journal of Botany 110(5):e16175.
Cooper, BJ, MJ Moore, NA Douglas, WL Wagner, MG Johnson, RP Overson, AJ McDonnell, RA Levin, RA Raguso, H Flores Olvera, H Ochoterena, JB Fant, KA Skogen, NJ Wickett. 2023. Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus. Systematic Biology 72(2):249-263.
Bechen, LL, MG Johnson, GT Broadhead, RA Levin, RP Overson, T Jogesh, JB Fant, RA Raguso, KA Skogen, NJ Wickett. 2022. Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae). BMC Genomics 23:124.
2020-2021
McDonnell, AJ, WJ Baker, S Dodsworth, F Forest, SW Graham, MG Johnson, L Pokorny, J Tate, S Wicke, NJ Wickett. 2021. Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics. Applications in Plant Sciences 9(7):e11443.
Baker, WJ, S Dodsworth, F Forest, SW Graham, MG Johnson, AJ McDonnell, L Pokorny, J Tate, S Wicke, NJ Wickett. 2021. Exploring Angiosperms353: an open, community toolkit for collaborative phylogenomic research on flowering plants. American Journal of Botany 108(7):1059–1065.
Baker, WJ, P Bailey, V Barber, A Barker, S Bellot, D Bishop, LR Botigué, G Brewer, T Carruthers, JJ Clarkson, J Cook, RS Cowan, S Dodsworth, N Epitawalage, E Fancoso, B Gallego, MG Johnson, JT Kim, K Leempoel, O Maurin, C McGinnie, L Pokorny, S Roy, M Stone, E Toledo, NJ Wickett, AR Zuntini, WL Eiserhardt, PJ Kersey, IJ Leitch, F Forest. 2021. A comprehensive phylogenomic platform for exploring the angiosperm tree of life. Systematic Biology: DOI:10.1093/sysbio/syab035.
Wenzell, KE, AJ McDonnell, NJ Wickett, JB Fant, KA Skogen. 2021. Incomplete reproductive isolation and low genetic differentiation despite floral divergence across varying geographic scales in Castilleja. American Journal of Botany 108(7):1270-1288.
Carey, SB, J Jenkins, JT Lovell, F Maumus, A Sreedasyam, AC Payton, S Shu, GP Tiley, N Fernandez-Pozo, K Barry, C Chen, M Wang, A Lipzen, C Daum, CA Saski, JC McBreen, RE Conrad, LM Kollar, S Olsson, S Huttunen, JB Landis, JG Burleigh, NJ Wickett, MG Johnson, SA Rensing, J Grimwood, J Schmutz, SF McDaniel. 2021. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. Science Advances 7(27):eabh2488.
Patsis, A, RP Overson, KA Skogen, NJ Wickett, MG Johnson, WL Wagner, RA Raguso, JB Fant, RA Levin. 2021. Elucidating the evolutionary history of Oenothera sect. Pachylophus (Onagraceae): A phylogenomic approach. Systematic Botany 46(3): IN PRESS.
Cooper, BJ, MJ Moore, NA Douglas, WL Wagner, MG Johnson, RP Overson, AJ McDonnell, RA Levin, RA Raguso, H Flores Olvera, H Ochoterena, JB Fant, KA Skogen, NJ Wickett. 2021. Target enrichment and extensive population sampling help untangle the recent, rapid radiation of Oenothera sect. Calylophus. bioRxiv PREPRINT
Bechen, LL, MG Johnson, GT Broadhead, RA Levin, RP Overson, T Jogesh, JB Fant, RA Raguso, KA Skogen, NJ Wickett. 2021. Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae). bioRxiv PREPRINT.
Ribeiro, CL, 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). Systematic Biology 70(3):558-575.
2018-2019
One Thousand Plant Transcriptomes Initiative. 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574:679-685. OPEN ACCESS
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. OPEN ACCESS
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. FREE ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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.
2016-2017
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. OPEN ACCESS
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. OPEN ACCESS
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 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. OPEN ACCESS
2014-2015
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. OPEN ACCESS
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 111(14): E4859-E4868. OPEN ACCESS
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. OPEN ACCESS
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.
2012-2013
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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. OPEN ACCESS
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.
2010-2011
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. OPEN ARCHIVE
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. 2011. FLOWERING LOCUS T Duplication Coordinates Reproductive and Vegetative Growth in Perennial Poplar. Proceedings of the National Academy of Sciences of the United States of America 108(26): 10756-10761.OPEN ACCESS
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. OPEN ACCESS
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.
2004-2009
Wickett NJ, Y Fan, PO Lewis & B Goffinet. 2008. Distribution and evolution of pseudogenes, gene losses and a gene rearrangement in the 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. FREE ACCESS
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. FREE ACCESS
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.
