2020-2021
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). In press, Systematic Biology.
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.