Similar Datasets
Project description:Transcriptome profiling of Phalaenopsis reveals that photoperiod regulates floral induction
| PRJNA955177 | ENA
Project description:Floral scent is an important factor in attracting pollinators and repelling florivores. In Phalaenopsis bellina (Orchidaceae), the major floral scent components are monoterpenoids. Previously, we determined that expression of GERANYL DIPHOSPHATE SYNTHASE (PbGDPS) is highly correlated with monoterpene biosynthesis in Phalaenosis orchids. Here, we found that both cis- and trans-regulation were present on the GDPS promoters, with trans-regulation playing a key role. To investigate the regulation of biosynthesis of floral scent, we compared the transcriptomic data of two Phalaenopsis orchids with contrasting scent phenotypes. Eight transcription factors (TFs) that exhibited sequential elevation in abundance through floral development in P. bellina were identified, and their transcript levels were higher in the scented orchid than the scentless one. Five of these TFs transactivated several structural genes involved in monoterpene biosynthesis including PbbHLH4, PbbHLH6, PbbZIP4, PbERF1, and PbNAC1. Ectopic transient expression of each of these TFs in scentless orchids resulted in stimulation of terpenoid biosynthesis. PbbHLH4 most profoundly induced monoterpene biosynthesis, with a 950-fold increase of monoterpenoid production in the scentless orchid. In conclusion, we determined that biosynthesis of orchid floral monoterpenes was sequentially regulated, with PbbHLH4 playing a crucial role for monoterpene biosynthesis.
| S-EPMC6093345 | biostudies-literature
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of plants. The goals of this study are to compare omparatively evaluated both sequence variation and gene expression at the transcriptomic level between two species. Methods: Pooled total RNA of P. floridana flower buds and young fruits, in triplicate, using Illumina HiSeqTM 2000. The sequence reads remove reads with adaptors or unknown nucleotides larger than 5% and low-quality reads using . qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Sequencing the Physalis transcriptome revealed 147,118 unigenes. When aligned to the tomato genome, we estimated that around 30,121 genes were expressed in the Physalis floral-fruit transcriptome, and 10,498 orthologous gene pairs were identified between P. floridana and S. pimpinellifolium.with a fold change ≥1.5 and FER value <0.001, 0.68% of the unigenes in the Physalis floral-fruit transcriptome were developmentally regulated at the floral-fruit transition, and Altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of floral-fruit transcriptomes, with biologic replicates, generated by RNA-seq technology.The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a organ or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2018-12-29 | GSE92998 | GEO
Project description:Phalaenopsis has a zygomorphic floral structure, including three outer tepals, two lateral inner tepals and a highly modified inner median tepal called labellum or lip; however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for floral organs of the Phalaenopsis wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after de novo assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression. PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes' expression patterns. PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. Our study provides new insights into how the orchid labellum differs and why the petal or sepal converts to a labellum in Phalaenopsis floral mutants.
| S-EPMC4430480 | biostudies-literature
Project description:Temperate maize was domesticated from its tropical ancestor, teosinte. Whereas temperate maize is an autonomous day-neutral plant, teosinte is an obligate short-day plant that requires uninterrupted long nights to induce flowering. Leaf-derived florigenic signals trigger reproductive growth in both teosinte and temperate maize. To study the genetic mechanisms underlying floral inductive pathways in maize and teosinte, mRNA and small RNA genome-wide expression analyses were conducted on leaf tissue from plants that were induced or not induced to flower. Transcriptome profiles reveal common differentially expressed genes during floral induction, but a comparison of candidate flowering time genes indicates that photoperiod and autonomous pathways act independently. Expression differences in teosinte are consistent with the current paradigm for photoperiod-induced flowering, where changes in circadian clock output trigger florigen production. Conversely, differentially expressed genes in temperate maize link carbon partitioning and flowering, but also show altered expression of circadian clock genes that are distinct from those altered upon photoperiodic induction in teosinte. Altered miRNA399 levels in both teosinte and maize suggest a novel common connection between flowering and phosphorus perception. These findings provide insights into the molecular mechanisms underlying a strengthened autonomous pathway that enabled maize growth throughout temperate regions.
| S-EPMC5972621 | biostudies-literature
Project description:Phalaenopsis amabilis, one of the most important flowers in the current international flower market, is a plant that undergoes vernalization and requires low temperature treatment for flowering. There have been few reports on the proteomic analysis of the development of flower buds. In this study, by using isobaric tags for relative and absolute quantification (iTRAQ), 4096 differentially expressed proteins were identified in P. amabilis under low temperature treatment, of which 42 were associated with early floral induction, and 18 were verified by mass spectrometry multi-reaction monitoring (MRM). Among the proteins associated with the vernalization pathway, PEQU_11434 (glycine-rich RNA-binding protein GRP1A-like) and PEQU_11045 (UDP-N-acetylglucosamine diphosphorylase) were upregulated compared to their expression in control flower buds. It was therefore inferred that O-GlcNAc glycosylation was involved in the posttranscriptional modification of VRN1 (API homolog) and that the GRP2 protein (glycine-rich RNA-binding protein) was glycosylated to relieve binding to the VRN1 mRNA precursor to promote the expression of VRN1, which initiates floral development. Furthermore, phytochromes A (PEQU_13449, PEQU_35378), B (PEQU_09249) and C (PEQU_41401) were downregulated under low temperature treatment compared to their expression in control flower buds, suggesting that they could repress the expression of the VRN2 gene and thus release its repression of VRN3 to enable the high-level expression of FTPEQU_19304 (FT, VRN3 homolog), which promotes VRN1 expression and then stimulates flowering.
2020-03-20 | PXD013908 | Pride
Project description:Our results showed that hundreds of differentially expressed genes (DEGs) were detected in floral sex initiation period, but thousands of DEGs were involved in stamens and ovules development process. Moreover, the DEGs were mainly showed up-regulation in male floral initiation, but mainly down-regulation in female floral initiation. Male floral initiation was associated with the flavonoid biosynthesis pathway while female floral initiation was related to the phytohormone signal transduction pathway. In addition, the floral organ identity genes played important roles in floral sex differentiation process and displayed a general conservation of the ABCDE model in J. curcas.
2018-03-21 | GSE102894 | GEO
Project description:Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that mediate floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-seq analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, the qem2 mutation is in CHROMATIN REMODELING 4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.
2020-03-02 | PXD016457 | Pride
Project description:Plants have evolved a unique and conserved developmental program that enables the conversion of leaves into floral organs. Elegant genetic and molecular work has identified key regulators of floral meristem identity. However, further understanding of flower meristem specification has been hampered by redundancy and by pleiotropic effects. The KNOXI gene STM transcription factor is a well-characterized regulator of shoot apical meristem maintenance. stm loss-of-function mutants arrest shortly after germination, and therefore the knowledge on later roles of STM, including flower development, is limited. Here, we uncover a role for STM in the specification of flower meristem identity. Silencing STM in the AP1 expression domain in the ap1-4 mutant background resulted in a complete leafy-like flower phenotype and an intermediate stm-2 allele enhanced the floral meristem identity phenotype of ap1-4. Transcriptional profiling of STM perturbation suggested that STM activity affects multiple meristem identity and flower transition genes, among them the F-Box gene UFO. In agreement, stm-2 enhanced the ufo-2 floral meristem fate phenotype, and ectopic UFO expression rescued the leafy flowers in genetic backgrounds with compromised AP1 and STM activities. This work suggests a molecular mechanism that underlies the activity of STM in the specification of flower meristem identity.
2018-05-04 | GSE113894 | GEO
Project description:The F1 population of Phalaenopsis Intermedia, which established from the cross between P. equestris and P. aphrodite was applied to build a high-density genetic map based on SSRs and SNPs from GBS methodology, with the digestion of by Hinp1 I and Hae III. In addition, another GBS was performed with enzymes ApeK I and Hae II to increase the SNP number for the GWAS analysis. We identified 10 SNPs highly associated with floral aesthetic trait, and among them, 4 were associated with flower color related. Genes with function related to anthocyanin biosynthesis were identified as the candidate genes. In addition, the flowering time-related gene SOC1 may contribute to flower color regulation in our discovery.
2022-03-09 | GSE176215 | GEO