Transcriptome profiling reveals regulatory mechanisms underlying corolla senescence in petunia

Wang, Hong; Chang, Xiaoxiao; Lin, Jing; YouHong, Chang; Chen, Jen-Chih; Reid, Michael S.; Jiang, Cai‐Zhong

doi:10.1038/s41438-018-0018-1

Cited by 35 publications

(30 citation statements)

References 55 publications

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“…The ABA-induced genes, PP2C , increased in their mRNA levels significantly from the phase of MA as we discovered, which could appear to dephosphorylate an essential component of the ABA pathway leading to the synthesis of hydrolytic enzymes and programmed cell death (PCD) [ 75 ]. This mediation proved coincident in petunia corolla senescence [ 49 ]. Whereas the three genes encoding PYL family proteins which act as abscisic acid sensors, were obviously down-regulated in LA compared with M, maybe demonstrating the transcriptional reduction of PYL homologs in extreme premature senescence.…”

Section: Discussionmentioning

confidence: 99%

“…With the rapid development of the RNA-seq technique for acquiring mRNA transcriptome profiling to investigate the probable function of genes, most Senescence-Associated Genes (SAGs) have been able to be characterized by such a technique. However, the transcriptome analyses of plant senescence has been operated only on a limited number of plants, including Arabidopsis [ 46 ], wheat [ 1 ], cotton [ 7 , 17 ], common tobacco [ 41 ], sorghum [ 47 ], maize [ 48 ], and petunia corolla [ 49 ], and more plants are required. Though the only transcriptome analysis of senescence in Nicotiana tabacum was reported by Li [ 41 ], it has laid focus on the metabolites of nutrient remobilization rather than the gene transcription regulating senescence.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome Analysis of Gene Expression Patterns Potentially Associated with Premature Senescence in Nicotiana tabacum L.

Zhao

et al. 2018

Molecules

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Senescence affects the remobilization of nutrients and adaption of the plant to the environment. Combined stresses can result in premature senescence in plants which exist in the field. In this study, transcriptomic analysis was performed on mature leaves and leaves in three stages of premature senescence to understand the molecular mechanism. With progressive premature senescence, a declining chlorophyll (chl) content and an increasing malonaldehyde (MDA) content were observed, while plasmolysis and cell nucleus pyknosis occurred, mitochondria melted, thylakoid lamellae were dilated, starch grains in chloroplast decreased, and osmiophilic granules increased gradually. Moreover, in total 69 common differentially expressed genes (DEGs) in three stages of premature senescing leaves were found, which were significantly enriched in summarized Gene Ontology (GO) terms of membrane-bounded organelle, regulation of cellular component synthesis and metabolic and biosynthetic processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the plant hormone signal transduction pathway was significantly enriched. The common DEGs and four senescence-related pathways, including plant hormone signal transduction, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, and regulation of autophagy were selected to be discussed further. This work aimed to provide potential genes signaling and modulating premature senescence as well as the possible dynamic network of gene expression patterns for further study.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Gene Expression Patterns Potentially Associated with Premature Senescence in Nicotiana tabacum L.

Zhao

et al. 2018

Molecules

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“…RNAseq samples of Arabidopsis and rice were obtained from different tissues and developmental stages under drought and salt stress conditions (Table S7). The data were filtered using Trim_galore, a high-throughput sequence quality confine analysis tool (Brown et al, 2017;Wang et al, 2018). Then, the filtered reads were mapped to the Arabidopsis and rice reference genomes using HISAT2 (Yang-Ming et al, 2016).…”

Section: Rna-seq Data and Quantificationmentioning

confidence: 99%

The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

et al. 2021

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Eukaryotic genes can be classified into intronless (no introns), intron-poor (three or fewer introns per gene) or intron-rich. Early eukaryotic genes were mostly intron-rich, and their alternative splicing into multiple transcripts, giving rise to different proteins, might have played pivotal roles in adaptation and evolution. Interestingly, extant plant genomes contain many gene families with one or sometimes few sub-families with genes that are intron-poor or intronless, and it remains unknown when and how these intron-poor or intronless genes have originated and evolved, and what their possible functions are. In this study, we identified 33 such gene families that contained intronless and intron-poor sub-families. Intronless genes seemed to have first emerged in early land plant evolution, while intron-poor sub-families seemed first to have appeared in green algae. In contrast to intron-rich genes, intronless genes in intron-poor sub-families occurred later, and were subject to stronger functional constraints. Based on RNA-seq analyses in Arabidopsis and rice, intronless or intron-poor genes in AP2, EF-hand_7, bZIP, FAD_binding_4, STE_STE11, CAMK_-CAMKL-CHK1 and C2 gene families were more likely to play a role in response to drought and salt stress, compared with intron-rich genes in the same gene families, whereas intronless genes in the B_lectin and S_locus_glycop gene family were more likely to participate in epigenetic processes and plant development. Understanding the origin and evolutionary trajectory, as well as the potential functions, of intronless and intron-poor sub-families provides further insight into plant genome evolution and the functional divergence of genes.

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“…However, the genetic regulatory mechanisms of flowering in A. amurensis under extremely low temperatures are unclear. Currently, both transcriptomics and proteomics have been widely used to identify genes in flowering in plants [21,22,23]. In the present study, we identified the key TFs involved in flowering in A. amurensis by combining transcriptomic and proteomic analyses.…”

Section: Introductionmentioning

confidence: 99%

Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics

Zhou

Sun

Dai

et al. 2019

Genes

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Temperature is one of the most important environmental factors affecting flowering in plants. Adonis amurensis, a perennial herbaceous flower that blooms in early spring in northeast China where the temperature can drop to −15 °C, is an ideal model for studying the molecular mechanisms of flowering at extremely low temperatures. This study first investigated global gene expression profiles at different developmental stages of flowering in A. amurensis by RNA-seq transcriptome and iTRAQ proteomics. Finally, 123 transcription factors (TFs) were detected in both the transcriptome and the proteome. Of these, 66 TFs belonging to 14 families may play a key role in multiple signaling pathways of flowering in A. amurensis. The TFs FAR1, PHD, and B3 may be involved in responses to light and temperature, while SCL, SWI/SNF, ARF, and ERF may be involved in the regulation of hormone balance. SPL may regulate the age pathway. Some members of the TCP, ZFP, MYB, WRKY, and bHLH families may be involved in the transcriptional regulation of flowering genes. The MADS-box TFs are the key regulators of flowering in A. amurensis. Our results provide a direction for understanding the molecular mechanisms of flowering in A. amurensis at low temperatures.

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Transcriptome profiling reveals regulatory mechanisms underlying corolla senescence in petunia

Cited by 35 publications

References 55 publications

Transcriptome Analysis of Gene Expression Patterns Potentially Associated with Premature Senescence in Nicotiana tabacum L.

Transcriptome Analysis of Gene Expression Patterns Potentially Associated with Premature Senescence in Nicotiana tabacum L.

The emergence and evolution of intron‐poor and intronless genes in intron‐rich plant gene families

Identification of Transcription Factors Involved in the Regulation of Flowering in Adonis Amurensis Through Combined RNA-seq Transcriptomics and iTRAQ Proteomics

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