Base de dados : MEDLINE
Pesquisa : G05.360.340.365 [Categoria DeCS]
Referências encontradas : 12924 [refinar]
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  1 / 12924 MEDLINE  
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[PMID]:29425824
[Au] Autor:Wang L; Zhu J; Li X; Wang S; Wu J
[Ad] Endereço:Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
[Ti] Título:Salt and drought stress and ABA responses related to bZIP genes from V. radiata and V. angularis.
[So] Source:Gene;651:152-160, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Mung bean and adzuki bean are warm-season legumes widely cultivated in China. However, bean production in major producing regions is limited by biotic and abiotic stress, such as drought and salt stress. Basic leucine zipper (bZIP) genes play key roles in responses to various biotic and abiotic stresses. However, only several bZIP genes involved in drought and salt stress in legumes, especially Vigna radiata and Vigna angularis, have been identified. In this study, we identified 54 and 50 bZIP proteins from whole-genome sequences of V. radiata and V. angularis, respectively. First, we comprehensively surveyed the characteristics of all bZIP genes, including their gene structure, chromosome distribution and motif composition. Phylogenetic trees showed that VrbZIP and VabZIP proteins were divided into ten clades comprising nine known and one unknown subgroup. The results of the nucleotide substitution rate of the orthologous gene pairs showed that bZIP proteins have undergone strong purifying selection: V. radiata and V. angularis diverged 1.25 million years ago (mya) to 9.20 mya (average of 4.95 mya). We also found that many cis-acting regulatory elements (CAREs) involved in abiotic stress and plant hormone responses were detected in the putative promoter regions of the bZIP genes. Finally, using the quantitative real-time PCR (qRT-PCR) method, we performed expression profiling of the bZIP genes in response to drought, salt and abscisic acid (ABA). We identified several bZIP genes that may be involved in drought and salt responses. Generally, our results provided useful and rich resources of VrbZIP and VabZIP genes for the functional characterization and understanding of bZIP transcription factors (TFs) in warm-season legumes. In addition, our results revealed important and interesting data - a subset of VrbZIP and VabZIP gene expression profiles in response to drought, salt and ABA stress. These results provide gene expression evidence for the selection of candidate genes under drought and salt stress for future study.
[Mh] Termos MeSH primário: Fatores de Transcrição de Zíper de Leucina Básica/genética
Genes de Plantas
Proteínas de Plantas/genética
Vigna/genética
[Mh] Termos MeSH secundário: Ácido Abscísico/farmacologia
Secas
Perfilação da Expressão Gênica
Genoma de Planta
Filogenia
Cloreto de Sódio/farmacologia
Estresse Fisiológico/genética
Vigna/classificação
Vigna/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Basic-Leucine Zipper Transcription Factors); 0 (Plant Proteins); 451W47IQ8X (Sodium Chloride); 72S9A8J5GW (Abscisic Acid)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180210
[St] Status:MEDLINE


  2 / 12924 MEDLINE  
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[PMID]:29409851
[Au] Autor:Tan M; Li G; Qi S; Liu X; Chen X; Ma J; Zhang D; Han M
[Ad] Endereço:College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, China.
[Ti] Título:Identification and expression analysis of the IPT and CKX gene families during axillary bud outgrowth in apple (Malus domestica Borkh.).
[So] Source:Gene;651:106-117, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cytokinins (CKs) play a crucial role in promoting axillary bud outgrowth and targeting the control of CK metabolism can be used to enhance branching in plants. CK levels are maintained mainly by CK biosynthesis (isopentenyl transferase, IPT) and degradation (dehydrogenase, CKX) genes in plants. A systematic study of the IPT and CKX gene families in apple, however, has not been conducted. In the present study, 12 MdIPTs and 12 MdCKXs were identified in the apple genome. Systematic phylogenetic, structural, and synteny analyses were performed. Expression analysis of these genes in different tissues was also assessed. MdIPT and MdCKX genes exhibit distinct expression patterns in different tissues. The response of MdIPT, MdCKX, and MdPIN1 genes to various treatments (6-BA, decapitation and Lovastatin, an inhibitor of CKs synthesis) that impact branching were also investigated. Results indicated that most of the MdIPT and MdCKX, and MdPIN1 genes were upregulated by 6-BA and decapitation treatment, but inhibited by Lovastatin, a compound that effectively suppresses axillary bud outgrowth induced by decapitation. These findings suggest that cytokinin biosynthesis is required for the activation of bud break and the export of auxin from buds in apple tree with intact primary shoot apex or decapitated apple tree. MdCKX8 and MdCKX10, however, exhibited little response to decapitation, but were significantly up-regulated by 6-BA and Lovastatin, a finding that warrants further investigation in order to understand their function in bud-outgrowth.
[Mh] Termos MeSH primário: Alquil e Aril Transferases/genética
Genes de Plantas
Malus/genética
Oxirredutases/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Compostos de Benzil/farmacologia
Mapeamento Cromossômico
Cromossomos de Plantas
Evolução Molecular
Flores/genética
Perfilação da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Genoma de Planta
Lovastatina/farmacologia
Malus/enzimologia
Malus/crescimento & desenvolvimento
Família Multigênica
Filogenia
Reguladores de Crescimento de Planta
Purinas/farmacologia
Sintenia
Regulação para Cima
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Benzyl Compounds); 0 (Plant Growth Regulators); 0 (Purines); 9LHU78OQFD (Lovastatin); EC 1.- (Oxidoreductases); EC 1.5.99.12 (cytokinin oxidase); EC 2.5.- (Alkyl and Aryl Transferases); EC 2.5.1.27 (adenylate isopentenyltransferase); KXG6A989PS (benzylaminopurine)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180208
[St] Status:MEDLINE


  3 / 12924 MEDLINE  
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[PMID]:28453674
[Au] Autor:Mohamadi H; Khan H; Birol I
[Ad] Endereço:Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
[Ti] Título:ntCard: a streaming algorithm for cardinality estimation in genomics data.
[So] Source:Bioinformatics;33(9):1324-1330, 2017 05 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Motivation: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k -mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k -mers, or even better, to build a histogram of k -mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools. However, calculating a k -mer histogram from large volumes of sequencing data is a challenging task. Results: Here, we present ntCard, a streaming algorithm for estimating the frequencies of k -mers in genomics datasets. At its core, ntCard uses the ntHash algorithm to efficiently compute hash values for streamed sequences. It then samples the calculated hash values to build a reduced representation multiplicity table describing the sample distribution. Finally, it uses a statistical model to reconstruct the population distribution from the sample distribution. We have compared the performance of ntCard and other cardinality estimation algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB in size, where the first two representing whole genome shotgun sequencing experiments on the human genome and the last one on the white spruce genome. Results show ntCard estimates k -mer coverage frequencies >15× faster than the state-of-the-art algorithms, using similar amount of memory, and with higher accuracy rates. Thus, our benchmarks demonstrate ntCard as a potentially enabling technology for large-scale genomics applications. Availability and Implementation: ntCard is written in C ++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ntCard. Contact: hmohamadi@bcgsc.ca or ibirol@bcgsc.ca. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Genômica/métodos
Análise de Sequência de DNA/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Tamanho do Genoma
Genoma Humano
Genoma de Planta
Seres Humanos
Modelos Estatísticos
Picea/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw832


  4 / 12924 MEDLINE  
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[PMID]:28453675
[Au] Autor:Drori E; Levy D; Smirin-Yosef P; Rahimi O; Salmon-Divon M
[Ad] Endereço:Agriculture and Oenology Research Department, Eastern R&D Center, 40700 Ariel, Israel.
[Ti] Título:CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files.
[So] Source:Bioinformatics;33(9):1392-1393, 2017 05 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Summary: Visualization of whole-genomic variations in a meaningful manner assists researchers in gaining new insights into the underlying data, especially when it comes in the context of whole genome comparisons. CircosVCF is a web based visualization tool for genome-wide variant data described in VCF files, using circos plots. The user friendly interface of CircosVCF supports an interactive design of the circles in the plot, and the integration of additional information such as experimental data or annotations. The provided visualization capabilities give a broad overview of the genomic relationships between genomes, and allow identification of specific meaningful SNPs regions. Availability and Implementation: CircosVCF was implemented in JavaScript and is available at http://www.ariel.ac.il/research/fbl/software. Contact: malisa@ariel.ac.il. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Genômica/métodos
Polimorfismo de Nucleotídeo Único
Análise de Sequência de DNA/métodos
Software
[Mh] Termos MeSH secundário: Genoma de Planta
Vitis/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw834


  5 / 12924 MEDLINE  
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[PMID]:29178822
[Au] Autor:Bowman MJ; Pulman JA; Liu TL; Childs KL
[Ad] Endereço:Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA.
[Ti] Título:A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa.
[So] Source:BMC Bioinformatics;18(1):522, 2017 Nov 25.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. When gene prediction programs are trained on a subset of grass genes with random GC content, they are effectively being trained on two classes of genes at once, and this can be expected to result in poor results when genes are predicted in new genome sequences. RESULTS: We find that gene prediction programs trained on grass genes with random GC content do not completely predict all grass genes with extreme GC content. We show that gene prediction programs that are trained with grass genes with high or low GC content can make both better and unique gene predictions compared to gene prediction programs that are trained on genes with random GC content. By separately training gene prediction programs with genes from multiple GC ranges and using the programs within the MAKER genome annotation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using the standard MAKER annotation protocol. Gene structure was improved in over 13% of genes, and 651 novel genes were predicted by the GC-specific MAKER protocol. CONCLUSIONS: We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa. We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content.
[Mh] Termos MeSH primário: Genoma de Planta
Anotação de Sequência Molecular/métodos
Oryza/genética
[Mh] Termos MeSH secundário: Composição de Bases
Cadeias de Markov
RNA de Plantas/química
RNA de Plantas/isolamento & purificação
RNA de Plantas/metabolismo
Ribossomos/metabolismo
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Plant)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1942-z


  6 / 12924 MEDLINE  
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[PMID]:29351563
[Au] Autor:Ates D; Aldemir S; Alsaleh A; Erdogmus S; Nemli S; Kahriman A; Ozkan H; Vandenberg A; Tanyolac B
[Ad] Endereço:Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey.
[Ti] Título:A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.
[So] Source:PLoS One;13(1):e0191375, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). RESULTS: The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. CONCLUSION: This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.
[Mh] Termos MeSH primário: Lens (Planta)/genética
[Mh] Termos MeSH secundário: Mapeamento Cromossômico/métodos
Sequência Consenso
DNA de Plantas/genética
Ligação Genética
Genoma de Planta
Polimorfismo de Nucleotídeo Único
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180120
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191375


  7 / 12924 MEDLINE  
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[PMID]:29257136
[Au] Autor:Nie SJ; Liu YQ; Wang CC; Gao SW; Xu TT; Liu Q; Chang HL; Chen YB; Yan PC; Peng W; Zheng TQ; Xu JL; Li ZK
[Ad] Endereço:Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, 420 Gong-Nong West Road, Suihua, Heilongjiang 152000, China.
[Ti] Título:Assembly of an early-matured japonica (Geng) rice genome, Suijing18, based on PacBio and Illumina sequencing.
[So] Source:Sci Data;4:170195, 2017 12 19.
[Is] ISSN:2052-4463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:The early-matured japonica (Geng) rice variety, Suijing18 (SJ18), carries multiple elite traits including durable blast resistance, good grain quality, and high yield. Using PacBio SMRT technology, we produced over 25 Gb of long-read sequencing raw data from SJ18 with a coverage of 62×. Using Illumina paired-end whole-genome shotgun sequencing technology, we generated 59 Gb of short-read sequencing data from SJ18 (23.6 Gb from a 200 bp library with a coverage of 59× and 35.4 Gb from an 800 bp library with a coverage of 88×). With these data, we assembled a single SJ18 genome and then generated a set of annotation data. These data sets can be used to test new programs for variation deep mining, and will provide new insights into the genome structure, function, and evolution of SJ18, and will provide essential support for biological research in general.
[Mh] Termos MeSH primário: Genoma de Planta
Oryza/genética
[Mh] Termos MeSH secundário: Análise de Sequência de DNA
[Pt] Tipo de publicação:DATASET; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180223
[Lr] Data última revisão:
180223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171220
[St] Status:MEDLINE
[do] DOI:10.1038/sdata.2017.195


  8 / 12924 MEDLINE  
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[PMID]:29257129
[Au] Autor:Pisupati R; Reichardt I; Seren Ü; Korte P; Nizhynska V; Kerdaffrec E; Uzunova K; Rabanal FA; Filiault DL; Nordborg M
[Ad] Endereço:Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, Vienna 1030, Austria.
[Ti] Título:Verification of Arabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples.
[So] Source:Sci Data;4:170184, 2017 12 19.
[Is] ISSN:2052-4463
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Large-scale studies such as the Arabidopsis thaliana '1,001 Genomes' Project require routine genotyping of stocks to avoid sample contamination. To genotype samples efficiently and economically, sequencing must be inexpensive and data processing simple. Here we present SNPmatch, a tool that identifies strains (or inbred lines, or accessions) by matching them to a SNP database. We tested the tool by performing low-coverage resequencing of over 2,000 strains from our lab seed stock collection. SNPmatch correctly genotyped samples from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.
[Mh] Termos MeSH primário: Arabidopsis
Técnicas de Genotipagem
[Mh] Termos MeSH secundário: Arabidopsis/classificação
Arabidopsis/genética
Genoma de Planta
Análise de Sequência de DNA
[Pt] Tipo de publicação:DATASET; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180223
[Lr] Data última revisão:
180223
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171220
[St] Status:MEDLINE
[do] DOI:10.1038/sdata.2017.184


  9 / 12924 MEDLINE  
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[PMID]:29232688
[Au] Autor:Raskina O
[Ad] Endereço:Institute of Evolution, University of Haifa, Haifa, Israel.
[Ti] Título:Genotype- and Cell-Specific Dynamics of Tandem Repeat Patterns in Aegilops speltoides Tausch (Poaceae, Triticeae).
[So] Source:Cytogenet Genome Res;153(2):105-116, 2017.
[Is] ISSN:1424-859X
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:In wild plant populations, chromosome rearrangements lead to the wide intraspecific polymorphisms in the abundance and patterns of highly repetitive DNA. However, despite the large amount of accumulated data, the impact of the complex repetitive DNA fraction on genome reorganization and functioning and the mechanisms balancing and maintaining the structural integrity of the genome are not fully understood. Homologous recombination is thought to play a key role in both genome reshuffling and stabilization, while the contribution of nonhomologous recombination seems to be undervalued. Here, tandem repeat patterns and dynamics during pollen mother cell development were addressed, with a focus on the meiotic recombination that determines chromosome/genome repatterning and stabilization under cross-pollination and artificial hybridization in wild goatgrass, Aegilops speltoides. Native plants from contrasting allopatric populations and artificially created intraspecific hybrids were investigated using a FISH approach. Cytogenetic analysis uncovered a wide spectrum of genotype- and cell-specific chromosomal rearrangements, suggesting intensive repatterning of both parental and hybrid genomes. The data obtained provide evidence that repetitive elements serve as overabundant and ubiquitous resources for maintaining chromosome architecture/genome integrity through homologous and nonhomologous recombination at the intraorganismal level, and genotype-specific repatterning underlies intrapopulation polymorphisms and intraspecific diversification in the wild.
[Mh] Termos MeSH primário: Cromossomos de Plantas/genética
DNA de Plantas/genética
Poaceae/genética
Sequências de Repetição em Tandem/genética
[Mh] Termos MeSH secundário: Cromossomos de Plantas/ultraestrutura
Cruzamentos Genéticos
Genoma de Planta
Genótipo
Recombinação Homóloga
Hibridização Genética
Hibridização in Situ Fluorescente
Meiose
Metagenômica
Polimorfismo Genético
Turquia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171213
[St] Status:MEDLINE
[do] DOI:10.1159/000484917


  10 / 12924 MEDLINE  
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[PMID]:29293569
[Au] Autor:Ding CJ; Liang LX; Diao S; Su XH; Zhang BY
[Ad] Endereço:State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
[Ti] Título:Genome-wide analysis of day/night DNA methylation differences in Populus nigra.
[So] Source:PLoS One;13(1):e0190299, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.
[Mh] Termos MeSH primário: Ritmo Circadiano
Metilação de DNA
Genoma de Planta
Populus/genética
[Mh] Termos MeSH secundário: Adaptação Fisiológica
Escuridão
Imunoprecipitação
Luz
Folhas de Planta/metabolismo
Populus/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190299



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