OneKP companion papers

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


Gane KS Wong, et al. Apr 2020. Sequencing and analyzing the transcriptomes of a thousand species across the tree of life for green plants. Annu. Rev. Plant Biol. 71: 741-765. PMID: 31851546

Zheng Li, Michael Barker. Feb 2020. Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions. GigaScience 9: giaa004. PMID: 32043527

David Bell, ... Sean Graham. Jan 2020. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. Am. J. Bot. 107: 91-115. PMID: 31814117

One Thousand Plant Transcriptomes Initiative. Oct 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574: 679-685. PMID: 31645766

... NEWS & VIEWS by Patrick Wincker. 11 Nov 2019. A thousand plants' phylogeny. Nat. Plants 5: 1106-1107. DOI: 10.1038/s41477-019-0555-0

... IN THE NEWS by Florence Rosier. 29 Oct 2019. Les plantes: une aventure évolutive éclairée par leur ADN. Le Monde

... IN THE NEWS by R Siva Kumar. 28 Oct 2019. Plants diversified from a common ancestor, reveals genetic data of 1,147 species. International Business Times

... IN THE NEWS by Jasmine Demers. 28 Oct 2019. Scientists build road map for 1 billion year evolution of green plants. Arizona Daily Star

... IN THE NEWS by Florida Museum of Natural History. 24 Oct 2019. 1 billion years of evolution illuminated by genetic sequencing of 1,100 plants.

... IN THE NEWS by Bob Weber. 24 Oct 2019. 'Everything is interrelated': Scientists write family tree for tree of life. The Canadian Press

EJ Carpenter, … Gane KS Wong. Oct 2019. Access to RNA-sequencing data from 1173 plant species: The 1000 Plant transcriptomes initiative (1KP). GigaScience 8: giz126. PMID: 31644802

Falicia Goh, ... Neil Clarke. Jul 2019. Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae. Sci. Rep. 9: 10482. PMID: 31324835

Matthew Johnson, Lisa Pokorny, ... Norman Wickett. Jul 2019. A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Syst. Biol. 68: 594-606. PMID: 30535394

Chenchen Zhao, Yuanyuan Wang, Kai Xun Chan, ... Doug Soltis, Barry Pogson, Zhong-Hua Chen. Mar 2019. Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land. Proc. Natl. Acad. Sci. USA. 116: 5015-5020. PMID: 30804180

Guo Wei, Xinlu Chen, … Feng Chen. Feb 2019. Terpene biosynthesis in red algae is catalyzed by microbial type but not typical plant terpene synthases. Plant Physiol. 179: 382-390. PMID: 30538166

Elena Govorunova, ... John Spudich. Jul 2018. Extending the time domain of neuronal silencing with cryptophyte anion channelrhodopsins. eNeuro 5: ENEURO.0174-18.2018. PMID: 30027111

Amanda Lane, ... James Leebens-Mack. May 2018. Phylogenomic analysis of the Ranunculales resolves branching events across the orderBot. J. Linean. Soc. 187: 157-166. DOI: 10.1093/botlinnean/boy015

Jacob Krüger Jensen, ... Jesper Harholt. May 2018. Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesisNew Phytol218: 1049-1060. PMID: 29460505

Sarah Unruh, ..... J. Chris Pires. April 2018.  Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae). Am. J. Bot. 105: 631-640. PMID: 29608785

Matthew Gitzendanner, ... Doug Soltis. Mar 2018. Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. Am. J. Bot. 105: 291-301. PMID: 29603143

Sumanth Mutte, ... Dolf Weijers. Mar 2018. Origin and evolution of the nuclear auxin response systemeLife 7: e33399. PMID: 29580381

Daniel Lang, ... Stefan Rensing. Feb 2018. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. The Plant J. 93: 515-533. PMID: 29237241

Dieter Hackenberg, ... Sona Pandey. Oct 2017. Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytol. 216: 562-575. PMID: 27634188

Katrin Luck, ... Tobias Köllner. Sep 2017. CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the formation of taxiphyllin in Taxus baccata. Plant Mol. Biol. 95: 169-180. PMID: 28795267

Ivana Spasevska, ... Jack Tuszynski. Aug 2017. Modeling the Colchicum autumnale tubulin and a comparison of its interaction with colchicine to human tubulin. Int. J. Mol. Sci. 18: E1676. PMID: 28767055

Rohan Bythell-Douglas, ... Tom Bennett. Jun 2017. Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues. BMC Biol. 15: 52. PMID: 28662667

Kim Johnson, Andrew Cassin, ... Monika Doblin, Carolyn Schultz. Jun 2017. Insights into the evolution of hydroxyproline-rich glycoproteins from 1000 plant transcriptomes. Plant Physiol. 174: 904-921. PMID: 28446636

Choun-Sea Lin, ... Ming-Che Shih. Jun 2017. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant J. 90: 994-1006. PMID: 28258650

Adam Bewick, .... Robert J. Schmitz. June 2017. The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biol. 18: 65. PMID: 28457232

Jing-Dan Han, ... Guang-Yuan Rao. Apr 2017. Evolutionary analysis of the LAFL genes involved in the land plant seed maturation program. Front. Plant Sci. 8: 439. PMID: 28421087

Elena Govorunova, ... John Spudich. Mar 2017. The expanding family of natural anion channelrhodopsins reveals large variations in kinetics, conductance, and spectral sensitivity. Sci. Rep. 7: 43358. PMID: 28256618

Stéphane Bourque, ... David Wendehenne, Valérie Nicolas-Francès. Dec 2016. The evolution of HD2 proteins in green plantsTrends Plant Sci. 21: 1008-1016. PMID: 27789157

Alejandra Vasco, ... Barbara A Ambrose. Nov 2016. Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes. New Phytol. 212: 745-758. PMID: 27385116

Qidong Jia, ... Feng Chen. Oct 2016. Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants. Proc. Natl. Acad. Sci. USA 113: 12328-12333. PMID: 27791023

Aude Maugarny-Calès, Beatriz Gonçalves, ... Patrick Laufs. Sep 2016. Apparition of the NAC transcription factors predates the emergence of land plants. Mol. Plant 9: 1345-1348. PMID: 27302340

Sean Stevenson, ... Andrew Cuming. Jun 2016. Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE, a regulator of ABA responses unique to basal land plants and required for desiccation tolerance. Plant Cell 28: 1310-1327. PMID: 27194706

Pradeep Yerramsetty, ... James Berry. Jun 2016. Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plantsBMC Evol. Biol. 16: 141. PMID: 27356975

Thomas Lane, ... C Neal Stewart Jr. May 2016. Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnol. 16: 47. PMID: 27245738

Matt Stata, ... Rowan Sage. May 2016. Mesophyll chloroplast investment in C3, C4 and C2 species of the genus Flaveria. Plant Cell Physiol. 57: 904-918. PMID: 26985020

Michael McKane,... James Leebens-Mack. Mar 2016. A phylogenomic assessment of ancient polyploidy and genome evolution across the PoalesGenome Biol. Evol. 8: 1150-1164. PMID: 26988252

Spencer T Glantz, ... Brian Y Chow. Mar 2016. Functional and topological diversity of LOV domain photoreceptors. Proc. Natl. Acad. Sci. USA 113: E1442- E1451. 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 Lyu, ... 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. The 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

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 Scott Edmunds. 29 Oct 2014. Uncovering the tangled roots of plant evolutionGigaBlog

... 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. DOI: 10.1086/676675

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

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

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

Steven Kelly, ... Gane KS Wong, Julian Hibberd. Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis.

Ming-Ju Amy Lyu, ... Xin-Guang Zhu. Molecular paths to an evolutionary jump during C4 evolution in the Flaveria genus and the major players.

Draft version Circulated