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Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

ABSTRACT: We used Illumina sequencing to investigate the global transcriptomic expression of hormonal pathway genes in ABA initiated strawberry receptacle ripening. Expression profiles of hormone synthetic and signaling genes further demonstrated the positive roles of ABA and GA, and the negative role of auxin in receptacle ripening. We also evaluated the transcript profiling of ethylene and JA pathway genes, and the results suggested that both ethylene and JA participated in receptacle ripening. Furthermore, two novel miRNAs and three conserved miRNAs were identified and validated to target genes in ABA and auxin pathways, respectively. Our analyses reveal the molecular mechanism of hormonal regulation during strawberry receptacle ripening. The data also provide an abundant of genetic information for molecular manipulation on non-climacteric fruit ripening.

ORGANISM(S): Fragaria x ananassa

PROVIDER: GSE63224 | GEO | 2016/10/27

SECONDARY ACCESSION(S): PRJNA267010

REPOSITORIES: GEO

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Comprehensive transcriptome analysis of phytohormone pathway genes and miRNAs in ABA initiated strawberry receptacle ripening

Project description:We used Illumina sequencing to investigate the global transcriptomic expression of hormonal pathway genes in ABA initiated strawberry receptacle ripening. Expression profiles of hormone synthetic and signaling genes further demonstrated the positive roles of ABA and GA, and the negative role of auxin in receptacle ripening. We also evaluated the transcript profiling of ethylene and JA pathway genes, and the results suggested that both ethylene and JA participated in receptacle ripening. Furthermore, two novel miRNAs and three conserved miRNAs were identified and validated to target genes in ABA and auxin pathways, respectively. Our analyses reveal the molecular mechanism of hormonal regulation during strawberry receptacle ripening. The data also provide an abundant of genetic information for molecular manipulation on non-climacteric fruit ripening. Sample 1: CK0 (Strawberry fruit two weeks after athesis treated with water, set as day 0); Sample 2: CK5 (fruit treated with water on day 5); Sample 3: CK8 (fruit treated with water on day 8); Sample 4: ABA5 (fruit treated with ABA on day 5); Sample 5: ABA8 (fruit treated with ABA on day 5); Sample 6: NDGA5 (fruit treated with water on day 5); Sample 7: NDGA8 (fruit treated with NDGA on day 8).

2016-10-27 | E-GEOD-63224 | biostudies-arrayexpress

The NAC transcription factor FaRIF controls fruit ripening in strawberry

Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

2021-02-20 | GSE167107 | GEO

RdDM is involved in epigenetic regulation of strawberry fruit ripening

Project description:DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.

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Transcriptomic studies in the development and ripening of strawberry fruits

Project description:Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over 32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.

2018-05-09 | GSE95300 | GEO

Transcriptomic studies in the development and ripening of strawberry fruits (Agilent)

2019-10-18 | GSE126220 | GEO

The ethylene-auxin crosstalk regulates the postharvest fruit ripening process in apple

Project description:The ripening of climacteric fruits, such as apple, is represented by a series of genetically programmed events orchestrated by the action of several hormones. In this work, we investigated the existence of a hormonal crosstalk between ethylene and auxin during the post-harvest ripening of three internationally known apple cultivars: ‘Golden Deli-cious’, ‘Granny Smith’ and ‘Fuji’. The normal climacteric ripening was impaired by the exogenous application of 1-methylcyclopropene (1-MCP) that effectively affected the production of ethylene and the physiological behaviour of specific ethylene-related qual-ity traits, such as fruit texture and the production of volatile organic compounds showed a de-novo accumulation of auxin following the application of 1-MCP. The RNA-Seq wide-transcriptome analysis evidenced as the competition at the level of the ethylene re-ceptors induced a cultivar-dependent transcription re-programming. The DEGs annota-tion carried out through the KEGG database identified as most genes were assigned to the plant hormone signaling transduction category, and specifically related to auxin and ethylene. The interplay between these two hormones was further assessed through a candidate gene analysis that highlighted a specific activation of GH3 and ILL genes, en-coding key steps in the process of the auxin homeostasis mechanism. Our results showed that a compromised ethylene metabolism at the onset of the climacteric ripening in apple can stimulate, in a cultivar-dependent fashion, an initial de-novo synthesis and de-conjugation of auxin as a tentative to restore a normal ripening progression.

2021-11-17 | GSE182822 | GEO

Effect of 1-methylcyclopropene (1-MCP) on preclimacteric nectarine (Prunus persica cv Stark Red Gold) fruit.

Project description:Peach is a climacteric fruit whose ripening is largely dependent on ethylene. Recently, it has been shown that auxin is able to autonomously regulate the expression of ripening related genes, and that a cross-talk between ethylene and auxin occurs during the ripening process. By using the non-destructing index of absorbance difference (IAD), mature nectarines were homogeneously grouped into three classes (0, 1 and 2) according to their ripening phase and treated with 1-methylcyclopropene (1-MCP), known to block ethylene receptors. 1-MCP responses differed in the three classes that were thus used to molecularly investigate the auxin-ethylene cross-talk during the transition from maturation to ripening and the accompanying switch of ethylene biosynthesis from System-1 to System-2. Microarray experiments showed that 1-MCP modified the expression of 121 genes (63 were up-regulated and 59 down-regulated). Besides inducing ethylene-, auxin- and ripening-repressed genes and repressing ethylene-, auxin- and ripening-induced genes, also genes induced by ripening, auxin and 1-MCP were discovered. The up-regulating effect of 1-MCP was observed for ctg134, similar to signalling peptides, for 1-aminocyclopropane-1-carboxylic acid synthase 1 (ACS1) and, interestingly, for many auxin-regulated genes, such as GH3, whose expression is widely used as a marker for free auxin. The latter finding, together with the induction of an IAA amidohydrolase, suggests that the 1-MCP application could have caused a rise in free auxin, thus leading to an increase in ethylene biosynthesis through the induction of the tightly regulated ACS1 gene.

2010-04-01 | GSE16224 | GEO

N6-methyladenosine mRNA methylomes in the MTA RNAi strawberry fruits and the controls

Project description:For exploring the influence of the m6A methyltransferase gene MTA silencing in the global m6A mRNA methylomes of strawberry fruits, we performed m6A-seq in the MTA RNAi strawberry fruits (RNAi-MTA) and the controls with three independently biological replicates. Results showed that MTA silencing induces the m6A hypomethylation of thousands of transcripts, including those of ripening and ABA pathway genes.

2021-05-20 | GSE174703 | GEO

Integrative approach combining transcriptomic assay with physical and metabolite analysis reveal novel clues about the regulatory mechanism governing the climacteric ripening physiology in apple (Malus x domestica Borkh.) [WGAA]

Project description:Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation. whole genome array specifically enriched of ripening related genes for apple (WGAA) with two cultivars (Golden Delicious and Granny Smith)

2016-08-23 | E-GEOD-78744 | biostudies-arrayexpress

Interference with ethylene perception at receptor level sheds light on auxin and transcriptional circuits associated with climacteric ripening of apple fruit (Malus x domestica Borkh.)

Project description:Apple (Malus x domestica Borkh.) is a model fruit species to study the metabolic changes occurring at the onset of ripening as well the physiological mechanism governed by the hormone ethylene. In this survey, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and polyphenolic compounds) was carried out throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms, a custom array dedicated to fruit ripening pathways (iRIPE) and a whole genome array specifically enriched of ripening related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor, were also highlighted. The suppression of ethylene modified and delayed the ethylene receptors turnover, leading to important modifications in the overall fruit physiology. The integrative comparative network analysis showed both negative and positive correlations between ripening related transcripts and accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of the ethylene perception besides affecting the ethylene and texture control, stimulated the de-repression of auxin related genes, transcription factors and photosynthethic genes. In the end, the comprehensive repertoire of results obtained here step forwards in the elucidation of the multi-layered control of ethylene, hypothesizing a possible hormonal cross-talk coupled with a transcriptional regulation. 48 samples analyzed; 8 stages have been identified over the fruit development and ripening (from flower to post harvest ripening) of apple fruit belonging to two apple cultivars (Golden Delicious and Granny Smith), ending with 16 samples (3 replacates for each sample)

2016-08-23 | E-GEOD-78745 | biostudies-arrayexpress

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