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1.
Food Chem ; 338: 127997, 2021 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-33091988

RESUMO

Flavonols are gaining increasing interests due to their diverse health benefits for humans. Broccoli is a main flavonol source in our diet, but the genetic variation of flavonols and their correlation with antioxidant capacity remain to be understood. Here, we examined variations of the two major flavonols kaempferol and quercetin in florets and leaves of 15 diverse broccoli accessions by ultra-performance liquid chromatography. Broccoli accumulated more kaempferol than quercetin in most of the accessions tested, with the ratios varying from 4.4 to 27.9 in leaves and 0.4 to 4.4 in florets. Total flavonoids showed 2.5-fold and 3.3-fold differences in leaves and florets of these accessions, respectively. Principle component analysis revealed that flavonols, along with the key biosynthetic pathway genes, correlated with antioxidant capacity related indicators. This study provides important information for broccoli flavonol genotypic variations and correlation with antioxidant capacity, and will facilitate the development of flavonol enriched cultivars in broccoli.


Assuntos
Antioxidantes/química , Brassica/genética , Flavonóis/análise , Variação Genética , Antioxidantes/metabolismo , Brassica/química , Brassica/metabolismo , Catalase/metabolismo , Cromatografia Líquida de Alta Pressão , Flavonóis/metabolismo , Genótipo , Humanos , Folhas de Planta/química , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/metabolismo , Análise de Componente Principal , RNA de Plantas/química , RNA de Plantas/metabolismo , Superóxido Dismutase/metabolismo
2.
Nat Commun ; 11(1): 6031, 2020 11 27.
Artigo em Inglês | MEDLINE | ID: mdl-33247135

RESUMO

Plant spermatogenesis is a complex process that directly affects crop breeding. A rapid change in gene abundance occurs at early meiosis prophase, when gene regulation is selective. However, how these genes are regulated remains unknown. Here, we show that rice reproductive phasiRNAs are essential for the elimination of a specific set of RNAs during meiotic prophase I. These phasiRNAs cleave target mRNAs in a regulatory manner such that one phasiRNA can target more than one gene, and/or a single gene can be targeted by more than one phasiRNA to efficiently silence target genes. Our investigation of phasiRNA-knockdown and PHAS-edited transgenic plants demonstrates that phasiRNAs and their nucleotide variations are required for meiosis progression and fertility. This study highlights the importance of reproductive phasiRNAs for the reprogramming of gene expression during meiotic progression and establishes a basis for future studies on the roles of phasiRNAs with a goal of crop improvement.


Assuntos
Regulação da Expressão Gênica de Plantas , Meiose/genética , Oryza/citologia , Oryza/genética , RNA de Plantas/metabolismo , Sequência de Bases , Fertilidade/genética , Gametogênese Vegetal/genética , Modelos Biológicos , Nucleotídeos/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Pólen/citologia , Pólen/genética , Clivagem do RNA , RNA de Plantas/genética , Reprodutibilidade dos Testes
3.
PLoS One ; 15(10): e0239230, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33057394

RESUMO

Trichosanthes kirilowii Maxim. (TK) is a dioecious plant in the Cucurbitaceae for which different sexes have separate medicinal uses. In order to study the genes related to sex determination, transcriptome sequencing was performed on flower buds of male and female plants using the high-throughput sequencing technology. A total of 145,975 unigenes and 7110 DEGs were obtained. There were 6776 DEGs annotated to 1234 GO terms and enriched to 18 functional groups, including five biological processes related to sugar metabolism. KEGG pathway analysis indicated genes involved in hormone transduction, hormone synthesis and carbohydrate metabolism. Many DEGs of TK are involved in reproductive organ formation, hormone signal transduction and regulatory networks. Combining the results of GO, KEGG and qRT-PCR, 11 sex determining candidate genes of TK were selected, including MYB80, MYB108, CER1, CBL9, ABCB19, SERK1, HSP81-3, ACS9, SEP3, AUX1 and YUC6. The results provide a foundation for the study of sex differentiation in TK.


Assuntos
Proteínas de Plantas/genética , Transcriptoma , Trichosanthes/genética , Metabolismo dos Carboidratos/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes/genética , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Reguladores de Crescimento de Planta/genética , Reguladores de Crescimento de Planta/metabolismo , Proteínas de Plantas/metabolismo , RNA de Plantas/química , RNA de Plantas/isolamento & purificação , RNA de Plantas/metabolismo , Transdução de Sinais/genética , Trichosanthes/crescimento & desenvolvimento
4.
Nat Commun ; 11(1): 5441, 2020 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-33116138

RESUMO

With global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification of SLG1 (Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice. SLG1 plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction of SLG1 results in plants with thermosensitive phenotype, while overexpression of SLG1 enhances the tolerance of plants to high temperature. SLG1 is differentiated between the two Asian cultivated rice subspecies, indica and japonica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance of indica rice varieties. Our results demonstrate that the allelic differentiation of SLG1 confers indica rice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe.


Assuntos
Genes de Plantas , Oryza/genética , Oryza/fisiologia , Termotolerância/genética , Termotolerância/fisiologia , Variação Genética , Aquecimento Global , Modelos Biológicos , Melhoramento Vegetal , Proteínas de Plantas/genética , Proteínas de Plantas/fisiologia , Regiões Promotoras Genéticas , Processamento Pós-Transcricional do RNA/genética , Processamento Pós-Transcricional do RNA/fisiologia , RNA de Plantas/metabolismo , RNA de Transferência/metabolismo , Tionucleotídeos/metabolismo
5.
Nat Commun ; 11(1): 5343, 2020 10 22.
Artigo em Inglês | MEDLINE | ID: mdl-33093443

RESUMO

Plants transmit signals long distances, as evidenced in grafting experiments that create distinct rootstock-scion junctions. Noncoding small RNA is a signaling molecule that is graft transmissible, participating in RNA-directed DNA methylation; but the meiotic transmissibility of graft-mediated epigenetic changes remains unclear. Here, we exploit the MSH1 system in Arabidopsis and tomato to introduce rootstock epigenetic variation to grafting experiments. Introducing mutations dcl2, dcl3 and dcl4 to the msh1 rootstock disrupts siRNA production and reveals RdDM targets of methylation repatterning. Progeny from grafting experiments show enhanced growth vigor relative to controls. This heritable enhancement-through-grafting phenotype is RdDM-dependent, involving 1380 differentially methylated genes, many within auxin-related gene pathways. Growth vigor is associated with robust root growth of msh1 graft progeny, a phenotype associated with auxin transport based on inhibitor assays. Large-scale field experiments show msh1 grafting effects on tomato plant performance, heritable over five generations, demonstrating the agricultural potential of epigenetic variation.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Lycopersicon esculentum/genética , Proteína MutS de Ligação de DNA com Erro de Pareamento/genética , Proteínas de Plantas/genética , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/fisiologia , Proteínas de Arabidopsis/fisiologia , Metilação de DNA , Epigênese Genética , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/fisiologia , Proteína MutS de Ligação de DNA com Erro de Pareamento/fisiologia , Mutação , Fenótipo , Melhoramento Vegetal , Proteínas de Plantas/fisiologia , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/fisiologia , Plantas Geneticamente Modificadas , RNA de Plantas/genética , RNA de Plantas/metabolismo , RNA Interferente Pequeno/genética , Transdução de Sinais/genética , Transdução de Sinais/fisiologia
6.
Nat Commun ; 11(1): 5191, 2020 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-33060587

RESUMO

In grasses, phased small interfering RNAs (phasiRNAs), 21- or 24-nucleotide (nt) in length, are predominantly expressed in anthers and play a role in regulating male fertility. However, their targets and mode of action on the targets remain unknown. Here we profile phasiRNA expression in premeiotic and meiotic spikelets as well as in purified male meiocytes at early prophase I, tetrads and microspores in rice. We show that 21-nt phasiRNAs are most abundant in meiocytes at early prophase I while 24-nt phasiRNAs are more abundant in tetrads and microspores. By performing highly sensitive degradome sequencing, we find that 21-nt phasiRNAs direct target mRNA cleavage in male germ cells, especially in meiocytes at early prophase I. These targets include 435 protein-coding genes and 71 transposons that show an enrichment for carbohydrate biosynthetic and metabolic pathways. Our study provides strong evidence that 21-nt phasiRNAs act in a target-cleavage mode and may facilitate the progression of meiosis by fine-tuning carbohydrate biosynthesis and metabolism in male germ cells.


Assuntos
Células Germinativas/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , RNA Mensageiro/metabolismo , RNA de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas , Meiose/fisiologia , Nucleotídeos , Oryza/embriologia , Oryza/genética , Proteínas de Plantas/genética , RNA Replicase/metabolismo , RNA de Plantas/genética , RNA Interferente Pequeno/metabolismo , Transcriptoma
7.
Plant Mol Biol ; 104(6): 629-645, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32909184

RESUMO

KEY MESSAGE: Rice aconitase gene OsACO1 is involved in the iron deficiency-signaling pathway for the expression of iron deficiency-inducible genes, either thorough enzyme activity or possible specific RNA binding for post-transcriptional regulation. Iron (Fe) is an essential element for virtually all living organisms. When plants are deficient in Fe, Fe acquisition systems are activated to maintain Fe homeostasis, and this regulation is mainly executed at the gene transcription level. Many molecules responsible for Fe uptake, translocation, and storage in plants have been identified and characterized. However, how plants sense Fe status within cells and then induce a transcriptional response is still unclear. In the present study, we found that knockdown of the OsACO1 gene, which encodes an aconitase in rice, leads to the down-regulation of selected Fe deficiency-inducible genes involved in Fe uptake and translocation in roots, and a decrease in Fe concentration in leaves, even when grown under Fe-sufficient conditions. OsACO1 knockdown plants showed a delayed transcriptional response to Fe deficiency compared to wild-type plants. In contrast, overexpression of OsACO1 resulted in the opposite effects. These results suggest that OsACO1 is situated upstream of the Fe deficiency-signaling pathway. Furthermore, we found that the OsACO1 protein potentially has RNA-binding activity. In vitro screening of RNA interactions with OsACO1 revealed that RNA potentially forms a unique stem-loop structure that interacts with OsACO1 via a conserved GGUGG motif within the loop structure. These results suggest that OsACO1 regulate Fe deficiency response either thorough enzyme activity catalyzing isomerization of citrate, or specific RNA binding for post-transcriptional regulation.


Assuntos
Aconitato Hidratase/genética , Ferro/metabolismo , Oryza/enzimologia , Aconitato Hidratase/metabolismo , Citratos/metabolismo , Regulação da Expressão Gênica de Plantas , Técnicas de Silenciamento de Genes , Genes de Plantas , Homeostase , Oryza/genética , Oryza/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , RNA de Plantas/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Transdução de Sinais
8.
Plant Physiol Biochem ; 155: 769-779, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32866790

RESUMO

Winter wheat not only provides adequate fresh forage grass in winter, but also ensures ample grain production in summer. The mechanisms underlying the regeneration of winter wheat after mowing or grazing are not well understood. In this study, the miRNA expression profile of winter wheat was determined using RNA sequencing and the endogenous auxin and cis-zeatin concentrations, as well as the expression of related miRNA-targeted genes, were measured. During the post-mowing regeneration of winter wheat, the concentrations of endogenous indole-3-acetic acid (IAA), methyl indole-3-acetate (ME-IAA), and indole-3-carboxaldehyde (ICA) decreased, while those of cis-zeatin (cZ) increased. Moreover, 15 novel miRNAs and three known miRNAs were found to be involved in the synthesis and signalling transduction of auxins and cytokinins (CKs). Among these miRNAs, miR1153-y, miR5059-x, miR2916-x, novel-miR1532-3p, novel-miR1060-3p, and novel-miR0890-3p, were found to be negatively correlated with the expression of their target genes including auxin response GH3.7, auxin response factor (ARF), type-A two-component response regulator (A-ARR), aldehyde dehydrogenase (ALDH), and O-glucosyltransferase (CISZOG). Furthermore, miR1153-y was identified as mediating the cleavage of GH3.7 by RACE assay. In turn, these genes inhibited the biosynthesis and signalling of IAA and activated CK signal transduction, resulting in the rapid regeneration of mowed winter wheat. This study revealed that some miRNAs exert a positive regulatory effect on the post-mowing regeneration of winter wheat by controlling the synthesis and signal transduction of IAA and CK, and our founding will aid developments in biotechnology aimed at improving the post-mowing regeneration ability of winter wheat.


Assuntos
Citocininas/metabolismo , Ácidos Indolacéticos/metabolismo , MicroRNAs/metabolismo , Triticum/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , RNA de Plantas/metabolismo , Transdução de Sinais , Triticum/metabolismo
9.
PLoS One ; 15(8): e0237457, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32780764

RESUMO

Onion (Allium cepa L.) is an important vegetable crop widely grown for diverse culinary and nutraceutical properties. Being a shallow-rooted plant, it is prone to drought. In the present study, transcriptome sequencing of drought-tolerant (1656) and drought-sensitive (1627) onion genotypes was performed to elucidate the molecular basis of differential response to drought stress. A total of 123206 and 139252 transcripts (average transcript length: 690 bases) were generated after assembly for 1656 and 1627, respectively. Differential gene expression analyses revealed upregulation and downregulation of 1189 and 1180 genes, respectively, in 1656, whereas in 1627, upregulation and downregulation of 872 and 1292 genes, respectively, was observed. Genes encoding transcription factors, cytochrome P450, membrane transporters, and flavonoids, and those related to carbohydrate metabolism were found to exhibit a differential expression behavior in the tolerant and susceptible genotypes. The information generated can facilitate a better understanding of molecular mechanisms underlying drought response in onion.


Assuntos
Secas , Regulação da Expressão Gênica de Plantas , Cebolas/genética , Metabolismo dos Carboidratos/genética , Perfilação da Expressão Gênica/métodos , Genótipo , Proteínas de Membrana Transportadoras/genética , RNA de Plantas/química , RNA de Plantas/metabolismo , Fatores de Transcrição/genética
10.
Gene ; 759: 145002, 2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-32726608

RESUMO

Recent evidence has shown that microRNAs are transferred from one species to another through cross-species transmission and exhibit biological activities in the receptor. However, the cross-kingdom regulation of pathogen virulence by plant-derived miRNAs is rarely reported. This study investigated the regulatory role of novel tomato miRNA miR1001 in the growth and development of Botrytis cinerea. Results showed that miR1001 inhibited the virulence of B. cinerea-infected plants, and the inhibitory effect of miR1001/miR1001* was stronger than that of miR1001. Moreover, miR1001 exerted a significant inhibitory effect on the conidiospore germination of B. cinerea. Degradome-seq experiment showed that miR1001 can directly target the Bcin03g02170.1 and Bcin10g01400.1 genes, which respectively encode the ATP-dependent metallopeptidase and cysteine-type endopeptidase, in B. cinerea. The interactions of both targets with miR1001 were further confirmed by using transient co-expression in tobacco. Real-time RT-PCR analysis showed that the expression levels of the two target genes were significantly downregulated in B. cinerea with miR1001 treatment. Our findings provide new evidence into the coevolution of pathogens and host plants, as well as new directions for the use of plant-derived miRNAs to control pathogens.


Assuntos
Botrytis/patogenicidade , Proteínas Fúngicas/genética , Interações Hospedeiro-Patógeno , Lycopersicon esculentum/genética , MicroRNAs/metabolismo , RNA de Plantas/metabolismo , Botrytis/fisiologia , Proteínas Fúngicas/metabolismo , Lycopersicon esculentum/microbiologia , MicroRNAs/genética , RNA de Plantas/genética , Esporos Fúngicos/fisiologia
11.
PLoS One ; 15(7): e0236588, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32706804

RESUMO

Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.


Assuntos
Resposta ao Choque Frio/genética , Metaboloma , Metabolômica/métodos , Sapindaceae/metabolismo , Transcriptoma , Aminoácidos/metabolismo , Catalase/metabolismo , Temperatura Baixa , Regulação da Expressão Gênica de Plantas , Malondialdeído/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/metabolismo , Análise de Componente Principal , RNA de Plantas/genética , RNA de Plantas/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Sapindaceae/genética , Transdução de Sinais/genética , Superóxido Dismutase/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
12.
PLoS One ; 15(7): e0236530, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32706831

RESUMO

Apple trees grafted on different rootstock types, including vigorous rootstock (VR), dwarfing interstock (DIR), and dwarfing self-rootstock (DSR), are widely planted in production, but the molecular determinants of tree branch architecture growth regulation induced by rootstocks are still not well known. In this study, the branch growth phenotypes of three combinations of 'Fuji' apple trees grafted on different rootstocks (VR: Malus baccata; DIR: Malus baccata/T337; DSR: T337) were investigated. The VR trees presented the biggest branch architecture. The results showed that the sugar content, sugar metabolism-related enzyme activities, and hormone content all presented obvious differences in the tender leaves and buds of apple trees grafted on these rootstocks. Transcriptomic profiles of the tender leaves adjacent to the top buds allowed us to identify genes that were potentially involved in signaling pathways that mediate the regulatory mechanisms underlying growth differences. In total, 3610 differentially expressed genes (DEGs) were identified through pairwise comparisons. The screened data suggested that sugar metabolism-related genes and complex hormone regulatory networks involved the auxin (IAA), cytokinin (CK), abscisic acid (ABA) and gibberellic acid (GA) pathways, as well as several transcription factors, participated in the complicated growth induction process. Overall, this study provides a framework for analysis of the molecular mechanisms underlying differential tree branch growth of apple trees grafted on different rootstocks.


Assuntos
Regulação da Expressão Gênica de Plantas , Malus/genética , Transdução de Sinais/genética , Açúcares/metabolismo , Ácido Abscísico/análise , Ácido Abscísico/metabolismo , Cromatografia Líquida de Alta Pressão , Citocininas/análise , Citocininas/metabolismo , Flores/genética , Flores/metabolismo , Giberelinas/análise , Giberelinas/metabolismo , Ácidos Indolacéticos/análise , Ácidos Indolacéticos/metabolismo , Malus/crescimento & desenvolvimento , Fenótipo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/metabolismo , Caules de Planta/genética , Caules de Planta/fisiologia , RNA de Plantas/genética , RNA de Plantas/metabolismo , Açúcares/análise , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , alfa-Glucosidases/genética , alfa-Glucosidases/metabolismo
13.
PLoS One ; 15(7): e0236586, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32726362

RESUMO

Short rotation woody biomass cultivars developed from fast-growing shrub species of willow (Salix spp.) have superior properties as perennial energy crops for the Northeast and Midwest US. However, the insect pest potato leafhopper (PLH) Empoasca fabae (Harris) can cause serious damage and reduce yield of susceptible genotypes. Currently, the willow cultivars in use display varying levels of susceptibility under PLH infestation. However, genes and markers for resistance to PLH are not yet available for marker-assisted selection in breeding. In this study, transcriptome differences between a resistant genotype 94006 (S. purpurea) and a susceptible cultivar 'Jorr' (S. viminalis), and their hybrid progeny were determined. Over 600 million RNA-Seq reads were generated and mapped to the Salix purpurea reference transcriptome. Gene expression analyses revealed the unique defense mechanism in resistant genotype 94006 that involves PLH-induced secondary cell wall modification. In the susceptible genotypes, genes involved in programed cell death were highly expressed, explaining the necrosis symptoms after PLH feeding. Overall, the discovery of resistance genes and defense mechanisms provides new resources for shrub willow breeding and research in the future.


Assuntos
Salix/genética , Transcriptoma , Animais , Apoptose/genética , Parede Celular/química , Parede Celular/metabolismo , Produtos Agrícolas , Perfilação da Expressão Gênica , Redes Reguladoras de Genes/genética , Genótipo , Hemípteros/fisiologia , Herbivoria , Interações Hospedeiro-Parasita/genética , Fenótipo , Análise de Componente Principal , RNA de Plantas/química , RNA de Plantas/metabolismo , Salix/parasitologia
14.
Sci Rep ; 10(1): 12573, 2020 07 28.
Artigo em Inglês | MEDLINE | ID: mdl-32724138

RESUMO

Purple-fleshed sweet potato (PFSP) is an important food crop, as it is a rich source of nutrients and anthocyanin pigments. Drought has become a major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted to identify drought stress-responsive genes using next-generation (NGS) and third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with a 30% solution of polyethylene glycol (PEG-6000) for 0, 1, 6, 12, and 48 h for second-generation sequencing. Leaf samples taken from upper third of sweet potato seedlings after 1, 6, 12, and 48 h of drought stress were used for the construction of cDNA libraries for third-generation sequencing; however, leaf samples from untreated plants were collected as controls. A total of 184,259,679 clean reads were obtained using second and third-generation sequencing and then assembled into 17,508 unigenes with an average length of 1,783 base pairs. Out of 17,508 unigenes, 642 (3.6%) unigenes failed to hit any homologs in any databases, which might be considered novel genes. A total of 2, 920, 1578, and 2,418 up-regulated unigenes and 3,834, 2,131, and 3,337 down-regulated unigenes from 1 h, 6 h, 12 h, and 48 h library were identified, respectively in drought stress versus control. In addition, after 6, 12, and 48 h of drought stress, 540 up-regulated unigenes, 486 down-regulated unigenes and 414 significantly differentially expressed unigenes were detected. It was found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine zipper (HD-ZIP), MYB, NAC (NAM, ATAF1/2, and CUC2), Thiol specific antioxidant and WRKY showed responses to drought stress. In total, 17,472 simple sequence repeats and 510,617 single nucleotide polymorphisms were identified based on transcriptome sequencing of the PFSP. About 96.55% of the obtained sequences are not available online in sweet potato genomics resources. Therefore, it will enrich annotated sweet potato gene sequences and enhance understanding of the mechanisms of drought tolerance through genetic manipulation. Moreover, it represents a sequence resource for genetic and genomic studies of sweet potato.


Assuntos
Ipomoea batatas/fisiologia , Proteínas de Plantas/genética , Poliploidia , RNA de Plantas/genética , Secas , Regulação da Expressão Gênica de Plantas , Ipomoea batatas/genética , Proteínas de Plantas/metabolismo , RNA de Plantas/metabolismo , Análise de Sequência de RNA , Estresse Fisiológico , Transcriptoma
15.
PLoS One ; 15(7): e0235975, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32649704

RESUMO

Rice cultivar "Weiyou916" (Oryza sativa L. ssp. Indica) were cultured with control (10 mM NO3-) and nitrate deficient solution (0 mM NO3-) for four weeks. Nitrogen (N) deficiency significantly decreased the content of N and P, dry weight (DW) of the shoots and roots, but increased the ratio of root to shoot in O. sativa. N deficiency decreased the photosynthesis rate and the maximum quantum yield of primary photochemistry (Fv/Fm), however, increased the intercellular CO2 concentration and primary fluorescence (Fo). N deficiency significantly increased the production of H2O2 and membrane lipid peroxidation revealed as increased MDA content in O. sativa leaves. N deficiency significantly increased the contents of starch, sucrose, fructose, and malate, but did not change that of glucose and total soluble protein in O. sativa leaves. The accumulated carbohydrates and H2O2 might further accelerate biosynthesis of lignin in O. sativa leaves under N limitation. A total of 1635 genes showed differential expression in response to N deficiency revealed by Illumina sequencing. Gene Ontology (GO) analysis showed that 195 DEGs were found to highly enrich in nine GO terms. Most of DEGs involved in photosynthesis, biosynthesis of ethylene and gibberellins were downregulated, whereas most of DEGs involved in cellular transport, lignin biosynthesis and flavonoid metabolism were upregulated by N deficiency in O. sativa leaves. Results of real-time quantitative PCR (RT-qPCR) further verified the RNA-Seq data. For the first time, DEGs involved oxygen-evolving complex, phosphorus response and lignin biosynthesis were identified in rice leaves. Our RNA-Seq data provided a global view of transcriptomic profile of principal processes implicated in the adaptation of N deficiency in O. sativa and shed light on the candidate direction in rice breeding for green and sustainable agriculture.


Assuntos
Flavonoides/metabolismo , Lignina/metabolismo , Nitratos/metabolismo , Oryza/genética , Fotossíntese , Carboidratos/análise , Clorofila A/química , Regulação da Expressão Gênica de Plantas , Peróxido de Hidrogênio/metabolismo , Malondialdeído/metabolismo , Oryza/metabolismo , Oxirredução , Folhas de Planta/genética , Folhas de Planta/metabolismo , Raízes de Plantas/metabolismo , Brotos de Planta/metabolismo , RNA de Plantas/química , RNA de Plantas/metabolismo , Análise de Sequência de RNA
16.
Nucleic Acids Res ; 48(14): 7700-7711, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32652016

RESUMO

Arabidopsis thaliana transcriptomes have been extensively studied and characterized under different conditions. However, most of the current 'RNA-sequencing' technologies produce a relatively short read length and demand a reverse-transcription step, preventing effective characterization of transcriptome complexity. Here, we performed Direct RNA Sequencing (DRS) using the latest Oxford Nanopore Technology (ONT) with exceptional read length. We demonstrate that the complexity of the A. thaliana transcriptomes has been substantially under-estimated. The ONT direct RNA sequencing identified novel transcript isoforms at both the vegetative (14-day old seedlings, stage 1.04) and reproductive stages (stage 6.00-6.10) of development. Using in-house software called TrackCluster, we determined alternative transcription initiation (ATI), alternative polyadenylation (APA), alternative splicing (AS), and fusion transcripts. More than 38 500 novel transcript isoforms were identified, including six categories of fusion-transcripts that may result from differential RNA processing mechanisms. Aided by the Tombo algorithm, we found an enrichment of m5C modifications in the mobile mRNAs, consistent with a recent finding that m5C modification in mRNAs is crucial for their long-distance movement. In summary, ONT DRS offers an advantage in the identification and functional characterization of novel RNA isoforms and RNA base modifications, significantly improving annotation of the A. thaliana genome.


Assuntos
Arabidopsis/genética , Sequenciamento por Nanoporos/métodos , RNA de Plantas/química , RNA de Plantas/metabolismo , Análise de Sequência de RNA/métodos , Transcriptoma , Citosina/metabolismo , Metilação , Isoformas de RNA/química , Isoformas de RNA/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , RNA-Seq
17.
Sci Rep ; 10(1): 12193, 2020 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-32699241

RESUMO

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12-mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins.


Assuntos
Resistência à Doença/genética , Genômica , Proteínas de Plantas/metabolismo , Vitis/metabolismo , Bases de Dados Genéticas , Cromatografia Gasosa-Espectrometria de Massas , Regulação da Expressão Gênica de Plantas , Genômica/métodos , Metaboloma , Peronospora/isolamento & purificação , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Folhas de Planta/metabolismo , Folhas de Planta/microbiologia , Proteínas de Plantas/genética , Análise de Componente Principal , RNA de Plantas/química , RNA de Plantas/genética , RNA de Plantas/metabolismo , RNA-Seq , Vitis/microbiologia
18.
Curr Opin Plant Biol ; 57: 52-60, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32634685

RESUMO

Intercellular communication in plants coordinates cellular functions during growth and development, and in response to environmental cues. RNAs figure prominently among the mobile signaling molecules used. Many hundreds of RNA species move over short and long distances, and can be mutually exchanged in biotic interactions. Understanding the specificity determinants of RNA mobility and the physiological relevance of this phenomenon are areas of active research. Here, we highlight the recent progress in our knowledge of small RNA and messenger RNA movement. Particular emphasis is given to novel insight into the specificity determinants of messenger RNA mobility, the role of small RNA movement in development, and the specificity of RNA exchange in plant-plant and plant-microbe interactions.


Assuntos
Plantas , Transporte de RNA , Comunicação Celular , Plantas/genética , Plantas/metabolismo , RNA Mensageiro/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo
19.
Mol Phylogenet Evol ; 150: 106878, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32512196

RESUMO

Stachyuraceae, an East Asian endemic family of shrubs or small trees, comprises a single genus, Stachyurus (c. 11 spp.). Despite previous extensive studies based on both morphology and molecular data, species relationships within Stachyurus are still unresolved. Here, we employed transcriptome data aiming to elucidate the evolutionary history of Stachyurus and investigate possible causes of phylogenetic incongruence among individual gene trees in this genus. Our transcriptome phylogeny strongly supports four major clades of Stachyurus, with S. praecox from Japan being resolved as sister to the remainder of the genus on the Asian mainland. The deciduous S. praecox in Japan appears to have originated in the late Miocene, while the remainder diversified and expanded on the mainland over late Miocene to Pliocene/early Pleistocene times. These latter episodes of diversification and expansion were likely promoted by changes in paleoclimate and orogeny (e.g., late Miocene uplift of the Hengduan Mts. and/or enforcement of the East Asian summer monsoon). Species of this genus evolved from a deciduous ancestor, followed by multiple and independent transitions in leaf habit, possibly reflecting climate-related adaptations. Phylogenetic incongruence observed among individual gene trees may be attributable to incomplete lineage sorting following ancient rapid diversification and frequent interspecific gene flow caused by hybridization events. In sum, this study demonstrates the potential usefulness of genome-wide phylogenetic incongruence and network analyses for reconstructing complex evolutionary histories in rapidly diversifying and naturally hybridizing species groups.


Assuntos
Magnoliopsida/classificação , Evolução Biológica , Hibridização Genética , Magnoliopsida/genética , Filogenia , Folhas de Planta/genética , RNA de Plantas/genética , RNA de Plantas/metabolismo , Transcriptoma
20.
Proc Natl Acad Sci U S A ; 117(26): 15316-15321, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32541063

RESUMO

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. At Arabidopsis thaliana FLC, antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3' processing factors, reduces FLC transcription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over the FLC gene body. SDG26 interacts with the RNA 3' processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repress FLC Overall, our work provides insights into RNA-mediated chromatin silencing.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Regulação da Expressão Gênica de Plantas/fisiologia , RNA Antissenso , RNA de Plantas/metabolismo , Transcrição Genética/fisiologia , Proteínas de Arabidopsis/genética , Cromatina , RNA de Plantas/genética
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