共查询到20条相似文献,搜索用时 31 毫秒
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Genome-wide analysis of gene expression during early Arabidopsis flower development 总被引:1,自引:0,他引:1 下载免费PDF全文
Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner. 相似文献
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Ekrem Dündar 《The Annals of applied biology》2009,154(1):33-41
Ten independent transposant lines with gene or enhancer traps (ET) inserted into the same gene (At2g01170) were identified in Arabidopsis thaliana . Transposon insertions were confirmed for each line. Only three of five ET lines and only one of the five gene trap (GT) lines displayed uidA (GUS) staining. The GUS (β-glucuronidase) expression patterns of the ET lines were different in all three lines. In the GT line, the GUS expression was restricted to the vascular tissue under all conditions examined. The variation in ET GUS expression suggests that each ET was controlled by different enhancer elements or the different elements of the trapped locus may give rise to different GUS expression patterns. Of five GT lines, three have the GUS gene in the same orientation as the At2g01170 open reading frame, yet only one yielded GUS staining. Regardless of the insertion construct, only those transposants with an insertion at the 3' end of the gene yielded GUS staining. Some transposants displayed a longer root phenotype in the presence of kanamycin that was also observed in 3' insertion sites in At2g01170. Taken together, these data show that insertions in the 5' end of the gene disrupted expression and emphasise the complexity encountered with ET and GT constructs to characterise the expression patterns of genes of interest based solely on GUS expression patterns. 相似文献
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Satoru Akama Rie Shimizu-Inatsugi Kentaro K. Shimizu Jun Sese 《Nucleic acids research》2014,42(6):e46
Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses. 相似文献
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Roux F Colomé-Tatché M Edelist C Wardenaar R Guerche P Hospital F Colot V Jansen RC Johannes F 《Genetics》2011,188(4):1015-1017
We extensively phenotyped 6000 Arabidopsis plants with experimentally perturbed DNA methylomes as well as a diverse panel of natural accessions in a common garden. We found that alterations in DNA methylation not only caused heritable phenotypic diversity but also produced heritability patterns closely resembling those of the natural accessions. Our findings indicate that epigenetically induced and naturally occurring variation in complex traits share part of their polygenic architecture and may offer complementary adaptation routes in ecological settings. 相似文献
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Genome-wide analysis of gene expression profiles associated with cell cycle transitions in growing organs of Arabidopsis 下载免费PDF全文
Beemster GT De Veylder L Vercruysse S West G Rombaut D Van Hummelen P Galichet A Gruissem W Inzé D Vuylsteke M 《Plant physiology》2005,138(2):734-743
Organ growth results from the progression of component cells through subsequent phases of proliferation and expansion before reaching maturity. We combined kinematic analysis, flowcytometry, and microarray analysis to characterize cell cycle regulation during the growth process of leaves 1 and 2 of Arabidopsis (Arabidopsis thaliana). Kinematic analysis showed that the epidermis proliferates until day 12; thereafter, cells expand until day 19 when leaves reach maturity. Flowcytometry revealed that endoreduplication occurs from the time cell division rates decline until the end of cell expansion. Analysis of 10 time points with a 6k-cDNA microarray showed that transitions between the growth stages were closely reflected in the mRNA expression data. Subsequent genome-wide microarray analysis on the three main stages allowed us to categorize known cell cycle genes into three major classes: constitutively expressed, proliferative, and inhibitory. Comparison with published expression data obtained from root zones corresponding to similar developmental stages and from synchronized cell cultures supported this categorization and enabled us to identify a high confidence set of 131 proliferation genes. Most of those had an M phase-dependent expression pattern and, in addition to many known cell cycle-related genes, there were at least 90 that were unknown or previously not associated with proliferation. 相似文献
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Pavan Umate 《Plant signaling & behavior》2011,6(3):335-338
The enzymes called lipoxygenases (LOXs) can dioxygenate unsaturated fatty acids, which leads to lipoperoxidation of biological membranes. This process causes synthesis of signaling molecules and also leads to changes in cellular metabolism. LOXs are known to be involved in apoptotic (programmed cell death) pathway, and biotic and abiotic stress responses in plants. Here, the members of LOX gene family in Arabidopsis and rice are identified. The Arabidopsis and rice genomes encode 6 and 14 LOX proteins, respectively, and interestingly, with more LOX genes in rice. The rice LOXs are validated based on protein alignment studies. This is the first report wherein LOXs are identified in rice which may allow better understanding the initiation, progression and effects of apoptosis, and responses to bitoic and abiotic stresses and signaling cascades in plants.Key words: apoptosis, biotic and abiotic stresses, genomics, jasmonic acid, lipidsLipoxygenases (linoleate:oxygen oxidoreductase, EC 1.13.11.-; LOXs) catalyze the conversion of polyunsaturated fatty acids (lipids) into conjugated hydroperoxides. This process is called hydroperoxidation of lipids. LOXs are monomeric, non-heme and non-sulfur, but iron-containing dioxygenases widely expressed in fungi, animal and plant cells, and are known to be absent in prokaryotes. However, a recent finding suggests the existence of LOX-related genomic sequences in bacteria but not in archaea.1 The inflammatory conditions in mammals like bronchial asthama, psoriasis and arthritis are a result of LOXs reactions.2 Further, several clinical conditions like HIV-1 infection,3 disease of kidneys due to the activation of 5-lipoxygenase,4,5 aging of the brain due to neuronal 5-lipoxygenase6 and atherosclerosis7 are mediated by LOXs. In plants, LOXs are involved in response to biotic and abiotic stresses.8 They are involved in germination9 and also in traumatin and jasmonic acid biochemical pathways.10,11 Studies on LOX in rice are conducted to develop novel strategies against insect pests12 in response to wounding and insect attack,13 and on rice bran extracts as functional foods and dietary supplements for control of inflammation and joint health.14 In Arabidopsis, LOXs are studied in response to natural and stress-induced senescence,15 transition to flowering,16 regulation of lateral root development and defense response.17The arachidonic, linoleic and linolenic acids can act as substrates for different LOX isozymes. A hydroperoxy group is added at carbons 5, 12 or 15, when arachidonic acid is the substrate, and so the LOXs are designated as 5-, 12- or 15-lipoxygenases. Sequences are available in the database for plant lipoxygenases (EC:1.13.11.12), mammalian arachidonate 5-lipoxygenase (EC:1.13.11.34), mammalian arachidonate 12-lipoxygenase (EC:1.13.11.31) and mammalian erythroid cell-specific 15-lipoxygenase (EC:1.13.11.33). The prototype member for LOX family, LOX-1 of Glycine max L. (soybean) is a 15-lipoxygenase. The LOX isoforms of soybean (LOX-1, LOX-2, LOX-3a and LOX-3b) are the most characterized of plant LOXs.18 In addition, five vegetative LOXs (VLX-A, -B, -C, -D, -E) are detected in soybean leaves.19 The 3-dimensional structure of soybean LOX-1 has been determined.20,21 LOX-1 was shown to be made of two domains, the N-terminal domain-I which forms a β-barrel of 146 residues, and a C-terminal domain-II of bundle of helices of 693 residues21 (Fig. 1). The iron atom was shown to be at the centre of domain-II bound by four coordinating ligands, of which three are histidine residues.22Open in a separate windowFigure 1Three-dimensional structure of soybean lipoxygenase L-1. The domain I (N-terminal) and domain II (C-terminal) are indicated. The catalytic iron atom is embedded in domain II (PDB ID-1YGE).21This article describes identification of LOX genes in Arabidopsis and rice. The Arabidopsis genome encodes for six LOX proteins23 (www.arabidopsis.org) (Locus Annotation Nomenclature A* B* C* AT1G55020 lipoxygenase 1 (LOX1) LOX1 859 98044.4 5.2049 AT1G17420 lipoxygenase 3 (LOX3) LOX3 919 103725.1 8.0117 AT1G67560 lipoxygenase family protein LOX4 917 104514.6 8.0035 AT1G72520 lipoxygenase, putative LOX6 926 104813.1 7.5213 AT3G22400 lipoxygenase 5 (LOX5) LOX5 886 101058.8 6.6033 AT3G45140 lipoxygenase 2 (LOX2) LOX2 896 102044.7 5.3177