Endogenous Arabidopsis messenger RNAs transported to distant tissues

[1]  Li Ni,et al.  The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species , 2009, PLoS Comput. Biol..

[2]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[3]  W. Scheible,et al.  MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis , 2008, The Plant journal : for cell and molecular biology.

[4]  Mark Stitt,et al.  Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w] , 2004, Plant Physiology.

[5]  F. Kragler.  RNA in the phloem: A crisis or a return on investment? , 2010 .

[6]  Rainer Hedrich,et al.  Identification of Arabidopsis thaliana phloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments. , 2008, The Plant journal : for cell and molecular biology.

[7]  Daniel Karcher,et al.  Horizontal genome transfer as an asexual path to the formation of new species , 2014, Nature.

[8]  C. dePamphilis,et al.  Genomic-scale exchange of mRNA between a parasitic plant and its hosts , 2014, Science.

[9]  J. Pritchard,et al.  A phloem-enriched cDNA library from Ricinus: insights into phloem function. , 2006, Journal of experimental botany.

[10]  R. Dirks,et al.  Graft-transmissible movement of inverted-repeat-induced siRNA signals into flowers. , 2014, The Plant journal : for cell and molecular biology.

[11]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[12]  Bjarni J. Vilhjálmsson,et al.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines , 2010 .

[13]  Yueyue Yu,et al.  Dynamics of a Mobile RNA of Potato Involved in a Long-Distance Signaling Pathway[W][OA] , 2006, The Plant Cell Online.

[14]  Axel Brennicke,et al.  RNA editing in plants and its evolution. , 2013, Annual review of genetics.

[15]  F. Kragler,et al.  Phloem-mobile signals affecting flowers: applications for crop breeding. , 2013, Trends in plant science.

[16]  J. Mu,et al.  LESION SIMULATING DISEASE1 Interacts with Catalases to Regulate Hypersensitive Cell Death in Arabidopsis1[C][W] , 2013, Plant Physiology.

[17]  Dena Leshkowitz,et al.  Characterization of phloem-sap transcription profile in melon plants , 2007 .

[18]  W. F. Thompson,et al.  Rapid isolation of high molecular weight plant DNA. , 1980, Nucleic acids research.

[19]  W. J. Lucas,et al.  Phloem long-distance trafficking of GIBBERELLIC ACID-INSENSITIVE RNA regulates leaf development. , 2005, The Plant journal : for cell and molecular biology.

[20]  Vincent Colot,et al.  Profiling histone modification patterns in plants using genomic tiling microarrays , 2005, Nature Methods.

[21]  N. Sinha,et al.  Developmental Changes Due to Long-Distance Movement of a Homeobox Fusion Transcript in Tomato , 2001, Science.

[22]  Charles W. Melnyk,et al.  Intercellular and systemic movement of RNA silencing signals , 2011, The EMBO journal.

[23]  T. Harada,et al.  Apple phloem cells contain some mRNAs transported over long distances , 2010, Tree Genetics & Genomes.

[24]  Lior Pachter,et al.  RESEARCH ARTICLE Open Access Identification and correction of systematic error in high-throughput sequence data , 2022 .

[25]  Asan,et al.  The genome of the cucumber, Cucumis sativus L. , 2009, Nature Genetics.

[26]  Xiaodong Bai,et al.  Transcriptomic Signatures of Ash (Fraxinus spp.) Phloem , 2011, PloS one.

[27]  W. J. Lucas,et al.  The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions , 2012, Nature Genetics.

[28]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[29]  W. J. Lucas,et al.  Proteolytic processing of CmPP36, a protein from the cytochrome b5 reductase family, is required for entry into the phloem translocation pathway: Peptide cleavage controls plasmodesmal transport , 2008 .

[30]  K. Oparka,et al.  THE GREAT ESCAPE: Phloem Transport and Unloading of Macromolecules1. , 2000, Annual review of plant physiology and plant molecular biology.

[31]  Mark Stitt,et al.  RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics , 2012, Nucleic Acids Res..

[32]  P. Waterhouse,et al.  Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template-Dependent, Nonvascular, Cell-to-Cell Movement1[W][OA] , 2012, Plant Physiology.

[33]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[34]  W. J. Lucas,et al.  Integrative plant biology: role of phloem long-distance macromolecular trafficking. , 2006, Annual review of plant biology.

[35]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[36]  J. Kehr,et al.  Long distance transport and movement of RNA through the phloem. , 2007, Journal of experimental botany.

[37]  M. Mann,et al.  Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.

[38]  Thomas J. Hardcastle,et al.  Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells , 2010, Science.

[39]  S. Somerville,et al.  A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Karsten M. Borgwardt,et al.  Whole-genome sequencing of multiple Arabidopsis thaliana populations , 2011, Nature Genetics.

[41]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[42]  M. Todesco,et al.  Target mimicry provides a new mechanism for regulation of microRNA activity , 2007, Nature Genetics.

[43]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[44]  Louise Jones,et al.  RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance , 2001, Current Biology.

[45]  W. Schulze,et al.  Metabolic labeling and membrane fractionation for comparative proteomic analysis of Arabidopsis thaliana suspension cell cultures. , 2013, Journal of visualized experiments : JoVE.

[46]  Matthew D. Schultz,et al.  Patterns of Population Epigenomic Diversity , 2013, Nature.