TY  - JOUR
A1  - Read, Betsy A.
A1  - Kegel, Jessica
A1  - Klute, Mary J.
A1  - Kuo, Alan
A1  - Lefebvre, Stephane C.
A1  - Maumus, Florian
A1  - Mayer, Christoph
A1  - Miller, John
A1  - Monier, Adam
A1  - Salamov, Asaf
A1  - Young, Jeremy
A1  - Aguilar, Maria
A1  - Claverie, Jean-Michel
A1  - Frickenhaus, Stephan
A1  - Gonzalez, Karina
A1  - Herman, Emily K.
A1  - Lin, Yao-Cheng
A1  - Napier, Johnathan
A1  - Ogata, Hiroyuki
A1  - Sarno, Analissa F.
A1  - Shmutz, Jeremy
A1  - Schroeder, Declan
A1  - de Vargas, Colomban
A1  - Verret, Frederic
A1  - von Dassow, Peter
A1  - Valentin, Klaus
A1  - Van de Peer, Yves
A1  - Wheeler, Glen
A1  - Dacks, Joel B.
A1  - Delwiche, Charles F.
A1  - Dyhrman, Sonya T.
A1  - Glöckner, Gernot
A1  - John, Uwe
A1  - Richards, Thomas
A1  - Worden, Alexandra Z.
A1  - Zhang, Xiaoyu
A1  - Grigoriev, Igor V.
A1  - Allen, Andrew E.
A1  - Bidle, Kay
A1  - Borodovsky, M.
A1  - Bowler, C.
A1  - Brownlee, Colin
A1  - Cock, J. Mark
A1  - Elias, Marek
A1  - Gladyshev, Vadim N.
A1  - Groth, Marco
A1  - Guda, Chittibabu
A1  - Hadaegh, Ahmad
A1  - Iglesias-Rodriguez, Maria Debora
A1  - Jenkins, J.
A1  - Jones, Bethan M.
A1  - Lawson, Tracy
A1  - Leese, Florian
A1  - Lindquist, Erika
A1  - Lobanov, Alexei
A1  - Lomsadze, Alexandre
A1  - Malik, Shehre-Banoo
A1  - Marsh, Mary E.
A1  - Mackinder, Luke
A1  - Mock, Thomas
A1  - Müller-Röber, Bernd
A1  - Pagarete, Antonio
A1  - Parker, Micaela
A1  - Probert, Ian
A1  - Quesneville, Hadi
A1  - Raines, Christine
A1  - Rensing, Stefan A.
A1  - Riano-Pachon, Diego Mauricio
A1  - Richier, Sophie
A1  - Rokitta, Sebastian
A1  - Shiraiwa, Yoshihiro
A1  - Soanes, Darren M.
A1  - van der Giezen, Mark
A1  - Wahlund, Thomas M.
A1  - Williams, Bryony
A1  - Wilson, Willie
A1  - Wolfe, Gordon
A1  - Wurch, Louie L.
T1  - Pan genome of the phytoplankton Emiliania underpins its global distribution
JF  - Nature : the international weekly journal of science
N2  - Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
Y1  - 2013
U6  - https://doi.org/10.1038/nature12221
SN  - 0028-0836
SN  - 1476-4687
VL  - 499
IS  - 7457
SP  - 209
EP  - 213
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Riano-Pachon, Diego Mauricio
A1  - Dreyer, Ingo
A1  - Müller-Röber, Bernd
T1  - Orphan transcripts in Arabidopsis thaliana : identification of several hundred previously unrecognized genes
N2  - Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome
Y1  - 2005
SN  - 0960-7412
ER  - 
TY  - GEN
A1  - Riano-Pachon, Diego Mauricio
A1  - Nagel, Axel
A1  - Neigenfind, Jost
A1  - Wagner, Robert
A1  - Basekow, Rico
A1  - Weber, Elke
A1  - Müller-Röber, Bernd
A1  - Diehl, Svenja
A1  - Kersten, Birgit
T1  - GabiPD : the GABI primary database - a plant integrative "omics" database
N2  - The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 137 
KW  - Phosphorylation sites
KW  - Arabidopsis thaliana
KW  - Information
KW  - Proteins
KW  - Families
Y1  - 2009
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45075
ER  - 
TY  - JOUR
A1  - Rohrmann, Johannes
A1  - Tohge, Takayuki
A1  - Alba, Rob
A1  - Osorio, Sonia
A1  - Caldana, Camila
A1  - McQuinn, Ryan
A1  - Arvidsson, Samuel Janne
A1  - van der Merwe, Margaretha J.
A1  - Riano-Pachon, Diego Mauricio
A1  - Müller-Röber, Bernd
A1  - Fei, Zhangjun
A1  - Nesi, Adriano Nunes
A1  - Giovannoni, James J.
A1  - Fernie, Alisdair
T1  - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development
JF  - The plant journal
N2  - Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.
KW  - transcription factor
KW  - Solanum lycopersicum
KW  - quantitative RT-PCR
KW  - microarray
KW  - metabolomics
KW  - fleshy fruit ripening
Y1  - 2011
U6  - https://doi.org/10.1111/j.1365-313X.2011.04750.x
SN  - 0960-7412
VL  - 68
IS  - 6
SP  - 999
EP  - 1013
PB  - Wiley-Blackwell
CY  - Malden
ER  -