Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

Toepel J, Albaum S, Arvidsson S, Goesmann A, La Russa M, Rogge K, Kruse O (2011)
BMC Genomics 12(1): 579.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
ABSTRACT: BACKGROUND: Chlamydomonas reinhardtii is widely accepted as a model organism regarding photosynthesis, circadian rhythm, cell mobility, phototaxis, and biotechnology. The complete annotation of the genome allows transcriptomic studies, however a new microarray platform was needed. Based on the completed annotation of Chlamydomonas reinhardtii a new microarray on an Agilent platform was designed using an extended JGI 3.1 genome data set which included 15000 transcript models. RESULTS: In total 44000 probes were determined (3 independent probes per transcript model) covering 93% of the transcriptome. Alignment studies with the recently published AUGUSTUS 10.2 annotation confirmed 11000 transcript models resulting in a very good coverage of 70% of the transcriptome (17000). Following the estimation of 10000 predicted genes in Chlamydomonas reinhardtii our new microarray, nevertheless, covers the expected genome by 90-95%. CONCLUSIONS: To demonstrate the capabilities of the new microarray, we analyzed transcript levels for cultures grown under nitrogen as well as sulfate limitation, and compared the results with recently published microarray and RNA-seq data. We could thereby confirm previous results derived from data on nutrient-starvation induced gene expression of a group of genes related to protein transport and adaptation of the metabolism as well as genes related to efficient light harvesting, light energy distribution and photosynthetic electron transport.
BMC Genomics
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Toepel J, Albaum S, Arvidsson S, et al. Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics. 2011;12(1): 579.
Toepel, J., Albaum, S., Arvidsson, S., Goesmann, A., La Russa, M., Rogge, K., & Kruse, O. (2011). Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics, 12(1), 579. doi:10.1186/1471-2164-12-579
Toepel, J., Albaum, S., Arvidsson, S., Goesmann, A., La Russa, M., Rogge, K., and Kruse, O. (2011). Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics 12:579.
Toepel, J., et al., 2011. Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics, 12(1): 579.
J. Toepel, et al., “Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii”, BMC Genomics, vol. 12, 2011, : 579.
Toepel, J., Albaum, S., Arvidsson, S., Goesmann, A., La Russa, M., Rogge, K., Kruse, O.: Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics. 12, : 579 (2011).
Toepel, Jörg, Albaum, Stefan, Arvidsson, S., Goesmann, Alexander, La Russa, Marco, Rogge, Kristin, and Kruse, Olaf. “Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii”. BMC Genomics 12.1 (2011): 579.
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13 Zitationen in Europe PMC

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Rai V, Karthikaichamy A, Das D, Noronha S, Wangikar PP, Srivastava S., OMICS 20(7), 2016
PMID: 27315140
Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle.
Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M., Plant Physiol 169(4), 2015
PMID: 26450704
Nitric oxide-triggered remodeling of chloroplast bioenergetics and thylakoid proteins upon nitrogen starvation in Chlamydomonas reinhardtii.
Wei L, Derrien B, Gautier A, Houille-Vernes L, Boulouis A, Saint-Marcoux D, Malnoë A, Rappaport F, de Vitry C, Vallon O, Choquet Y, Wollman FA., Plant Cell 26(1), 2014
PMID: 24474630
Risk and information evaluation of prioritized genes for complex traits: application to bipolar disorder.
Kao CF, Chuang LC, Kuo PH., Am J Med Genet B Neuropsychiatr Genet 165B(7), 2014
PMID: 25123107
Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii.
Malasarn D, Kropat J, Hsieh SI, Finazzi G, Casero D, Loo JA, Pellegrini M, Wollman FA, Merchant SS., J Biol Chem 288(15), 2013
PMID: 23439652
New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics.
Toepel J, Illmer-Kephalides M, Jaenicke S, Straube J, May P, Goesmann A, Kruse O., Plant Biotechnol J 11(6), 2013
PMID: 23551401
Nitrogen and sulfur deprivation differentiate lipid accumulation targets of Chlamydomonas reinhardtii.
Cakmak T, Angun P, Ozkan AD, Cakmak Z, Olmez TT, Tekinay T., Bioengineered 3(6), 2012
PMID: 22892589

42 References

Daten bereitgestellt von Europe PubMed Central.

Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii.
Eberhard S, Jain M, Im CS, Pollock S, Shrager J, Lin Y, Peek AS, Grossman AR., Curr. Genet. 49(2), 2005
PMID: 16333659
Hemin and magnesium-protoporphyrin IX induce global changes in gene expression in Chlamydomonas reinhardtii.
Voss B, Meinecke L, Kurz T, Al-Babili S, Beck CF, Hess WR., Plant Physiol. 155(2), 2010
PMID: 21148414
The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR., Science 318(5848), 2007
PMID: 17932292
EST assembly supported by a draft genome sequence: an analysis of the Chlamydomonas reinhardtii transcriptome.
Jain M, Shrager J, Harris EH, Halbrook R, Grossman AR, Hauser C, Vallon O., Nucleic Acids Res. 35(6), 2007
PMID: 17355987
Power of deep sequencing and agilent microarray for gene expression profiling study.
Feng L, Liu H, Liu Y, Lu Z, Guo G, Guo S, Zheng H, Gao Y, Cheng S, Wang J, Zhang K, Zhang Y., Mol. Biotechnol. 45(2), 2010
PMID: 20432071
Estimating accuracy of RNA-Seq and microarrays with proteomics.
Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P., BMC Genomics 10(), 2009
PMID: 19371429
RNA-Seq: a method for comprehensive transcriptome analysis
RNA-Seq analysis to capture the transcriptome landscape of a single cell.
Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA., Nat Protoc 5(3), 2010
PMID: 20203668
Rapid whole-genome mutational profiling using next-generation sequencing technologies.
Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM., Genome Res. 18(10), 2008
PMID: 18775913
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y., Genome Res. 18(9), 2008
PMID: 18550803
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.
Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ., BMC Genomics 11(), 2010
PMID: 20444259
Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.
Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS., Science 329(5988), 2010
PMID: 20616280
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.
Gonzalez-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR., Plant Cell 22(6), 2010
PMID: 20587772
Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism.
Miller R, Wu G, Deshpande RR, Vieler A, Gartner K, Li X, Moellering ER, Zauner S, Cornish AJ, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, Shiu SH, Benning C., Plant Physiol. 154(4), 2010
PMID: 20935180
Anaerobic acclimation in Chlamydomonas reinhardtii: anoxic gene expression, hydrogenase induction, and metabolic pathways.
Mus F, Dubini A, Seibert M, Posewitz MC, Grossman AR., J. Biol. Chem. 282(35), 2007
PMID: 17565990
Transcriptome for photobiological hydrogen production induced by sulfur deprivation in the green alga Chlamydomonas reinhardtii.
Nguyen AV, Thomas-Hall SR, Malnoe A, Timmins M, Mussgnug JH, Rupprecht J, Kruse O, Hankamer B, Schenk PM., Eukaryotic Cell 7(11), 2008
PMID: 18708561
Acclimation to singlet oxygen stress in Chlamydomonas reinhardtii.
Ledford HK, Chin BL, Niyogi KK., Eukaryotic Cell 6(6), 2007
PMID: 17435007
Analysis of light and CO(2) regulation in Chlamydomonas reinhardtii using genome-wide approaches.
Im CS, Zhang Z, Shrager J, Chang CW, Grossman AR., Photosyn. Res. 75(2), 2003
PMID: 16245082
The interplay of proton, electron, and metabolite supply for photosynthetic H2 production in Chlamydomonas reinhardtii.
Doebbe A, Keck M, La Russa M, Mussgnug JH, Hankamer B, Tekce E, Niehaus K, Kruse O., J. Biol. Chem. 285(39), 2010
PMID: 20581114
Phylogenetic and molecular analysis of hydrogen-producing green algae.
Timmins M, Thomas-Hall SR, Darling A, Zhang E, Hankamer B, Marx UC, Schenk PM., J. Exp. Bot. 60(6), 2009
PMID: 19342428
Hydrogen production. Green algae as a source of energy.
Melis A, Happe T., Plant Physiol. 127(3), 2001
PMID: 11706159
Proteomic analysis of hydrogen photoproduction in sulfur-deprived Chlamydomonas cells.
Chen M, Zhao L, Sun YL, Cui SX, Zhang LF, Yang B, Wang J, Kuang TY, Huang F., J. Proteome Res. 9(8), 2010
PMID: 20509623
Fatty acid profiling of Chlamydomonas reinhardtii under nitrogen deprivation.
James GO, Hocart CH, Hillier W, Chen H, Kordbacheh F, Price GD, Djordjevic MA., Bioresour. Technol. 102(3), 2010
PMID: 21146403
Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation.
Bolling C, Fiehn O., Plant Physiol. 139(4), 2005
PMID: 16306140
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP., Nucleic Acids Res. 30(4), 2002
PMID: 11842121
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
An ancient light-harvesting protein is critical for the regulation of algal photosynthesis.
Peers G, Truong TB, Ostendorf E, Busch A, Elrad D, Grossman AR, Hippler M, Niyogi KK., Nature 462(7272), 2009
PMID: 19940928
Analysis of LhcSR3, a protein essential for feedback de-excitation in the green alga Chlamydomonas reinhardtii.
Bonente G, Ballottari M, Truong TB, Morosinotto T, Ahn TK, Fleming GR, Niyogi KK, Bassi R., PLoS Biol. 9(1), 2011
PMID: 21267060
Cysteine modification of a specific repressor protein controls the translational status of nucleus-encoded LHCII mRNAs in Chlamydomonas.
Wobbe L, Blifernez O, Schwarz C, Mussgnug JH, Nickelsen J, Kruse O., Proc. Natl. Acad. Sci. U.S.A. 106(32), 2009
PMID: 19666611
Improvement of light to biomass conversion by de-regulation of light-harvesting protein translation in Chlamydomonas reinhardtii.
Beckmann J, Lehr F, Finazzi G, Hankamer B, Posten C, Wobbe L, Kruse O., J. Biotechnol. 142(1), 2009
PMID: 19480949
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
An evaluation framework for statistical tests on microarray data.
Dondrup M, Huser AT, Mertens D, Goesmann A., J. Biotechnol. 140(1-2), 2009
PMID: 19297690
Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii.
Dent RM, Haglund CM, Chin BL, Kobayashi MC, Niyogi KK., Plant Physiol. 137(2), 2005
PMID: 15653810


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