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

Published

Sandra K Floyd, ... John L Bowman. [Epub ahead of print] Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Mol. Phylogenet. Evol. PMID: 25263420.

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. Jun 2014. Horizontal gene transfer: accidental inheritance drives adaptationCurr Biol. 24: R562-R564. PMID: 24937281

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

... 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 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 Office.

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

... PERSPECTIVE by Jeffery Kovach, Rebecca Lamb. 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

Norman J Wickett, ... Gane KS Wong, Jim Leebens-Mack. A phylotranscriptomics analysis of the origin and early diversification of land plants.

Naim Matasci, ... Jim Leebens-Mack, Gane KS Wong. Data access for the 1,000 Plants (1KP) project.

In Review

Megan M Augustin, … Toni M Kutchan. Accelerating biochemical pathway elucidation in non-model systems: formation of the antineoplastic cyclopamine in Veratrum californicum.

Steven B Cannon, ... Jim Leebens-Mack. Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes.

Ya Yang, ... Stephen Smith. Dissecting molecular evolution in a hyperdiverse plant clade using transcriptome sequencing.

Jesse D Hollister, ... Stephen I Wright, Marc TJ Johnson. Recurrent loss of sex drives deleterious mutation accumulation in Oenothera.

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

Ming-Ju Amy Lv, ... Xin-Guang Zhu. RNA-Seq based reconstruction of the phylogenetic tree of the genus Flaveria (Asteraceae).

Ming-Che Shih, ... Choun-Sea Lin. The locations of ndh genes of chloroplast origin in the Orchidaceae family.

Huizi Duan-Mu, ... Yanming Zhu. Gene expression profiling of wild soybean roots under alkaline stress.

Draft awaiting comments

Tracey Ruhlman, ... Choun-Sea Lin. Coordinate loss of plastid and nuclear expression of NDH proteins across the seed plant phylogeny.

  


   

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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