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  1 / 8492 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


  2 / 8492 MEDLINE  
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[PMID]:29351555
[Au] Autor:Xue Y; Chen B; Win AN; Fu C; Lian J; Liu X; Wang R; Zhang X; Chai Y
[Ad] Endereço:College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
[Ti] Título:Omega-3 fatty acid desaturase gene family from two ω-3 sources, Salvia hispanica and Perilla frutescens: Cloning, characterization and expression.
[So] Source:PLoS One;13(1):e0191432, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Omega-3 fatty acid desaturase (ω-3 FAD, D15D) is a key enzyme for α-linolenic acid (ALA) biosynthesis. Both chia (Salvia hispanica) and perilla (Perilla frutescens) contain high levels of ALA in seeds. In this study, the ω-3 FAD gene family was systematically and comparatively cloned from chia and perilla. Perilla FAD3, FAD7, FAD8 and chia FAD7 are encoded by single-copy (but heterozygous) genes, while chia FAD3 is encoded by 2 distinct genes. Only 1 chia FAD8 sequence was isolated. In these genes, there are 1 to 6 transcription start sites, 1 to 8 poly(A) tailing sites, and 7 introns. The 5'UTRs of PfFAD8a/b contain 1 to 2 purine-stretches and 2 pyrimidine-stretches. An alternative splice variant of ShFAD7a/b comprises a 5'UTR intron. Their encoded proteins harbor an FA_desaturase conserved domain together with 4 trans-membrane helices and 3 histidine boxes. Phylogenetic analysis validated their identity of dicot microsomal or plastidial ω-3 FAD proteins, and revealed some important evolutionary features of plant ω-3 FAD genes such as convergent evolution across different phylums, single-copy status in algae, and duplication events in certain taxa. The qRT-PCR assay showed that the ω-3 FAD genes of two species were expressed at different levels in various organs, and they also responded to multiple stress treatments. The functionality of the ShFAD3 and PfFAD3 enzymes was confirmed by yeast expression. The systemic molecular and functional features of the ω-3 FAD gene family from chia and perilla revealed in this study will facilitate their use in future studies on genetic improvement of ALA traits in oilseed crops.
[Mh] Termos MeSH primário: Ácidos Graxos Dessaturases/genética
Genes de Plantas
Perilla frutescens/enzimologia
Perilla frutescens/genética
Proteínas de Plantas/genética
Salvia/enzimologia
Salvia/genética
[Mh] Termos MeSH secundário: Regiões 5' não Traduzidas
Processamento Alternativo
Sequência de Aminoácidos
Clonagem Molecular
Sequência Conservada
Evolução Molecular
Ácidos Graxos Dessaturases/química
Ácidos Graxos Dessaturases/metabolismo
Regulação Enzimológica da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Família Multigênica
Especificidade de Órgãos
Filogenia
Proteínas de Plantas/química
Proteínas de Plantas/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA de Plantas/genética
RNA de Plantas/metabolismo
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Homologia de Sequência de Aminoácidos
Estresse Fisiológico
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (5' Untranslated Regions); 0 (Plant Proteins); 0 (RNA, Messenger); 0 (RNA, Plant); 0 (Recombinant Proteins); EC 1.14.19.- (Fatty Acid Desaturases); EC 1.14.99.- (omega-3 fatty acid desaturase)
[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.0191432


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[PMID]:29382326
[Au] Autor:Chen X; Wu RZ; Zhu YQ; Ren ZM; Tong YL; Yang F; Dai GH
[Ad] Endereço:Institute of Basic Medicine, Zhejiang Academy of Traditional Chinese Medicine, No. 132, Tianmushan Road, Xihu District, Hangzhou, Zhejiang, China.
[Ti] Título:Study on the inhibition of Mfn1 by plant-derived miR5338 mediating the treatment of BPH with rape bee pollen.
[So] Source:BMC Complement Altern Med;18(1):38, 2018 Jan 30.
[Is] ISSN:1472-6882
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Recent studies have found that plant derived microRNA can cross-kingdom regulate the expression of genes in humans and other mammals, thereby resisting diseases. Can exogenous miRNAs cross the blood-prostate barrier and entry prostate then participate in prostate disease treatment? METHODS: Using HiSeq sequencing and RT-qPCR technology, we detected plant miRNAs that enriched in the prostates of rats among the normal group, BPH model group and rape bee pollen group. To forecast the functions of these miRNAs, the psRobot software and TargetFinder software were used to predict their candidate target genes in rat genome. The qRT-PCR technology was used to validate the expression of candidate target genes. RESULTS: Plant miR5338 was enriched in the posterior lobes of prostate gland of rats fed with rape bee pollen, which was accompanied by the improvement of BPH. Among the predicted target genes of miR5338, Mfn1 was significantly lower in posterior lobes of prostates of rats in the rape bee pollen group than control groups. Further experiments suggested that Mfn1 was highly related to BPH. CONCLUSIONS: These results suggesting that plant-derived miR5338 may involve in treatment of rat BPH through inhibiting Mfn1 in prostate. These results will provide more evidence for plant miRNAs cross-kingdom regulation of animal gene, and will provide preliminary theoretical and experimental basis for development of rape bee pollen into innovative health care product or medicine for the treatment of BPH.
[Mh] Termos MeSH primário: Proteínas de Membrana/antagonistas & inibidores
MicroRNAs/farmacologia
Proteínas Mitocondriais/antagonistas & inibidores
Pólen
Próstata/efeitos dos fármacos
Hiperplasia Prostática/metabolismo
RNA de Plantas/farmacologia
[Mh] Termos MeSH secundário: Animais
Abelhas
Peso Corporal/efeitos dos fármacos
Masculino
Proteínas de Membrana/metabolismo
Proteínas Mitocondriais/metabolismo
Tamanho do Órgão/efeitos dos fármacos
RNA de Plantas/farmacocinética
Ratos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Membrane Proteins); 0 (MicroRNAs); 0 (Mitochondrial Proteins); 0 (RNA, Plant); 0 (mitofusin 1 protein, rat)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180301
[Lr] Data última revisão:
180301
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180201
[St] Status:MEDLINE
[do] DOI:10.1186/s12906-018-2107-y


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[PMID]:29360842
[Au] Autor:Liu F; Yang Y; Gao J; Ma C; Bi Y
[Ad] Endereço:College of Life Science, Shandong Normal University, Jinan, China.
[Ti] Título:A comparative transcriptome analysis of a wild purple potato and its red mutant provides insight into the mechanism of anthocyanin transformation.
[So] Source:PLoS One;13(1):e0191406, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In this study, a red mutant was obtained through in vitro regeneration of a wild purple potato. High-performance liquid chromatography and Mass spectrometry analysis revealed that pelargonidin-3-O-glucoside and petunidin-3-O-glucoside were main anthocyanins in the mutant and wild type tubers, respectively. In order to thoroughly understand the mechanism of anthocyanin transformation in two materials, a comparative transcriptome analysis of the mutant and wild type was carried out through high-throughput RNA sequencing, and 295 differentially expressed genes (DEGs) were obtained. Real-time qRT-PCR validation of DEGs was consistent with the transcriptome date. The DEGs mainly influenced biological and metabolic pathways, including phenylpropanoid biosynthesis and translation, and biosynthesis of flavone and flavonol. In anthocyanin biosynthetic pathway, the analysis of structural genes expressions showed that three genes, one encoding phenylalanine ammonia-lyase, one encoding 4-coumarate-CoA ligase and one encoding flavonoid 3',5'-hydroxylasem were significantly down-regulated in the mutant; one gene encoding phenylalanine ammonia-lyase was significantly up-regulated. Moreover, the transcription factors, such as bZIP family, MYB family, LOB family, MADS family, zf-HD family and C2H2 family, were significantly regulated in anthocyanin transformation. Response proteins of hormone, such as gibberellin, abscisic acid and brassinosteroid, were also significantly regulated in anthocyanin transformation. The information contributes to discovering the candidate genes in anthocyanin transformation, which can serve as a comprehensive resource for molecular mechanism research of anthocyanin transformation in potatoes.
[Mh] Termos MeSH primário: Antocianinas/biossíntese
Antocianinas/genética
Solanum tuberosum/genética
Solanum tuberosum/metabolismo
[Mh] Termos MeSH secundário: Vias Biossintéticas/genética
Coenzima A Ligases/genética
Sistema Enzimático do Citocromo P-450/genética
Perfilação da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Genes de Plantas
Glucosídeos/biossíntese
Glucosídeos/genética
Sequenciamento de Nucleotídeos em Larga Escala
Mutação
Fenilalanina Amônia-Liase/genética
Pigmentação/genética
Reguladores de Crescimento de Planta/genética
Proteínas de Plantas/genética
Tubérculos/genética
Tubérculos/metabolismo
RNA de Plantas/genética
Fatores de Transcrição/genética
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Anthocyanins); 0 (Glucosides); 0 (Plant Growth Regulators); 0 (Plant Proteins); 0 (RNA, Plant); 0 (Transcription Factors); 6988-81-4 (petunidin-3-glucoside); 8H1WZY9R6P (pelargonidin-3-glucoside); 9035-51-2 (Cytochrome P-450 Enzyme System); EC 1.14.- (flavonoid 3',5'-hydroxylase); EC 4.3.1.24 (Phenylalanine Ammonia-Lyase); EC 6.2.1.- (Coenzyme A Ligases); EC 6.2.1.12 (4-coumarate-CoA ligase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180227
[Lr] Data última revisão:
180227
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180124
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191406


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[PMID]:29352281
[Au] Autor:Al-Harrasi I; Al-Yahyai R; Yaish MW
[Ad] Endereço:Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
[Ti] Título:Differential DNA methylation and transcription profiles in date palm roots exposed to salinity.
[So] Source:PLoS One;13(1):e0191492, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation. To achieve these, whole-genome bisulfite sequencing (WGBS) was employed and mRNA was sequenced from salinity-treated and untreated roots. The WGBS analysis included 324,987,795 and 317,056,091 total reads of the control and the salinity-treated samples, respectively. The analysis covered about 81% of the total genomic DNA with about 40% of mapping efficiency of the sequenced reads and an average read depth of 17-fold coverage per DNA strand, and with a bisulfite conversion rate of around 99%. The level of methylation within the differentially methylated regions (DMRs) was significantly (p < 0.05, FDR ≤ 0.05) increased in response to salinity specifically at the mCHG and mCHH sequence contexts. Consistently, the mass spectrometry and the enzyme-linked immunosorbent assay (ELISA) showed that there was a significant (p < 0.05) increase in the global DNA methylation in response to salinity. mRNA sequencing revealed the presence of 6,405 differentially regulated genes with a significant value (p < 0.001, FDR ≤ 0.05) in response to salinity. Integration of high-resolution methylome and transcriptome analyses revealed a negative correlation between mCG methylation located within the promoters and the gene expression, while a positive correlation was noticed between mCHG/mCHH methylation rations and gene expression specifically when plants grew under control conditions. Therefore, the methylome and transcriptome relationships vary based on the methylated sequence context, the methylated region within the gene, the protein-coding ability of the gene, and the salinity treatment. These results provide insights into interplay among DNA methylation and gene expression, and highlight the effect of salinity on the nature of this relationship, which may involve other genetic and epigenetic players under salt stress conditions. The results obtained from this project provide the first draft map of the differential methylome and transcriptome of date palm when exposed to an abiotic stress.
[Mh] Termos MeSH primário: Metilação de DNA
Phoeniceae/genética
Phoeniceae/metabolismo
Salinidade
[Mh] Termos MeSH secundário: Adaptação Fisiológica/genética
DNA de Plantas/genética
DNA de Plantas/metabolismo
Epigênese Genética
Perfilação da Expressão Gênica
Genes de Plantas
Anotação de Sequência Molecular
Phoeniceae/crescimento & desenvolvimento
Fotossíntese
Raízes de Plantas/genética
Raízes de Plantas/crescimento & desenvolvimento
Raízes de Plantas/metabolismo
Regiões Promotoras Genéticas
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA de Plantas/genética
RNA de Plantas/metabolismo
Sequenciamento Completo do Genoma
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (DNA, Plant); 0 (RNA, Messenger); 0 (RNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180121
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191492


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[PMID]:29372965
[Au] Autor:Punina EO; Machs EM; Krapivskaya EE; Rodionov AV
[Ti] Título:[Polymorphic sites in transcribed spacers of 35S rRNA genes as an indicator of origin of the Paeonia cultivars].
[So] Source:Genetika;53(2):181-91, 2017 Feb.
[Is] ISSN:0016-6758
[Cp] País de publicação:Russia (Federation)
[La] Idioma:rus
[Ab] Resumo:Region ITS1­5.8S rDNA­ITS2 is sequenced in 27 varieties of cultivated ornamental peonies, ten of which presumably originate from Paeonia lactiflora, one from P. officinalis, 13 from hybridization of P. lactiflora and P. peregrina, or P. officinalis, and three are Itoh hybrids. Comparative analysis of distribution patterns of polymorphic sites (PS) for the obtained DNA sequences and data from GenBank is carried out. Hypotheses of origin of the studied varieties, except for two, which, as previously assumed, originate from hybridization of P. lactiflora and P. peregrina, are confirmed. It is shown that the sequence ITS1­5.8S rDNA­ITS2 is a good genetic marker for cultivars of the P. lactiflora group and Itoh hybrids, and that the PS distribution patterns in these sequences can provide valuable information on the kinship and origin of individual varieties. However, insufficient knowledge of wild species from the P. officinalis kinship group limits the use of this marker in the study of varieties obtained through interspecific hybridization within the Paeonia section.
[Mh] Termos MeSH primário: Genes de Plantas
Genes de RNAr
Paeonia/genética
Polimorfismo Genético
RNA de Plantas/genética
RNA Ribossômico/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Plant); 0 (RNA, Ribosomal)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180216
[Lr] Data última revisão:
180216
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180127
[St] Status:MEDLINE


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[PMID]:29262706
[Au] Autor:Yumnam JS; Rai M; Tyagi W
[Ad] Endereço:School of Crop Improvement, College of Post-Graduate Studies, Central Agricultural University (Imphal) , Umiam, Meghalaya 793103.
[Ti] Título:In silico characterisation of novel rice transcripts differentially expressed in phosphorus dificient conditions suggests a role of these transcripts in multiple abiotic stresses.
[So] Source:Acta Biol Hung;68(4):398-411, 2017 Dec.
[Is] ISSN:0236-5383
[Cp] País de publicação:Hungary
[La] Idioma:eng
[Ab] Resumo:Phosphorus deficiency adversely affects crop productivity. The mechanism of tolerance in plants is not well understood. The current study successfully annotated a set of highly significant (Log RPKM ≥3) nine novel sequences up-regulated in P deficient condition identified from a low P tolerant rice genotype. Sequence annotation identified two transcripts (Os01g37260 and Os02g11060) carrying known domains, F-box and WD, respectively. Multiple Expectation maximization for Motif Elicitation (MEME) revealed presence of conserved domains like D[LP][HY][CL]D[CM][DT]C[AP][DQ][IQ]C, [EH][DN]HN[HS] [ER][FY][EP]I[HN]H which might play a role in phosphorus deficiency tolerance. Analysis of the upstream regions indicated presence of stress responsive elements like E Box, ABRE, and MYBCORE suggesting regulation of the novel transcripts by DNA binding. Protein localization prediction tool suggests that these novel proteins might be targeted to nucleus, chloroplast and cell wall. Transcripts Os02g03640 and Os02g10250 revealed potential target sites for microRNA binding suggesting role of novel miRNAs in low phosphorus response. Our analysis suggests that an F-box protein, Os01g37260 (OSFBx14) might be a promising candidate gene playing a role in multiple abiotic stresses including P deficiency.
[Mh] Termos MeSH primário: Regulação da Expressão Gênica de Plantas
MicroRNAs/biossíntese
Oryza/metabolismo
Fósforo/deficiência
RNA de Plantas/biossíntese
Estresse Fisiológico
[Mh] Termos MeSH secundário: MicroRNAs/genética
Oryza/genética
Fósforo/metabolismo
RNA de Plantas/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (RNA, Plant); 27YLU75U4W (Phosphorus)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180216
[Lr] Data última revisão:
180216
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171222
[St] Status:MEDLINE
[do] DOI:10.1556/018.68.2017.4.6


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[PMID]:29320569
[Au] Autor:Guo WL; Chen BH; Chen XJ; Guo YY; Yang HL; Li XZ; Wang GY
[Ad] Endereço:School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China.
[Ti] Título:Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew.
[So] Source:PLoS One;13(1):e0190175, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line "112-2" using RNA sequencing (RNA-Seq). The inbred line "112-2" has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line "112-2" at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant "112-2" were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar "Jiujiangjiaoding"). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM.
[Mh] Termos MeSH primário: Ascomicetos/fisiologia
Cucurbita/genética
Perfilação da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Genes de Plantas
Doenças das Plantas/genética
Folhas de Planta/metabolismo
[Mh] Termos MeSH secundário: Resistência à Doença
Biblioteca Gênica
Ontologia Genética
Redes e Vias Metabólicas/genética
Fotossíntese/genética
Reguladores de Crescimento de Planta/fisiologia
Folhas de Planta/microbiologia
RNA de Plantas/biossíntese
RNA de Plantas/genética
Análise de Sequência de RNA
Transdução de Sinais/genética
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Growth Regulators); 0 (RNA, Plant); 0 (Transcription Factors)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180214
[Lr] Data última revisão:
180214
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190175


  9 / 8492 MEDLINE  
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[PMID]:29320527
[Au] Autor:Balic I; Vizoso P; Nilo-Poyanco R; Sanhueza D; Olmedo P; Sepúlveda P; Arriagada C; Defilippi BG; Meneses C; Campos-Vargas R
[Ad] Endereço:Universidad Andrés Bello, Facultad Ciencias Biológicas, Centro de Biotecnología Vegetal, Santiago, Chile.
[Ti] Título:Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless.
[So] Source:PLoS One;13(1):e0190087, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless. Functional analysis showed a transcriptional increase in genes related with degradation processes of chlorophyll, lipids, macromolecules recycling and nucleosomes organization; accompanied by a decrease in genes related with chloroplasts integrity and amino acid synthesis pathways. It was possible to identify several processes described during leaf senescence, particularly close to harvest. Before this point, the results suggest a high transcriptional activity associated with the regulation of gene expression, cytoskeletal organization and cell wall metabolism, which can be related to growth of berries and firmness loss characteristic to this stage of development. This high metabolic activity could be associated with an increase in the transcription of genes related with glycolysis and respiration, unexpected for a non-climacteric fruit ripening.
[Mh] Termos MeSH primário: Frutas/crescimento & desenvolvimento
Regulação da Expressão Gênica no Desenvolvimento
Regulação da Expressão Gênica de Plantas
Genes de Plantas
Transcriptoma
Vitis/genética
[Mh] Termos MeSH secundário: Frutas/metabolismo
Perfilação da Expressão Gênica
Ontologia Genética
Redes e Vias Metabólicas/genética
Fenótipo
Proteínas de Plantas/genética
RNA de Plantas/biossíntese
RNA de Plantas/genética
RNA de Plantas/isolamento & purificação
Reação em Cadeia da Polimerase em Tempo Real
Vitis/crescimento & desenvolvimento
Vitis/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Proteins); 0 (RNA, Plant)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180214
[Lr] Data última revisão:
180214
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190087


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[PMID]:29273556
[Au] Autor:Sobhani Najafabadi A; Naghavi MR
[Ad] Endereço:Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box: 85135-487, Isfahan, Iran. Electronic address: ahmad.sobhani@ut.ac.ir.
[Ti] Título:Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes.
[So] Source:Gene;645:41-47, 2018 Mar 01.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Ferula gummosa is a well-known medicinal and industrial plant for its oleo-gum-resin named galbanum. So far, there is no information about the role of miRNAs on the production of terpenes as the major secondary metabolite of galbanum. In the present study, RNA-seq data on the root and flower of the plant were used to predict miRNAs and their targets using computational approaches. Additionally, biological network analyses were used to unravel the direct or indirect regulatory effects of miRNAs on the targets involved in terpene biosynthesis. For the first time, 220 miRNAs from 94 families have been reported in F. gummosa. miR5658, miR1533, miR5021, miR414, and miR1436 are the top five miRNAs with high abundance. Gene ontology (GO) analysis of the identified targets showed that in the biological process category, the miRNA-regulated genes were highly involved in transcription. According to the KEGG and PlantCyc results, six miRNAs from five miRNA families including miR2919, miR5251, miR838, miR5021, and miR5658 were found to be related to the pathway of terpene biosynthesis. Moreover, network analysis showed that three terpene-regulating TFs namely SPL7, SPL11, and ATHB13 are putatively regulated by three miRNAs including miR1533, miR5021, and miR5658 respectively. Differential gene expression results showed that the expression levels of these miRNAs are negatively correlated to the expression levels of both TFs and their co-expressed terpene biosynthesis genes.
[Mh] Termos MeSH primário: Ferula/genética
Perfilação da Expressão Gênica/métodos
MicroRNAs/genética
Análise de Sequência de RNA/métodos
[Mh] Termos MeSH secundário: Regulação da Expressão Gênica de Plantas
Ontologia Genética
Redes Reguladoras de Genes
Proteínas de Plantas/genética
RNA de Plantas/genética
Metabolismo Secundário
Terpenos/metabolismo
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs); 0 (Plant Proteins); 0 (RNA, Plant); 0 (Terpenes); 0 (Transcription Factors)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180129
[Lr] Data última revisão:
180129
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171224
[St] Status:MEDLINE



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