Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment.
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ABSTRACT:
SUBMITTER: Ye Y
PROVIDER: S-EPMC8216796 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Flowering time is an important factor determining yield and seed quality in maize. A change in flowering time is a strategy used to survive abiotic stresses. Among abiotic stresses, drought can increase anthesis-silking intervals (ASI), resulting in negative effects on maize yield. We have analyzed the correlation between flowering time and drought stress using RNA-seq and bioinformatics tools. Our results identified a total of 619 genes and 126 transcripts whose expression was altered by drought stress in the maize B73 leaves under short-day condition. Among drought responsive genes, we also identified 20 genes involved in flowering times. Gene Ontology (GO) enrichment analysis was used to predict the functions of the drought-responsive genes and transcripts. GO categories related to flowering time included reproduction, flower development, pollen-pistil interaction, and post-embryonic development. Transcript levels of several genes that have previously been shown to affect flowering time, such as PRR37, transcription factor HY5, and CONSTANS, were significantly altered by drought conditions. Furthermore, we also identified several drought-responsive transcripts containing C2H2 zinc finger, CCCH, and NAC domains, which are frequently involved in transcriptional regulation and may thus have potential to alter gene expression programs to change maize flowering time. Overall, our results provide a genome-wide analysis of differentially expressed genes (DEGs), novel transcripts, and isoform variants expressed during the reproductive stage of maize plants subjected to drought stress and short-day condition. Further characterization of the drought-responsive transcripts identified in this study has the potential to advance our understanding of the mechanisms that regulate flowering time under drought stress.
| S-EPMC5331056 | biostudies-literature
Project description:Xanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink's medium and from infected strawberry cv. Elsanta plants were isolated and sequenced using the Illumina MiSeq platform. The expression profiles of the bacteria in Wilbrink's medium and in planta were very diverse. Of the 3939 CDSs recorded, 1995 had significantly different expression in planta (966 and 1029 genes were down- and upregulated, respectively). Among the genes showing increased expression in planta, those with eggNOG/COG (evolutionary genealogy of genes: Non-supervised Orthologous Groups/Cluster of Orthologous Groups) categories associated with bacterial cell motility, signal transduction, transport and metabolism of inorganic ions and carbohydrates and transcription were overrepresented. Among the genes with the most increased expression in planta, genes primarily associated with flagella synthesis and chemotaxis were found. It is also interesting to note that out of the 31 genes localized on a plasmid, 16 were expressed differently in planta, which may indicate their potential role in plant-pathogen interactions. Many genes with differentiated expression that were localized on chromosome and plasmid encode proteins of unknown function.
| S-EPMC7688646 | biostudies-literature
Project description:Berry fruits are well known to contain large amounts of polyphenol compounds. Among them, flavan-3-ol derivatives are a group of secondary metabolism compounds currently attracting a great deal of attention owing to their health benefits. Not only the fruits, but also the leaves of raspberry plants, are highly esteemed for tea making around the world and are largely used for food. In this report, we discuss the results of our study on the effect of light and temperature on polyphenol accumulation in raspberry leaves. When raspberry was cultivated in a plant factory unit and light intensity, wavelength, and temperature were varied, the amount of total polyphenol increased under blue light. Quantitative determination of (+)-catechin, (⁻)-epicatechin, procyanidin B4, flavan-3-ol trimer, which are flavan-3-ol derivatives, was carried out using HPLC, whereby we confirmed their increase under blue light. Semi-quantitative RT-PCR showed correlation between chalcone synthase (CHS) gene expression and the amounts of the compounds measured in the leaves.
| S-EPMC6468916 | biostudies-literature
Project description:Exposure to blue light of the facultative phototrophic proteobacterium Rhodobacter sphaeroides grown semiaerobically results in repression of the puc and puf operons involved in photosystem formation. To reveal the genome-wide effects of blue light on gene expression and the underlying photosensory mechanisms, transcriptome profiles of R. sphaeroides during blue-light irradiation (for 5 to 135 min) were analyzed. Expression of most photosystem genes was repressed upon irradiation. Downregulation of photosystem development may be used to prevent photooxidative damage occurring when the photosystem, oxygen, and high-intensity light are present simultaneously. The photoreceptor of the BLUF-domain family, AppA, which belongs to the AppA-PpsR antirepressor-repressor system, is essential for maintenance of repression upon prolonged irradiation (S. Braatsch et al., Mol. Microbiol. 45:827-836, 2002). Transcriptome data suggest that the onset of repression is also mediated by the AppA-PpsR system, albeit via an apparently different sensory mechanism. Expression of several genes, whose products may participate in photooxidative damage defense, including deoxypyrimidine photolyase, glutathione peroxidase, and quinol oxidoreductases, was increased. Among the genes upregulated were genes encoding two sigma factors: sigmaE and sigma38. The consensus promoter sequences for these sigma factors were predicted in the upstream sequences of numerous upregulated genes, suggesting that coordinated action of sigmaE and sigma38 is responsible for the upregulation. Based on the dynamics of upregulation, the anti-sigmaE factor ChrR or its putative upstream partner is proposed to be the primary sensor. The identified transcriptome responses provided a framework for deciphering blue-light-dependent signal transduction pathways in R. sphaeroides.
| S-EPMC524910 | biostudies-literature
Project description:Excess Manganese (Mn) is toxic to plants and reduces crop production. Although physiological and molecular pathways may drive plant responses to Mn toxicity, few studies have evaluated Mn tolerance capacity in roots and leaves. As a result, the processes behind Mn tolerance in various plant tissue or organ are unclear. The reactivity of peanut (Arachis hypogaea) to Mn toxicity stress was examined in this study. Mn oxidation spots developed on peanut leaves, and the root growth was inhibited under Mn toxicity stress. The physiological results revealed that under Mn toxicity stress, the activities of antioxidases and the content of proline in roots and leaves were greatly elevated, whereas the content of soluble protein decreased. In addition, manganese and iron ion content in roots and leaves increased significantly, but magnesium ion content decreased drastically. The differentially expressed genes (DEGs) in peanut roots and leaves in response to Mn toxicity were subsequently identified using genome-wide transcriptome analysis. Transcriptomic profiling results showed that 731 and 4589 DEGs were discovered individually in roots and leaves, respectively. Furthermore, only 310 DEGs were frequently adjusted and controlled in peanut roots and leaves, indicating peanut roots and leaves exhibited various toxicity responses to Mn. The results of qRT-PCR suggested that the gene expression of many DEGs in roots and leaves was inconsistent, indicating a more complex regulation of DEGs. Therefore, different regulatory mechanisms are present in peanut roots and leaves in response to Mn toxicity stress. The findings of this study can serve as a starting point for further research into the molecular mechanism of important functional genes in peanut roots and leaves that regulate peanut tolerance to Mn poisoning.
| S-EPMC9867376 | biostudies-literature
Project description:BackgroundLight has significant effect on the growth and development of Saccharina japonica, but there are limited reports on blue light mediated physiological responses and molecular mechanism. In this study, high-throughput paired-end RNA-sequencing (RNA-Seq) technology was applied to transcriptomes of S. japonica exposed to blue light and darkness, respectively. Comparative analysis of gene expression was designed to correlate the effect of blue light and physiological mechanisms on the molecular level.Principal findingsRNA-seq analysis yielded 70,497 non-redundant unigenes with an average length of 538 bp. 28,358 (40.2%) functional transcripts encoding regions were identified. Annotation through Swissprot, Nr, GO, KEGG, and COG databases showed 25,924 unigenes compared well (E-value <10(-5)) with known gene sequences, and 43 unigenes were putative BL photoreceptor. 10,440 unigenes were classified into Gene Ontology, and 8,476 unigenes were involved in 114 known pathways. Based on RPKM values, 11,660 (16.5%) differentially expressed unigenes were detected between blue light and dark exposed treatments, including 7,808 upregulated and 3,852 downregulated unigenes, suggesting S. japonica had undergone extensive transcriptome re-orchestration during BL exposure. The BL-specific responsive genes were indentified to function in processes of circadian rhythm, flavonoid biosynthesis, photoreactivation and photomorphogenesis.SignificanceTranscriptome profiling of S. japonica provides clues to potential genes identification and future functional genomics study. The global survey of expression changes under blue light will enhance our understanding of molecular mechanisms underlying blue light induced responses in lower plants as well as facilitate future blue light photoreceptor identification and specific responsive pathways analysis.
| S-EPMC3384632 | biostudies-literature
Project description:In an effort to better understand the mechanism by which blue light inhibits the growth of Staphylococcus aureus in culture, a whole transcriptome analysis of S. aureus isolate BUSA2288 was performed using RNA-Seq to analyze the differential gene expression in response to blue light exposure. RNA was extracted from S. aureus cultures pooled from 24 1 ml well samples that were each illuminated with a dose of 250 J/cm(2) of 465 nm blue light and from control cultures grown in the dark. Complementary DNA libraries were generated from enriched mRNA samples and sequenced using the Illumina MiSeq Next Generation Sequencer. Here we report one type of analysis that identified 32 candidate genes for further investigation. Blue light has been shown to be bactericidal against S. aureus and is a potential alternative therapy for antibiotic resistant organisms. The mechanism for the inactivation of bacteria is hypothesized to involve reactive oxygen species. These RNA-Seq results provide data that may be used to test this hypothesis. The RNA-Seq data generated by these experiments is deposited in Gene Expression Omnibus (Gene accession GSE62055) and may be found at NCBI (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62055).
| S-EPMC4906118 | biostudies-literature
Project description:IntroductionBlueberry (Vaccinium corymbosum L.) is a popular fruit with an abundance of anthocyanins in its leaves and fruits. Light is one of the pivotal environmental elements that affects plant growth and development, but the regulatory mechanism between light quality and anthocyanin formation is poorly understood.MethodsAn integrated transcriptome and metabolome analysis was performed to investigate the effects of white (control), blue (B), red (R), and red/blue (60R/40B) light on blueberry growth and reveal the potential pathway controlling anthocyanin biosynthesis in blueberry leaves.ResultsThe anthocyanin content was significantly improved by the blue and red/blue light when compared with white light, whereas there was a significant reduction in the photosynthesis under the blue light, showing an inverse trend to that of anthocyanin accumulation. Transcriptomic analysis resulted in the assembly of 134,709 unigenes. Of these, 22 were differentially expressed genes (DEGs) that participate in the anthocyanin biosynthesis pathway, with the majority being significantly up-regulated under the blue light. Most of the photosynthesis-related genes that were down-regulated were expressed during anthocyanin accumulation. Targeted metabolome profiling identified 44 metabolites associated with anthocyanin biosynthesis. The contents of most of these metabolites were higher under blue light than the other light conditions, which was consistent with the transcriptome results. The integrated transcriptome and metabolome analysis suggested that, under blue light, leucoanthocyanidin dioxygenase (LDOX), O-methyltransferase (OMT), and UDP-glucose flavonoid glucosyltransferase (UFGT) were the most significantly expressed, and they promoted the synthesis of cyanidin (Cy), malvidin (Mv), and pelargonidin (Pg) anthocyanidins, respectively. The expression levels of dihydroflavonol 4-reductase (DFR) and OMT, as well as the accumulation of delphinidin (Dp), peonidin (Pn), and petunidin (Pt), were significantly increased by the red/blue light.DiscussionThe blue and red/blue lights promoted anthocyanin biosynthesis via inducing the expression of key structural genes and accumulation of metabolites involved in anthocyanin synthesis pathway. Moreover, there was a possible feedback regulating correlation between anthocyanin biosynthesis and photosynthesis under different light qualities in blueberry leaves. This study would provide a theoretical basis for elucidating the underlying regulatory mechanism of anthocyanin biosynthesis of V. corymbosum.
| S-EPMC9772006 | biostudies-literature
Project description:In a previous study, we found that blue-light irradiation kills insects such as fruit flies, mosquitos, and flour beetles. However, the lethal effects of blue light on coleopteran field crop pests have not been investigated. Chrysomelidae, a major family in phytophagous beetles, includes many species of crop pests. We investigated the lethal effect of blue light on chrysomelid beetles by examining the mortality of the strawberry leaf beetle Galerucella grisescens irradiated with different wavelengths of blue light during the non-mobile egg or pupal stage by using light-emitting diodes. Fifty to seventy percent of beetles irradiated with 407, 417, 438, or 465-nm lights at 15?×?1018 photons·m-2·s-1 during the egg stage died before hatching; ca. 90% of hatchlings irradiated with 438-nm light during the egg stage died before eclosion; and 35-55% of beetles irradiated with 407, 417, 454, and 465-nm lights at the same intensity during the pupal stage died before eclosion. Field crop pests are considered to have high tolerance to blue light because they are usually exposed to sunlight in their natural habitats. However, this study suggests that blue light can kill some field crop as well as household insect pests.
| S-EPMC5457428 | biostudies-literature
Project description:Lettuce (Lactuca sativa) is grown in various parts of the world for use as a leafy vegetable. Although the use of light-emitting diode (LED) in controlled plant production systems has been successfully used to enhance nutritional quality and plant growth efficiently, the molecular basis of lettuce's response to varying light spectra is not studied. Using next-generation sequencing, we have analyzed the transcriptomes of leaf lettuce (Lactuca sativa var. 'New Red Fire') grown hydroponically in a modular agricultural production system under three different types of LED lighting: red, blue, and white light. Illumina HiSeq sequencing platform was used to generate paired-end sequence reads (58 Gb raw and 54 Gb clean data) of the transcriptome of lettuce leaves exposed to varying light spectra. The de novo assembled final transcriptome contained 74,096 transcripts. Around 53% and 39% of the assembled transcripts matched to the UniProt and RefSeq RNA sequences, respectively. The validation of the differentially expressed transcripts using RT-qPCR showed complete agreement with RNA-Seq data for 27 transcripts. A comparison of the blue versus red light treatments showed the highest number of significantly differentially expressed transcripts. Among the transcripts significantly up-regulated in blue-light-exposed leaves compared to white-light-exposed leaves, ~ 26% were involved in the 'response to stress'. Among the transcripts significantly upregulated under red light compared to white light, ~ 6% were associated with 'nucleosome assembly' and other processes, such as 'oxidation-reduction process' and 'response to water deprivation' were significantly enriched. Thus, the result from the current study provides deeper insights into differential gene expression patterns and associated functional aspects under varying light qualities.
| S-EPMC9797559 | biostudies-literature