EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods

Firnhaber C, Pühler A, Küster H (2005)
Planta 222(2): 269-283.

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To evaluate the molecular mechanisms during pod and seed formation in legumes, starting with the development of reproductive organs, we constructed two cDNA libraries from developing flowers (MtFLOW) and pods including seeds (MtPOSE) of the model plant Medicago truncatula Gaertner. A total of 2,516 expressed sequence tags (ESTs) clustered into 1,776 non-redundant sequences (2k-set), which were annotated and assigned to functional classes. While about 30% of the ESTs encoded proteins of yet unknown function, typical annotations pointed to seed storage proteins, LTPs and lipoxygenases. The 2k-set was used to upgrade Mt6k-RIT microarrays (Kuster et al. in J Biotechnol 108: 95, 2004) to Mt8k versions representing approximately 6,300 nonredundant M. truncatula genes. These were used to perform time course expression profiling studies based on hybridizations of samples that covered eight different developmental stages from flower buds to almost mature pods versus leaves as a common reference. About 180 up- and 70 downregulated genes were typically found for each stage and in total, 782 genes were either twofold up- or downregulated in at least one of the eight stages investigated. Based on this set, a combination of self-organizing map and hierarchical clustering revealed genes displaying expression regulation during characteristic stages of M. truncatula flower and pod development. Amongst those, several genes encoded proteins related to seed metabolism and development including novel regulators and proteins involved in signaling.
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Planta
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222
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2
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269-283
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Firnhaber C, Pühler A, Küster H. EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta. 2005;222(2):269-283.
Firnhaber, C., Pühler, A., & Küster, H. (2005). EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta, 222(2), 269-283. doi:10.1007/s00425-005-1543-3
Firnhaber, C., Pühler, A., and Küster, H. (2005). EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta 222, 269-283.
Firnhaber, C., Pühler, A., & Küster, H., 2005. EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta, 222(2), p 269-283.
C. Firnhaber, A. Pühler, and H. Küster, “EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods”, Planta, vol. 222, 2005, pp. 269-283.
Firnhaber, C., Pühler, A., Küster, H.: EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods. Planta. 222, 269-283 (2005).
Firnhaber, Christian, Pühler, Alfred, and Küster, Helge. “EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods”. Planta 222.2 (2005): 269-283.

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Daten bereitgestellt von Europe PubMed Central.

From embryo sac to oil and protein bodies: embryo development in the model legume Medicago truncatula.
Wang XD, Song Y, Sheahan MB, Garg ML, Rose RJ., New Phytol 193(2), 2012
PMID: 21988647
Analysis of expressed sequence tags in Brassica napus cotyledons damaged by crucifer flea beetle feeding.
Gruber M, Wu L, Links M, Gjetvaj B, Durkin J, Lewis C, Sharpe A, Lydiate D, Hegedus D., Genome 55(2), 2012
PMID: 22276855
Transcriptional network analysis of the tryptophan-accumulating rice mutant during grain filling.
Kim DS, Lee KJ, Yim WC, Kim JB, Ha BK, Kim SH, Kang SY., Mol Genet Genomics 287(9), 2012
PMID: 22836167
Genome-wide analysis of gene expression profiles during ear development of maize.
Zhu Y, Fu J, Zhang J, Liu T, Jia Z, Wang J, Jin Y, Lian Y, Wang M, Zheng J, Hou W, Wang G., Plant Mol Biol 70(1-2), 2009
PMID: 19160056
Intersection of two signalling pathways: extracellular nucleotides regulate pollen germination and pollen tube growth via nitric oxide.
Reichler SA, Torres J, Rivera AL, Cintolesi VA, Clark G, Roux SJ., J Exp Bot 60(7), 2009
PMID: 19363208
Proteomic analysis of the development and germination of date palm (Phoenix dactylifera L.) zygotic embryos.
Sghaier-Hammami B, Valledor L, Drira N, Jorrin-Novo JV., Proteomics 9(9), 2009
PMID: 19402047
Post-genomics studies of developmental processes in legume seeds.
Thompson R, Burstin J, Gallardo K., Plant Physiol 151(3), 2009
PMID: 19675147
Peanut gene expression profiling in developing seeds at different reproduction stages during Aspergillus parasiticus infection.
Guo B, Chen X, Dang P, Scully BT, Liang X, Holbrook CC, Yu J, Culbreath AK., BMC Dev Biol 8(), 2008
PMID: 18248674
Reserve accumulation in legume seeds.
Gallardo K, Thompson R, Burstin J., C R Biol 331(10), 2008
PMID: 18926489
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance.
Terol J, Conesa A, Colmenero JM, Cercos M, Tadeo F, Agustí J, Alós E, Andres F, Soler G, Brumos J, Iglesias DJ, Götz S, Legaz F, Argout X, Courtois B, Ollitrault P, Dossat C, Wincker P, Morillon R, Talon M., BMC Genomics 8(), 2007
PMID: 17254327
Legume transcription factors: global regulators of plant development and response to the environment.
Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JM, Chueng F, Town CD., Plant Physiol 144(2), 2007
PMID: 17556517
Using genomics to study legume seed development.
Le BH, Wagmaister JA, Kawashima T, Bui AQ, Harada JJ, Goldberg RB., Plant Physiol 144(2), 2007
PMID: 17556519
Genetic and genomic analysis of legume flowers and seeds.
Domoney C, Duc G, Ellis TH, Ferrándiz C, Firnhaber C, Gallardo K, Hofer J, Kopka J, Küster H, Madueño F, Munier-Jolain NG, Mayer K, Thompson R, Udvardi M, Salon C., Curr Opin Plant Biol 9(2), 2006
PMID: 16480914
Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs.
Huang Y, Zhang L, Zhang J, Yuan D, Xu C, Li X, Zhou D, Wang S, Zhang Q., Plant Mol Biol 62(4-5), 2006
PMID: 16941221

61 References

Daten bereitgestellt von Europe PubMed Central.

ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development.
Alba R, Fei Z, Payton P, Liu Y, Moore SL, Debbie P, Cohn J, D'Ascenzo M, Gordon JS, Rose JK, Martin G, Tanksley SD, Bouzayen M, Jahn MM, Giovannoni J., Plant J. 39(5), 2004
PMID: 15315633
Orchestrating nuclear functions: ubiquitin sets the rhythm.
Bach I, Ostendorff HP., Trends Biochem. Sci. 28(4), 2003
PMID: 12713902
Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome.
Becker JD, Boavida LC, Carneiro J, Haury M, Feijo JA., Plant Physiol. 133(2), 2003
PMID: 14500793
From elicitins to lipid-transfer proteins: a new insight in cell signalling involved in plant defence mechanisms.
Blein JP, Coutos-Thevenot P, Marion D, Ponchet M., Trends Plant Sci. 7(7), 2002
PMID: 12119165
And then there were many: MADS goes genomic.
De Bodt S, Raes J, Van de Peer Y, Theissen G., Trends Plant Sci. 8(10), 2003
PMID: 14557044
Characterization of a tissue-specific and developmentally regulated beta-1,3-glucanase gene in pea (Pisum sativum).
Buchner P, Rochat C, Wuilleme S, Boutin JP., Plant Mol. Biol. 49(2), 2002
PMID: 11999373
Sink limitation induces the expression of multiple soybean vegetative lipoxygenase mRNAs while the endogenous jasmonic acid level remains low.
Bunker TW, Koetje DS, Stephenson LC, Creelman RA, Mullet JE, Grimes HD., Plant Cell 7(8), 1995
PMID: 7549487
Differential regulation of a family of apyrase genes from Medicago truncatula.
Cohn JR, Uhm T, Ramu S, Nam YW, Kim DJ, Penmetsa RV, Wood TC, Denny RL, Young ND, Cook DR, Stacey G., Plant Physiol. 125(4), 2001
PMID: 11299390

DR, Plant Cell 9(), 1997
BIOSYNTHESIS AND ACTION OF JASMONATES IN PLANTS.
Creelman RA, Mullet JE., Annu. Rev. Plant Physiol. Plant Mol. Biol. 48(), 1997
PMID: 15012267
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
Gene expression during anthesis and senescence in Iris flowers.
van Doorn WG, Balk PA, van Houwelingen AM, Hoeberichts FA, Hall RD, Vorst O, van der Schoot C, van Wordragen MF., Plant Mol. Biol. 53(6), 2003
PMID: 15082930
Cluster analysis and display of genome-wide expression patterns.
Eisen MB, Spellman PT, Brown PO, Botstein D., Proc. Natl. Acad. Sci. U.S.A. 95(25), 1998
PMID: 9843981
Expression profiling in Medicago truncatula identifies more than 750 genes differentially expressed during nodulation, including many potential regulators of the symbiotic program.
El Yahyaoui F, Kuster H, Ben Amor B, Hohnjec N, Puhler A, Becker A, Gouzy J, Vernie T, Gough C, Niebel A, Godiard L, Gamas P., Plant Physiol. 136(2), 2004
PMID: 15466239
Analysis of expressed sequence tags of flower buds in Lotus japonicus.
Endo M, Kokubun T, Takahata Y, Higashitani A, Tabata S, Watanabe M., DNA Res. 7(3), 2000
PMID: 10907852
Generation of 919 expressed sequence tags from immature flower buds and gene expression analysis using expressed sequence tags in the model plant Lotus japonicus.
Endo M, Hakozaki H, Kokubun T, Masuko H, Takahata Y, Tsuchiya T, Higashitani A, Tabata S, Watanabe M., Genes Genet. Syst. 77(4), 2002
PMID: 12419900
The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume, Lotus japonicus.
Endo M, Matsubara H, Kokubun T, Masuko H, Takahata Y, Tsuchiya T, Fukuda H, Demura T, Watanabe M., FEBS Lett. 514(2-3), 2002
PMID: 11943157
Proteomics of Medicago truncatula seed development establishes the time frame of diverse metabolic processes related to reserve accumulation.
Gallardo K, Le Signor C, Vandekerckhove J, Thompson RD, Burstin J., Plant Physiol. 133(2), 2003
PMID: 12972662
Microarray analysis of developing Arabidopsis seeds.
Girke T, Todd J, Ruuska S, White J, Benning C, Ohlrogge J., Plant Physiol. 124(4), 2000
PMID: 11115875

S, J Plant Physiol 158(), 2001
Phosphorylation of soybean nodulin 26 on serine 262 enhances water permeability and is regulated developmentally and by osmotic signals.
Guenther JF, Chanmanivone N, Galetovic MP, Wallace IS, Cobb JA, Roberts DM., Plant Cell 15(4), 2003
PMID: 12671092
Evidence supporting a role of jasmonic acid in Arabidopsis leaf senescence.
He Y, Fukushige H, Hildebrand DF, Gan S., Plant Physiol. 128(3), 2002
PMID: 11891244
Transcriptional programs of early reproductive stages in Arabidopsis.
Hennig L, Gruissem W, Grossniklaus U, Kohler C., Plant Physiol. 135(3), 2004
PMID: 15247381

N, Mol Plant-Microbe Interact 16(), 2003
Comparative analysis of the Arabidopsis pollen transcriptome.
Honys D, Twell D., Plant Physiol. 132(2), 2003
PMID: 12805594

W, Plant Mol Biol 53(), 2004
Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis.
Journet EP, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer MJ, Niebel A, Schiex T, Jaillon O, Chatagnier O, Godiard L, Micheli F, Kahn D, Gianinazzi-Pearson V, Gamas P., Nucleic Acids Res. 30(24), 2002
PMID: 12490726

GC, Func Plant Biol 31(), 2004
Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula.
Kuster H, Hohnjec N, Krajinski F, El YF, Manthey K, Gouzy J, Dondrup M, Meyer F, Kalinowski J, Brechenmacher L, van Tuinen D, Gianinazzi-Pearson V, Puhler A, Gamas P, Becker A., J. Biotechnol. 108(2), 2004
PMID: 15129719
MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome.
Lamblin AF, Crow JA, Johnson JE, Silverstein KA, Kunau TM, Kilian A, Benz D, Stromvik M, Endre G, VandenBosch KA, Cook DR, Young ND, Retzel EF., Nucleic Acids Res. 31(1), 2003
PMID: 12519981
An optimized protocol for analysis of EST sequences.
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J., Nucleic Acids Res. 28(18), 2000
PMID: 10982889
Microarray and differential display identify genes involved in jasmonate-dependent anther development.
Mandaokar A, Kumar VD, Amway M, Browse J., Plant Mol. Biol. 52(4), 2003
PMID: 13677466

M, Mol Plant-Microbe Interact 17(), 2004
Medicago truncatula.
May GD, Dixon RA., Curr. Biol. 14(5), 2004
PMID: 15028229
Methods for transcriptional profiling in plants. Be fruitful and replicate.
Meyers BC, Galbraith DW, Nelson T, Agrawal V., Plant Physiol. 135(2), 2004
PMID: 15173570
Peptide and amino acid transporters are differentially regulated during seed development and germination in faba bean.
Miranda M, Borisjuk L, Tewes A, Dietrich D, Rentsch D, Weber H, Wobus U., Plant Physiol. 132(4), 2003
PMID: 12913151
Transfer cells: cells specialized for a special purpose.
Offler CE, McCurdy DW, Patrick JW, Talbot MJ., Annu Rev Plant Biol 54(), 2003
PMID: 14502998
Medicago truncatula, going where no plant has gone before.
Oldroyd GE, Geurts R., Trends Plant Sci. 6(12), 2001
PMID: 11738372
From pollen tubes to infection threads: recruitment of Medicago floral pectic genes for symbiosis.
Rodriguez-Llorente ID, Perez-Hormaeche J, El Mounadi K, Dary M, Caviedes MA, Cosson V, Kondorosi A, Ratet P, Palomares AJ., Plant J. 39(4), 2004
PMID: 15272876
Contrapuntal networks of gene expression during Arabidopsis seed filling.
Ruuska SA, Girke T, Benning C, Ohlrogge JB., Plant Cell 14(6), 2002
PMID: 12084821
Pistil factors controlling pollination.
Sanchez AM, Bosch M, Bots M, Nieuwland J, Feron R, Mariani C., Plant Cell 16 Suppl(), 2004
PMID: 15010514
Global expression profiling applied to plant development.
Schnable PS, Hochholdinger F, Nakazono M., Curr. Opin. Plant Biol. 7(1), 2004
PMID: 14732441
Members of the aquaporin family in the developing pea seed coat include representatives of the PIP, TIP, and NIP subfamilies.
Schuurmans JA, van Dongen JT, Rutjens BP, Boonman A, Pieterse CM, Borstlap AC., Plant Mol. Biol. 53(5), 2003
PMID: 15010602
Stamen structure and function.
Scott RJ, Spielman M, Dickinson HG., Plant Cell 16 Suppl(), 2004
PMID: 15131249
Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation.
Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR., Proc. Natl. Acad. Sci. U.S.A. 96(6), 1999
PMID: 10077610
POLLEN GERMINATION AND TUBE GROWTH.
Taylor LP, Hepler PK., Annu. Rev. Plant Physiol. Plant Mol. Biol. 48(), 1997
PMID: 15012271

K, Plant Physiol 131(), 2003
Mapping the proteome of barrel medic (Medicago truncatula).
Watson BS, Asirvatham VS, Wang L, Sumner LW., Plant Physiol. 131(3), 2003
PMID: 12644662
Genome-wide analysis of spatial gene expression in Arabidopsis flowers.
Wellmer F, Riechmann JL, Alves-Ferreira M, Meyerowitz EM., Plant Cell 16(5), 2004
PMID: 15100403
A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil.
White JA, Todd J, Newman T, Focks N, Girke T, de Ilarduya OM, Jaworski JG, Ohlrogge JB, Benning C., Plant Physiol. 124(4), 2000
PMID: 11115876
Seed maturation: genetic programmes and control signals.
Wobus U, Weber H., Curr. Opin. Plant Biol. 2(1), 1999
PMID: 10047566

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