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The following are oneKP papers that have been written and are in varying stages of review or publication.



Matt Stata,... Rowan Sage. [Epub ahead of print] Mesophyll chloroplast investment in C3, C4 and C2 species of the genus Flaveria. Plant Cell Physiol. PMID: 26985020

Spencer T Glantz, ... Brian Y Chow. [Epub ahead of print] Functional and topological diversity of LOV domain photoreceptorsProc. Natl. Acad. Sci. USA. PMID: 26929367

Sylvain Jeandroz, ... David Wendehenne. Mar 2016. Occurrence, structure, and evolution of nitric oxide synthase-like proteins in the plant kingdom. Sci. Signal. 9: re2. PMID: 26933064

Roland Hellinger, ... Christian Gruber. Nov 2015. Peptidomics of circular cysteine-rich plant peptides: Analysis of the diversity of cyclotides from Viola tricolor by transcriptome and proteome mining. J. Proteome Res. 14: 4851-4862. PMID: 26399495

Huizi Duan-Mu, ... Yanming Zhu. Nov 2105. Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress. Funct. Integr. Genomics 15: 651-660. PMID: 25874911

Pierre-Marc Delaux, ... Jean-Michel Ané. Oct 2015. Algal ancestor of land plants was preadapted for symbiosis. Proc. Natl. Acad. Sci. USA 112: 13390-13395. PMID: 26438870

... IN THE NEWS by Staff Writer. 5 Oct 2015. Ancient alga knew how to survive on land before it left water and evolved into the first plantScienceDaily.

Samuel Brockington, ... Stephen Smith. Sep 2015. Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales. New Phytol. 207: 1170-1180. PMID: 25966996

Fay-Wei Li, ... Sarah Mathews, Kathleen M. Pryer. Aug 2015. The origin and evolution of phototropins. Front. Plant Sci. 6: 637. PMID: 26322073

Ya Yang, ... Stephen Smith. Aug 2015.Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Mol. Biol. Evol. 32: 2001-2014. PMID: 25837578

Fay-Wei Li, ... Kathleen M. Pryer, Sarah Mathews. Jul 2015. Phytochrome diversity in green plants and the origin of canonical plant phytochromes. Nat. Commun. 6: 7852. PMID: 26215968

... IN THE NEWS by Staff Writer. 28 Jul 2015. Plants inherited ability to sense red light from ancient algae.

Carl J Rothfels, ... Kathleen M Pryer. Jul 2015. The evolutionary history of ferns inferred from 25 low-copy nuclear genesAm. J. Bot. 102: 1089-1107. PMID: 26199366

Ming-Ju Amy Lv, ... Xin-Guang Zhu. Jun 2015. RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evol. Biol. 15: 116. PMID: 26084484

Megan M Augustin, … Toni M Kutchan. Jun 2015. Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells. Plant J. 82: 991-1003. PMID: 25939370

Burkhard Becker, ... Michael Melkonian. Jun 2015. The origin and evolution of the plant cell surface: algal integrin-associated proteins and a new family of integrin-like cytoskeleton-ECM linker proteins. Genome Biol. Evol. 7: 1580-1589. PMID: 25977459

Jesse D Hollister, ... Stephen I Wright, Marc TJ Johnson. Apr 2015. Recurrent loss of sex is associated with accumulation of deleterious mutations in OenotheraMol. Biol. Evol. 32: 896-905, PMID: 25534028

... IN THE NEWS by Elaine Smith. 12 Jan 2015. Research affirms sexual reproduction avoids harmful mutations.

Choun-Sea Lin, ... Ming-Che Shih. Mar 2015. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Sci. Rep. 5: 9040. PMID: 25761566

Steven B Cannon, ... James Leebens-Mack. Jan 2015. Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumesMol. Biol. Evol. 32: 193-210. PMID: 25349287

Sandra K Floyd, ... John L Bowman. Dec 2014. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Mol. Phylogenet. Evol. 81: 159-173. PMID: 25263420

Norman J Wickett, ... Gane KS Wong, Jim Leebens-Mack. Nov 2014. Phylotranscriptomic analysis of the origin and early diversification of land plantsProc. Natl. Acad. Sci. USA 111: E4859-E4868. PMID: 25355905

... IN THE NEWS by Bill Mah. 4 Nov 2104. World’s largest plant DNA project at University of Alberta starting to sprout new discoveriesEdmonton Journal.

... IN THE NEWS by Jim Erickson. 28 Nov 2014. A look back in time at key events in plant evolution. R&D Magazine.

... IN THE NEWS by James Hataway and Shelley Littin. 28 Oct 2014. Research uses DNA to study key events in plant evolutionUA News.

Naim Matasci, ... Jim Leebens-Mack, Gane KS Wong. Oct 2014. Data access for the 1,000 Plants (1KP) projectGigaScience 3: 17. PMID: 25625010

Daniel R Hochbaum, Yongxin Zhao, ... Adam E Cohen. Aug 2014. All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nat. Methods 11: 825-833. PMID: 24952910

Tom Bennett, ... C Jill Harrison. Aug 2014. Paralogous radiations of PIN proteins with multiple origins of noncanonical PIN structure. Mol. Biol. Evol. 31: 2042-2060. PMID: 24758777

Vitor H Maia, ... Douglas E Soltis. Jul/Aug 2014. Angiosperm phylogeny based on 18S/26S rDNA sequence data: Constructing a large data set using next-generation sequence dataInt. J. Plant Sci. 175: 613-650. PMID: unavailable

Pascal-Antoine Christin, ... Erika J Edwards. Jul  2014. Shared origins of a key enzyme during the evolution of C4 and CAM metabolism. J. Exp. Bot. 65: 3609-3621. PMID: 24638902

Natalia Pabón-Mora, ... Barbara A Ambrose. Jun 2014. Evolution of fruit development genes in flowering plants. Front. Plant Sci. 5: 300. PMID: 25018763

Yinlong Xie, ... Gane KS Wong, Jun Wang. Jun 2014. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30: 1660-1666. PMID: 24532719

Goro Tanifuji, ... John M Archibald. May 2014. Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algaeBMC Genomics 15: 374. PMID: 24885563

Fay-Wei Li, ... Sarah Mathews, Kathleen M Pryer. May 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc. Natl. Acad. Sci. USA 111: 6672-6677. PMID: 24733898

... DISPATCH by Endymion Cooper. 16 Jun 2014. Horizontal gene transfer: accidental inheritance drives adaptationCurr Biol. 24: R562-R564. PMID: 24937281

... RESEARCH HIGHLIGHT by Bryony Jones. 29 Apr 2014. Evolution: Planting genes. Nat. Rev. Genet. 15: 362-362. PMID: 24776772

... IN THE NEWS by Jennifer Huizen. 15 Jul 2015. Can the Fern That Cooled the Planet Do It Again? Scientific American.

... IN THE NEWS by Jennifer Frazer. 6 May 2014. In darkened forests, ferns stole gene from an unlikely source — and then from each otherScientific American.

... IN THE NEWS by Geoffrey Carr. 19 Apr 2014. Fern evolution: Time and chance. The survival of ferns to the present depended on an ancient accidentEconomist.

... IN THE NEWS by Carl Zimmer. 17 Apr 2014. Plants that practice genetic engineeringNew York Times.

... IN THE NEWS by Ed Yong. 14 Apr 2014. Genetic gift may have turned ferns into masters of shadowNational Geographic.

... IN THE NEWS by Vijay Shankar Balakrishnan. 14 Apr 2014. Hornworts loan genes to ferns for shady environments. Decoded Science.

Saemundur Sveinsson, ... Quentin CB Cronk. Apr 2014. Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. Ann. Bot. 113: 753-761. PMID: 24380843

Nathan C Klapoetke, ... Gane KS Wong, Edward S Boyden. Mar 2014. Independent optical excitation of distinct neural populationNat. Methods 11: 338-346. PMID: 24509633

... IN THE NEWS by Carolyn Beans and Chidinma Okparanta. 23 Dec 2014. Using lights to illuminate biology: Lighting up brain cells. LiveScience.

... IN THE NEWS by Anne Trafton. 9 Feb 2014. Optogenetic toolkit goes multicolor. New light-sensitive proteins allow scientists to study how multiple sets of neurons interact with each other. MIT News.

Camille Sayou, ... Francois Parcy, Renaud Dumas. Feb 2014. A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificityScience 343: 645-648. PMID: 24436181

... 6 Feb 2015. Comment on “A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity” by Jacob Brunkard, et al. Science 347: 621. PMID: 25657240

... 6 Feb 2015. Response to Comment on “A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity” by Samuel Brockington, et al. Science 347: 621. PMID: 25657241

... PERSPECTIVE by Jeffery Kovach, Rebecca Lamb. 7 Feb 2014. Evolution: There can be only oneScience 343: 623-624. PMID: 24503845

Carl J Rothfels, ... Kathleen M Pryer. Oct 2013. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One 8: e76957. PMID: 24116189

Johannes Koehbach, ... Christian W Gruber. Sep 2013. Cyclotide discovery in Gentianales revisited - identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plantsBiopolymers 100: 438-452. PMID: 23897543

Xinshuai Qi, André S Chanderbali, ... Pamela S Soltis. Jul 2013. Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants. BMC Evol. Biol. 13: 143. PMID: 23834366

Marc TJ Johnson, ... Gane KS Wong. Nov 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 7: e50226. PMID: 23185583

Jack A Tuszynski, ... Gane KS Wong. Nov 2012. Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin. Pharm. Res. 29: 3007-3021. PMID: 22833053

Yuannian Jiao, ... Claude W dePamphilis. Jan 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 13: R3. PMID: 22280555


Accepted for Publication


In Review

Sean Stevenson, ... Andrew Cuming. Forward genetics in Physcomitrella identifies an ABA response regulator unique to basal land plants, required for desiccation tolerance.

Alejandra Vasco, ... Barbara A Ambrose. Challenging the paradigms of leaf evolution: Class III HD-Zip expression in ferns and lycophytes.

Pradeep Yerramsetty, ... James Berry. Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants.

Dieter Hackenberg, ... Sona Pandey. Lost and found? The contradictory evolution of heterotrimeric Gα proteins and their regulatory RGS proteins in the plant lineage.

Thomas Lane, ... C Neal Stewart Jr. Distribution of ABC transporter genes across the plant kingdom


Draft version Circulated

Qidong Jia, ... Feng Chen. Microbial type terpene synthase genes occur widely and specifically in nonseed plants.

Aude Maugarny, Beatriz Gonçalves, ... Patrick Laufs. Apparition of the NAC transcription factors predates the emergence of land plants.

Ming-Ju Amy Lyu, ... Xin-Guang Zhu. Comparative transcriptomics study reveals two distinct phases of C4 evolution.

Stéphane Bourque, ... David Wendehenne, Valérie Nicolas-Francès. Type-2 HDACs: their evolution through the plant kingdom.

Amanda Lane, ... James Leebens-Mack. Phylogenomics of the Ranunculales with resolution of the Papaveraceae.




To give a flavour of what else is to come the following is a (somewhat outdated) list of research projects.

Note also that each of the gene family experts (see capstone paper) is likely to publish their own paper.

Species Tree Estimation by Phylogenomics

Pilot Project/Deep Green - Lead Jim Leebens-Mack (University of Georgia): About 100 1kp transcriptome assemblies were used to estimate streptophyte relationships. This project - as described on a separate wiki page -  aims to develop phylogenomic analysis pipelines and assess the scalability of these pipelines while at the same time testing hypothesized relationships among streptophytic algal lineages and land plants. Results of the supermatrix and supertree analyses are also providing insights into bryophyte and seed plant relationships. Lead authors Norm Wickett (Chicago Botanic Garden) and Siavash Mirarab and Nam Nguyen (Warnow Lab, University of Texas)have competed analyses on the TACC cluster. Data submission to NCBI under way.  Manuscript draft circulating, to be submitted this summer (2013).

1KP-Wide Plastome Analysis - Leads Brad Ruhfel (Eastern Kentucky University), Matt Gitzendanner (Soltis Lab, University of Florida), and Gordon Burleigh (University of Florida)

1KP-Wide Mitochondrial Analysis - Leads Brad Ruhfel (Eastern Kentucky University), Stull et al. (Soltis Lab, University of Florida) 

Seed Plant Relationships - Leads Sarah Mathews (Harvard), Sean Graham (University of British Columbia), and Dennis Stevenson (New York Botanical Gardens)

Origin and early diversification of the viridiplantae - Lead Michael Melkonian (University of Cologne)

Genome Evolution in Phylogenetic Context

Testing Relationship between Polyploidy and Diversification in Angiosperm History - Lead Doug Soltis (University of Florida)

Testing Relationship between Polyploidy and the Origin of Nodulation in Legumes - Lead Steve Cannon (USDA, Iowa State): Gene tree estimation and analysis by Alex Harkess (Leebens-Mack Lab, University of Georgia). Analyses mostly completed, manuscript started, submission early fall of 2013. 

Inferring the timing of the Rho and Sigma Whole Genome Duplication events within the Poales - Lead Jim Leebens-Mack (University of Georgia): Transcriptome data generated through the Monocot AToL project is being combined with 1kp transcriptomes generated for species within the Poales to resolve the timing of the Rho and Sigma paleopolyploidy events that have been identified in synteny analyses of the rice and sorghum genomes. Gene tree estimation and analysis by Michael McKain (Leebens-Mack Lab, University of Georgia). Work completed for Michael McKain's dissertation.  Manuscript to be submitted by end of summer, 2013.

Assessing the timing of genome duplications and diversification in the Brassicales - Lead J-Chris Pires (University of Missouri)

Biological Innovations 

Life history shift within land plants from dominant gametophyte to dominant sporophyte phases - Lead Sean Graham (University of British Columbia)

Morphological and anatomical transformations - Lead Dennis Stevenson (New York Botanical Gardens): focused on GO terms and similar

Evolution without Photosynthesis - Claude dePamphilis (Penn State University) using subet of 1KP from parasitic and mycotrophic species

C3/C4 transitions within the Asteraceae genus Flaveria - Leads Julian Hibberd (University of Cambridge) and Xinguang Zhu (CAS-MPG Partner Institute for Computational Biology)

Comparative analysis of C3 and C4 transcriptomes across diverse angiosperm lineages - Lead Julian Hibberd (University of Cambridge)

Alkaloid Biosynthesis - Lead Toni Kutchan (Danforth Plant Science Center): Comparative analysis of alkaloid biosynthesis pathways across the poppy family. John Kerry (Leebens-Mack Lab, University of Georgia) is currently analyzing data.

Multiple origins of cryophilic chlorophytes - Leads Ron Hoham (Colgate University), Jim Leebens-Mack (University of Georgia), and Michael Melkonian (University of Cologne)

Carbohydrate metabolism of brown and red algae - Leads Shaungxiu Wu and Jun Yu (Chinese Academy of Sciences and Beijing Institute of Genomics)

Algal metabolism (not necessarily restricted to lipids) - Lead Neil Clarke (Genome Institute of Singapore)

Gene Interactions and Regulatory Networks

Chromatin proteome - Lead Rich Jorgensen (LANGEBIO-CINVESTAV)

Phosphorus signaling - Leads Patrick Finnegan, Ricarda Jost, et al. (University of Western Australia)

DNA recognition motifs - Lead Neal Stewart (University of Tennessee)

Ecological Genomics

Extremophyte species - Lead Neal Stewart (University of Tennessee)

Mechanisms of salt tolerance - Leads Michael Deyholos (University of Alberta), Hans Bohnert and John Cheeseman (University of Illinois)

Morning glories as a model for weedy/invasive plants - Leads Gina Baucom (University of Cincinnati) and John Stinchcombe (University of Toronto)

Genomics of sexual recombination and segregation - Lead Marc Johnson (University of Toronto at Mississauga)

Landscape phenomics - Lead Andrew Lowe (University of Adelaide)

Population genomics of cycads and their cyanobacteria - Lead Angelica Cibrian (LANGEBIO-CINVESTAV)

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