Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha

[1]  P. Bhalla,et al.  Transcriptome-wide profiling and expression analysis of transcription factor families in a liverwort, Marchantia polymorpha , 2013, BMC Genomics.

[2]  D. Wagner,et al.  A molecular framework for auxin-mediated initiation of flower primordia. , 2013, Developmental cell.

[3]  J. Bowman Walkabout on the long branches of plant evolution. , 2013, Current opinion in plant biology.

[4]  Jean-Michel Claverie,et al.  The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation , 2012, Genome Biology.

[5]  Martin Vingron,et al.  Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..

[6]  L. Dolan,et al.  Morphological evolution in land plants: new designs with old genes , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

[7]  T. Sakurai,et al.  In Silico Analysis of Transcription Factor Repertoires and Prediction of Stress-Responsive Transcription Factors from Six Major Gramineae Plants , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[8]  Michael S. Barker,et al.  The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants , 2011, Science.

[9]  E. Grotewold,et al.  Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. , 2011, The Plant journal : for cell and molecular biology.

[10]  Richard M. Clark,et al.  The Arabidopsis lyrata genome sequence and the basis of rapid genome size change , 2011, Nature Genetics.

[11]  Fatih Ozsolak,et al.  RNA sequencing: advances, challenges and opportunities , 2011, Nature Reviews Genetics.

[12]  Akhilesh K. Tyagi,et al.  De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[13]  E. Scarpella,et al.  Simultaneous activation of SHR and ATHB8 expression defines switch to preprocambial cell state in Arabidopsis leaf development , 2011, Developmental dynamics : an official publication of the American Association of Anatomists.

[14]  Liang Tang,et al.  PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database , 2010, Nucleic Acids Res..

[15]  Jean-Michel Claverie,et al.  The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex[C][W] , 2010, Plant Cell.

[16]  B. Mueller‐Roeber,et al.  Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity , 2010, Genome biology and evolution.

[17]  D. Robertson,et al.  Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae1[W] , 2010, Plant Physiology.

[18]  H. Saedler,et al.  MIKC* MADS-box proteins: conserved regulators of the gametophytic generation of land plants. , 2010, Molecular biology and evolution.

[19]  L. Dolan,et al.  Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants , 2009, Molecular biology and evolution.

[20]  Birgit Kersten,et al.  PlnTFDB: updated content and new features of the plant transcription factor database , 2009, Nucleic Acids Res..

[21]  He Zhang,et al.  Computational identification of plant transcription factors and the construction of the PlantTFDB database. , 2010, Methods in molecular biology.

[22]  C. Delwiche,et al.  Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes , 2010, BMC Plant Biology.

[23]  C. Airoldi Determination of sexual organ development , 2010, Sexual Plant Reproduction.

[24]  J. Chris Pires,et al.  Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes , 2009, Chromosome Research.

[25]  S. Chen,et al.  Soybean Trihelix Transcription Factors GmGT-2A and GmGT-2B Improve Plant Tolerance to Abiotic Stresses in Transgenic Arabidopsis , 2009, PloS one.

[26]  T. Wada,et al.  The Trihelix Transcription Factor GTL1 Regulates Ploidy-Dependent Cell Growth in the Arabidopsis Trichome[W][OA] , 2009, The Plant Cell Online.

[27]  A. Salamov,et al.  Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas , 2009, Science.

[28]  Xiang Li,et al.  Repression of Seed Maturation Genes by a Trihelix Transcriptional Repressor in Arabidopsis Seedlings[W] , 2009, The Plant Cell Online.

[29]  T. Joshi,et al.  Update on Legume Transcription Factors Legume Transcription Factor Genes: What Makes Legumes So Special? , 2009 .

[30]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[31]  Felipe F. Aceituno,et al.  The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana , 2008, BMC Genomics.

[32]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[33]  U. Goodenough,et al.  Early Sexual Origins of Homeoprotein Heterodimerization and Evolution of the Plant KNOX/BELL Family , 2008, Cell.

[34]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[35]  J. Bennetzen,et al.  The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , 2008, Science.

[36]  Xin Chen,et al.  PlantTFDB: a comprehensive plant transcription factor database , 2007, Nucleic Acids Res..

[37]  Rongcheng Lin,et al.  Transposase-Derived Transcription Factors Regulate Light Signaling in Arabidopsis , 2007, Science.

[38]  B. Shuai,et al.  LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins , 2007, Nucleic acids research.

[39]  Nicholas H. Putnam,et al.  The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation , 2007, Proceedings of the National Academy of Sciences.

[40]  John L. Bowman,et al.  Green Genes—Comparative Genomics of the Green Branch of Life , 2007, Cell.

[41]  N. Rajewsky,et al.  The evolution of gene regulation by transcription factors and microRNAs , 2007, Nature Reviews Genetics.

[42]  N. R. Friedman,et al.  The VARL Gene Family and the Evolutionary Origins of the Master Cell-Type Regulatory Gene, regA, in Volvox carteri , 2007, Journal of Molecular Evolution.

[43]  Ingo Dreyer,et al.  PlnTFDB: an integrative plant transcription factor database , 2007, BMC Bioinformatics.

[44]  Dirk Inzé,et al.  Cell cycle regulation in plant development. , 2006, Annual review of genetics.

[45]  L. Forrest,et al.  Unraveling the evolutionary history of the liverworts (Marchantiophyta): multiple taxa, genomes and analyses , 2006 .

[46]  B. De Baets,et al.  Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Brian C. Thomas,et al.  Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. , 2006, Genome research.

[48]  Leah Barrera,et al.  The transcriptional regulatory code of eukaryotic cells--insights from genome-wide analysis of chromatin organization and transcription factor binding. , 2006, Current opinion in cell biology.

[49]  J. Bowman,et al.  Evolution of Class III Homeodomain–Leucine Zipper Genes in Streptophytes , 2006, Genetics.

[50]  S. Piippo,et al.  Illuminating the evolutionary history of liverworts (Marchantiophyta)—towards a natural classification , 2006, Cladistics : the international journal of the Willi Hennig Society.

[51]  M. Bienz The PHD finger, a nuclear protein-interaction domain. , 2006, Trends in biochemical sciences.

[52]  D. Moreira,et al.  Global dispersal and ancient cryptic species in the smallest marine eukaryotes. , 2006, Molecular biology and evolution.

[53]  Wen-Hsiung Li,et al.  Transcription Factor Families Have Much Higher Expansion Rates in Plants than in Animals1 , 2005, Plant Physiology.

[54]  Klaus Richter,et al.  A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[55]  J. Fletcher,et al.  ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis , 2005, Development.

[56]  G. Theißen,et al.  Characterization of MADS-box genes in charophycean green algae and its implication for the evolution of MADS-box genes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Addie Nina Olsen,et al.  NAC transcription factors: structurally distinct, functionally diverse. , 2005, Trends in plant science.

[58]  Keiji Nishida,et al.  Cyanidioschyzon merolae Genome. A Tool for Facilitating Comparable Studies on Organelle Biogenesis in Photosynthetic Eukaryotes1[w] , 2005, Plant Physiology.

[59]  Felix Grewe,et al.  Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants. , 2004, Molecular biology and evolution.

[60]  P. Brewer,et al.  PETAL LOSS, a trihelix transcription factor gene, regulates perianth architecture in the Arabidopsis flower , 2004, Development.

[61]  Nobutaka Mitsuda,et al.  VOZ; isolation and characterization of novel vascular plant transcription factors with a one-zinc finger from Arabidopsis thaliana. , 2004, Plant & cell physiology.

[62]  Pamela J Green,et al.  Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? , 2004, Genome Biology.

[63]  A. Weber,et al.  EST-analysis of the thermo-acidophilic red microalga Galdieriasulphuraria reveals potential for lipid A biosynthesis and unveils the pathway of carbon export from rhodoplasts , 2004, Plant Molecular Biology.

[64]  Cordelia Bolle,et al.  The role of GRAS proteins in plant signal transduction and development , 2004, Planta.

[65]  E. Liscum,et al.  Genetics of Aux/IAA and ARF action in plant growth and development , 2002, Plant Molecular Biology.

[66]  H. Fredericq,et al.  Red (R), Far-red (FR) photoreversible control of growth and chlorophyll content in light-grown thalli ofMarchantia polymorpha L. , 1966, Naturwissenschaften.

[67]  J. Kim,et al.  The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. , 2003, The Plant journal : for cell and molecular biology.

[68]  C. Wellman,et al.  Fragments of the earliest land plants , 2003, Nature.

[69]  R. Tjian,et al.  Transcription regulation and animal diversity , 2003, Nature.

[70]  W. Atchley,et al.  Phylogenetic Analysis of Plant Basic Helix-Loop-Helix Proteins , 2003, Journal of Molecular Evolution.

[71]  William McGinnis,et al.  Evolution of transcription factor function. , 2003, Current opinion in genetics & development.

[72]  R. Marmorstein Structure of SET domain proteins: a new twist on histone methylation. , 2003, Trends in biochemical sciences.

[73]  E. Grotewold,et al.  Recently Duplicated Maize R2R3 Myb Genes Provide Evidence for Distinct Mechanisms of Evolutionary Divergence after Duplication1 , 2003, Plant Physiology.

[74]  S. Beckert,et al.  Divergent Intron Conservation in the Mitochondrial nad2 Gene: Signatures for the Three Bryophyte Classes (Mosses, Liverworts, and Hornworts) and the Lycophytes , 2002, Journal of Molecular Evolution.

[75]  E. Koonin,et al.  The role of lineage-specific gene family expansion in the evolution of eukaryotes. , 2002, Genome research.

[76]  D. Bouchez,et al.  A Novel Family of Calmodulin-binding Transcription Activators in Multicellular Organisms* , 2002, The Journal of Biological Chemistry.

[77]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[78]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[79]  R. Copley,et al.  DDT -- a novel domain in different transcription and chromosome remodeling factors. , 2001, Trends in biochemical sciences.

[80]  S. Carroll Chance and necessity: the evolution of morphological complexity and diversity , 2001, Nature.

[81]  R. R. Samaha,et al.  Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. , 2000, Science.

[82]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[83]  Z. Liu,et al.  LEUNIG, a putative transcriptional corepressor that regulates AGAMOUS expression during flower development. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[84]  H. Saedler,et al.  MADS-Box gene diversity in seed plants 300 million years ago. , 2000, Molecular biology and evolution.

[85]  T. Eulgem,et al.  The WRKY superfamily of plant transcription factors. , 2000, Trends in plant science.

[86]  J. Bowman,et al.  The YABBY gene family and abaxial cell fate. , 2000, Current opinion in plant biology.

[87]  I. Winicov Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa , 2000, Planta.

[88]  M. Takemura,et al.  Characterization of a Novel Gene Encoding a Putative Single Zinc-finger Protein, ZIM, Expressed during the Reproductive Phase in Arabidopsis thaliana , 2000, Bioscience, biotechnology, and biochemistry.

[89]  H. Kranz,et al.  c-MYB oncogene-like genes encoding three MYB repeats occur in all major plant lineages. , 2000, The Plant journal : for cell and molecular biology.

[90]  Claudia Kappen,et al.  The Homeodomain: An Ancient Evolutionary Motif in Animals and Plants , 2000, Comput. Chem..

[91]  K. Yamato,et al.  Comparison of expressed sequence tags from male and female sexual organs of Marchantia polymorpha. , 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

[92]  P. Sieber,et al.  Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[93]  E. Grotewold,et al.  Maize R2R3 Myb genes: Sequence analysis reveals amplification in the higher plants. , 1999, Genetics.

[94]  B. Snel,et al.  Domains in plexins: links to integrins and transcription factors. , 1999, Trends in biochemical sciences.

[95]  T. MacRae,et al.  Transcription factors and their genes in higher plants functional domains, evolution and regulation. , 1999, European journal of biochemistry.

[96]  G. Angenent,et al.  Arabidopsis STERILE APETALA, a multifunctional gene regulating inflorescence, flower, and ovule development. , 1999, Genes & development.

[97]  I. Capesius,et al.  Plant Mitochondrial RNA Editing , 1999, Journal of Molecular Evolution.

[98]  K. Yamato,et al.  Expressed sequence tags from immature female sexual organ of a liverwort, Marchantia polymorpha. , 1999, DNA research : an international journal for rapid publication of reports on genes and genomes.

[99]  J. Ecker,et al.  Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. , 1998, Genes & development.

[100]  D. Weigel,et al.  A genetic framework for floral patterning , 1998, Nature.

[101]  Yangrae Cho,et al.  The gain of three mitochondrial introns identifies liverworts as the earliest land plants , 1998, Nature.

[102]  G. Hagen,et al.  The ARF family of transcription factors and their role in plant hormone-responsive transcription , 1998, Cellular and Molecular Life Sciences CMLS.

[103]  E. Meyerowitz,et al.  The AP2/EREBP family of plant transcription factors. , 1998, Biological chemistry.

[104]  M. Van Montagu,et al.  The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[105]  Peter R. Crane,et al.  The origin and early evolution of plants on land , 1997, Nature.

[106]  C. Martin,et al.  MYB transcription factors in plants. , 1997, Trends in genetics : TIG.

[107]  J. Lipsick One billion years of Myb. , 1996, Oncogene.

[108]  M. Purugganan,et al.  Molecular evolution of flower development: diversification of the plant MADS-box regulatory gene family. , 1995, Genetics.

[109]  F. Katagiri,et al.  Plant transcription factors: present knowledge and future challenges. , 1992, Trends in genetics : TIG.

[110]  F. Wann SOME OF THE FACTORS INVOLVED IN THE SEXUAL REPRODUCTION OF MARCHANTIA POLYMORPHA , 1925 .