News

New people, pictures, publications, and other activity. Move your cursor over each image for information and links.

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Congratulations to Matt Johnson, who will be taking his waffle talents to Texas Tech as an Assistant Professor starting in Fall, 2017!

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Matt Johnson's Last Supper (before heading to Texas). A Far-Northerner's attempt at a smoked brisket.

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Norm and the Matts enjoying the 115 degree heat index in Shenzhen for the International Botanical Congress, 2017

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Matt Parks having lunch in Shenzhen with world famous fern biologist Fay-Wei Li!

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Tania, a big pot of sea creatures, and gypsum endemic Mike Moore in Shenzhen.

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Engaging the public with a moss table at the celebration of World Environment Day at the Chicago Botanic Garden

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Matt Johnson, Elliot Gardner, and Norm recently led a HybSeq workshop at Kew. Thank you to Lisa Pokorny for being such
a great host!

Click here to view some of the workshop materials.

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No big deal. Just an Adiantum collected by Darwin (Kew herbarium).

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Elliot enjoying the company
of cacti at Kew

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Bioinformatics and bocce:
A natural combination.

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HybPiper, a modular pipeline for processing target enrichment data is now available!

Click here for the pipeline and here for the paper in APPS.

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Bryologists doing what bryologists do. The Nitztal, Germany.

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The lab taking a mid-day break to see the noon showing of
Rogue One

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Titan arum twins at the Chicago Botanic Garden!

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Donut Day! For our holiday lab excursion, we did a donut tour of downtown Chicago. The post-tour analysis showed that the Donut Vault has the best donuts in town.

Collection site in the Scottish highlands of the underground liverwort Aneura mirabilis, the only non-photosynthetic bryophyte.

People

Interested in joining us? Send Norm an email to find out about opportunities in the lab: nwickett@chicagobotanic.org.

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Norm Wickett

PhD (2007) University of Connecticut
I'm interested in understanding life history evolution in bryophytes, and the application of phylogenomics and comparative genomics to the study of plant diversification. I use gene trees, transcriptomics, and draft genome sequencing to understand how processes such as gene-family diversification (possibly through whole-genome duplication), shifts in selection, and horizontal gene transfer have influenced the evolution of land plants.

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Colby Witherup

MS (2013) Northwestern University
I'm interested in the possibility of selection on meiosis and related genes in pre- and post-polyploid plant populations. I am currently examining the evolutionary history of meiosis-related genes in sequenced plant genomes to identify patterns of conservation and change across the plant phylogeny.

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Matt Parks

PhD (2011) Oregon State
My research investigates phylogenomic and population genomic histories using whole-genome and targeted- enrichment sequencing. I have used these methods to resolve species relationships of pines and to understand climate-driven demographic changes in Adelie penguins.

Current Project: The role of Horizontal Gene Transfer and Genome Duplication in diatoms - genome assembly/annotation, transcriptome analysis (lead bioinformatician).

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Tania Jogesh

PhD (2014) University of Illinois
I'm a chemical ecologist interested in the ecology and evolution of chemically-mediated plant-insect interactions, particularly in cases where floral volitiles may attract both pollinators and herbivores, leading to conflicting selection on floral chemistry.

Current Project: Dimensions of Biodiversity (scent-mediated diversification of evening primroses and moths) - field team leader, experimental arrays, chemical analysis of floral scent.

Lab Alumni

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Matt Johnson

PhD (2013) Duke University
Former postdoc on the Moss Tree of Life project

Currently: Assistant Professor in the Department of Biological Sciences at Texas Tech University

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Rick Overson

PhD (2011) Arizona State
Former postdoc on the Landscapes of Linalool (Dimensions) project

Currently: Researcher in the Cease Lab at Arizona State University

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Claire Malley

MA (2016) Northwestern University
Methods in Orthology Detection and Application to the Moss Phylogeny

Currently: Bioinformatician at Johns Hopkins University

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Kristen Laricchia

MA (2014) Northwestern University
Transcriptome Analysis of Domesticated Breadfruit and its Wild Relatives

Currently: Associate Computational Biologist at the Broad Institute

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Laura Briscoe

MA (2012) Northwestern University
Using Molecules and Morphology to Better Understand the Liverwort Family Acrobolbaceae

Currently: Collections Manager, Steere Herbarium, New York Botanical Garden

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Lindsey Bechen

BA (2016) Amherst College
Floral morphology and patterns of gene expression associated with floral fragrance variation

Currently: Research Assistant at the Chicago Botanic Garden

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Amanda Patsis

BA (2017) Amherst College
A phylogenomic approach to inferring relationships in Oenothera sect. Pachylophus

Currently: Project Manager at Epic

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Anni Wang

BA (2018) Florida State
Comparative analysis of rates of protein conservation and divergence in diatom genomes

Currently: Fourth year student at Florida State University

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Marissa Ashner

Illinois Institute of Technology
Positional conservation of introns throughout diatom evolution

Currently: Fourth year student at Illinois Institute of Technology

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Nina Denne

Illinois Math & Science Academy
Characterization of transposable elements in diatom genomes

Currently: First year student at Carleton College

Buxbaumia aphylla, a moss with a massive sporophyte and highly reduced gametophyte.

Projects and Links

We work with a diversity of organisms in the Wickett Lab including (but not limited to) bryophytes, diatoms, and angiosperms. We also use a diversity of methods, but all of our projects include a high-throughput sequencing component, phylogenetic methods (gene trees and species trees) and a significant amount of bioinformatics. All of our projects share a common thread - understanding the molecular processes that coincide with the origin of fundamental life history traits and the relationship between these processes/traits and diversification. The primary, NSF-funded projects of the lab are described here.

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Moss Phylogeny

Assembling the Pleurocarpous (Moss) Tree of Life: Resolving the rapid radiation using genomics and transcriptomics

Pleurocarpous mosses comprise the most speciose lineage of mosses and most of this diversity arose through a rapid radiation in the Jurassic. For this project, we are using transcriptome sequencing and Hyb-Seq (sequence capture) methods to resolve enigmatic relationships within pleurocarps, and to reconstruct genomics processes (e.g. genome duplication) that may be associated with the radiation. (Photo: Blanka Shaw)

Collaborators: Bernard Goffinet (University of Connecticut), Jon Shaw (Duke).

(NSF Award DEB-1239992)

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Floral Scent in Onagraceae

Dimensions of Biodiversity: Landscapes of Linalool - Scent mediated diversification of flowers and moths across Western North America

Onagraceae (evening primrose family) is one of the most diverse groups of night-blooming plants in North America. We are investigating the role of floral scent in the diversification of this group and of its pollinators and seed predators, which may be attracted to the plants by the same scent. This project will result in a new genomes and genomic resources for the tribe Onagreae and a species-level phylogeny based on hundreds of nuclear markers. (Photo: Krissa Skogen)

Collaborators: Krissa Skogen (lead PI) and Jeremie Fant (Chicago Botanic Garden), Rob Raguso (Cornell), Rachel Levin (Amherst College).

(NSF Award DEB-1342873)

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Diatom Diversification

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 genomic drivers of the phylogenetic and functional diversification of diatoms, a hyperdiverse lineage of photosynthetic microalgae. Transcriptome and genome sequences will be used to reconstruct the timing of horizontal gene transfers and whole-genome duplications to determine whether these events coincide with major diversifications or the origins of important functional traits. (Photo: Andy Alverson)

Collaborator: Andy Alverson (University of Arkansas)

(NSF Award DEB-1353152)

The Beagle Channel. Photo taken from the Chilean island of Navarino, home of the Omora Ethnobotanical Park.

Publications

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 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 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. 2011. 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 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 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.

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.